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Sample records for solution-phase parallel synthesis

  1. Bis-enaminone based parallel solution-phase synthesis of 1,4-dihydropyridine derivatives.

    PubMed

    Baskovc, Jernej; Bevk, David; Stanovnik, Branko; Svete, Jurij

    2009-01-01

    Two variations of a parallel solution-phase synthesis of N-substituted dimethyl 4-oxo-1,4-dihydropyridine-3,5-dicarboxylates 4 and methyl 3-oxo-3,5-dihydro-2H-pyrazolo[4,3-c]pyridine-7-carboxylates 9 from dimethyl acetone-1,3-dicarboxylate (1) were developed. The first synthetic method comprises preparation of the bis-enaminone reagents 2 and 8 and their cyclization with primary amines 3 via double substitution of both dimethylamino groups to give dihydropyridines (DHPs) 4 and 9, respectively. Another variation consists of preparation of the monoenaminone reagents 5 and 10, followed by substitution of the dimethylamino group with primary amines 3, and cyclization of the so formed intermediates 6 with N,N-dimethylformamide dimethylacetal (DMFDMA). In this manner, a library of 46 analytically pure compounds, 24 intermediates 6, 11, and 13, and 22 final dihydropyridines 4 and 9 was obtained employing just a simple filtration workup.

  2. Solution phase parallel synthesis and evaluation of MAPK inhibitory activities of close structural analogues of a Ras pathway modulator.

    PubMed

    Lu, Yingchun; Sakamuri, Sukumar; Chen, Quin-Zene; Keng, Yen-Fang; Khazak, Vladimir; Illgen, Katrin; Schabbert, Silke; Weber, Lutz; Menon, Sanjay R

    2004-08-02

    A solution phase parallel synthesis approach was undertaken to rapidly explore the structure-activity relationship of an inhibitor of the Ras/Raf protein interaction identified from a small molecule compound library. Evaluation of the MAPK pathway signaling inhibitory activity of the synthesized analogues as well as their antiproliferative activity and ability to inhibit soft agar growth were performed.

  3. Solution-phase parallel synthesis of acyclic nucleoside libraries of purine, pyrimidine, and triazole acetamides.

    PubMed

    Pathak, Ashish K; Pathak, Vibha; Reynolds, Robert C

    2014-09-08

    Molecular diversity plays a pivotal role in modern drug discovery against phenotypic or enzyme-based targets using high throughput screening technology. Under the auspices of the Pilot Scale Library Program of the NIH Roadmap Initiative, we produced and report herein a diverse library of 181 purine, pyrimidine, and 1,2,4-triazole-N-acetamide analogues which were prepared in a parallel high throughput solution-phase reaction format. A set of assorted amines were reacted with several nucleic acid N-acetic acids utilizing HATU as the coupling reagent to produce diverse acyclic nucleoside N-acetamide analogues. These reactions were performed using 24 well reaction blocks and an automatic reagent-dispensing platform under inert atmosphere. The targeted compounds were purified on an automated purification system using solid sample loading prepacked cartridges and prepacked silica gel columns. All compounds were characterized by NMR and HRMS, and were analyzed for purity by HPLC before submission to the Molecular Libraries Small Molecule Repository (MLSMR) at NIH. Initial screening through the Molecular Libraries Probe Production Centers Network (MLPCN) program, indicates that several analogues showed diverse and interesting biological activities.

  4. A strategy for the solution-phase parallel synthesis of N-(pyrrolidinylmethyl)hydroxamic acids.

    PubMed

    Takayanagi, M; Flessner, T; Wong, C H

    2000-06-16

    Both five- and six-membered iminocyclitols have proven to be useful transition-state analogue inhibitors of glycosidases. They also mimic the transition-state sugar moiety of the nucleoside phosphate sugar in glycosyltransferase-catalyzed reactions. Described here is the development of a general strategy toward the parallel synthesis of a five-membered iminocyclitol linked to a hydroxamic acid group designed to mimic the transition state of GDP-fucose complexed with Mn(II) in fucosyltransferase reactions. The iminocyclitol 8 containing a protected hydroxylamine unit was prepared from D-mannitol. The hydroxamic acid moiety was introduced via the reaction of 8 with various acid chlorides. The strategy is generally applicable to the construction of libraries for identification of glycosyltransferase inhibitors.

  5. Plate-to-plate fluorous solid-phase extraction for solution-phase parallel synthesis.

    PubMed

    Zhang, Wei; Lu, Yimin; Nagashima, Tadamichi

    2005-01-01

    A commercially available Argonaut VacMaster-96 plate-to-plate solid-phase extraction (SPE) station equipped with 24 FluoroFlash cartridges is employed for parallel purification of fluorous reaction mixtures. Each cartridge charged with 3 g of fluorous silica gel has the capability to produce up to 100 mg of purified small molecules. The 24-well receiving plate has a standard footprint that can be directly concentrated in a Genevac vacuum centrifuge. Important issues such as sample loading, product cross-contamination, cartridge reuse, and reproducibility are investigated. The SPE system has been demonstrated in the purification of three small libraries that were produced involving amine scavenging reactions with fluorous isatoic anhydride, amide coupling reactions with 2-chloro-4,6-bis[(perfluorohexyl)propyloxy]-1,3,5-triazine (fluorous CDMT), and amide coupling reactions with a newly developed fluorous Mukaiyama condensation reagent.

  6. The Zymark BenchMate™. A compact, fully-automated solution-phase reaction work-up facility for multiple parallel synthesis

    PubMed Central

    Hamlin, Gordon A.

    2000-01-01

    The rapid growth of multiple parallel synthesis in our laboratories has created a demand for a robust, easily accessed automated system for solution-phase reaction work-up, since the manual work-up of large numbers of small-scale reactions is both time-consuming and tedious, and is a rate limiting step in the generation of large numbers of compounds for test. Work-up in chemical organic synthesis consists of a series of post-reaction operations designed using differential chemical properties to remove excess reagent or starting material, reagent products and, where possible reaction by-products. Careful consideration of post-reaction operations as a clean-up step can obviate the requirement for purification. Generally, work-up can be resolved into four operations: filtration, solvent addition (dilution, trituration), washing and separation (partition) and it is the selection and ordering of these four basic operations that constitutes a chemical work-up. Following the proven success of centralized Zymate robotic systems in the compilation, execution and work-up of complex reaction sequences, a centralized chemical work-up service has been in operation for over 12 months. It now seemed prudent that the needs of multiple parallel synthesis would be better served by the development of a compact, automated system, capable of operating in a standard chemistry laboratory fume-hood. A Zymark BenchMate platform has been configured to perform the four basic operations of chemical solution work-up. A custom-built filtration station, incorporating an integrated tipping facility for the sample tube has also been developed. Compilation of each work-up is through a set of Visual Basic procedure screens, each dedicated to a particular work-up scenario. Methods are compiled at the chemist's own PC and transferred to the BenchMate via a diskette. PMID:18924692

  7. Solution-Phase Synthesis of Dipeptides: A Capstone Project That Employs Key Techniques in an Organic Laboratory Course

    ERIC Educational Resources Information Center

    Marchetti, Louis; DeBoef, Brenton

    2015-01-01

    A contemporary approach to the synthesis and purification of several UV-active dipeptides has been developed for the second-year organic laboratory. This experiment exposes students to the important technique of solution-phase peptide synthesis and allows an instructor to highlight the parallel between what they are accomplishing in the laboratory…

  8. Solution-Phase Synthesis of Cesium Lead Halide Perovskite Nanowires.

    PubMed

    Zhang, Dandan; Eaton, Samuel W; Yu, Yi; Dou, Letian; Yang, Peidong

    2015-07-29

    Halide perovskites have attracted much attention over the past 5 years as a promising class of materials for optoelectronic applications. However, compared to hybrid organic-inorganic perovskites, the study of their pure inorganic counterparts, like cesium lead halides (CsPbX3), lags far behind. Here, a catalyst-free, solution-phase synthesis of CsPbX3 nanowires (NWs) is reported. These NWs are single-crystalline, with uniform growth direction, and crystallize in the orthorhombic phase. Both CsPbBr3 and CsPbI3 are photoluminescence active, with composition-dependent temperature and self-trapping behavior. These NWs with a well-defined morphology could serve as an ideal platform for the investigation of fundamental properties and the development of future applications in nanoscale optoelectronic devices based on all-inorganic perovskites.

  9. Aerosol spray pyrolysis & solution phase synthesis of nanostructures

    NASA Astrophysics Data System (ADS)

    Zhang, Hongwang

    This dissertation focuses on the synthesis of nanomaterials by both solution phase and gas phase methods. By the solution phase method, we demonstrate the synthesis of Au/CdS binary hybrid nanoparticles and the Au-induced growth of CdS nanorods. At higher reaction temperature, extremely uniform CdS nanorods were obtained. The size of the Au seed nanoparticles has an important influence on the length and diameter of the nanorods. In addition, preparation of peanut-like FePt-CdS hybrid nanoparticles by spontaneous epitaxial nucleation and growth of CdS onto FePt-seed nanoparticles in high-temperature organic solution is reported. The FePt-CdS hybrid nanoparticles reported here are an example of a bifunctional nanomaterial that combines size-dependent magnetic and optical properties. In the gas phase method, a spray pyrolysis aerosol synthesis method was used to produce tellurium dioxide nanoparticles and zinc sulfide nanoparticles. Tellurite glasses (amorphous TeO2 based materials) have two useful optical properties, high refractive index and high optical nonlinearity, that make them attractive for a range of applications. In the work presented here, TeO2 nanoparticles were prepared by spray pyrolysis of an aqueous solution of telluric acid, Te(OH)6. This laboratory-scale process is capable of producing up to 80 mg/hr of amorphous TeO2-nanoparticles with primary particle diameters from 10 to 40 nm, and allows their synthesis in significant quantities from an inexpensive and environmentally friendly precursor. Furthermore, both Er3+ doped and Er3+ and Yb3+ co-doped tellurium dioxide nanoparticles were synthesized by spray pyrolysis of an aqueous mixture of telluric acid with erbium/ytterbium salts, which exhibit the infrared to green visible upconversion phenomena. ZnS nanoparticles (NPs) were prepared by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor. The home-built scanning mobility particle spectrometer (SMPS) is a useful tool for

  10. Solution-phase synthesis of smaller cuprous oxide nanocubes

    SciTech Connect

    Zhang Hui; Cui Zuolin

    2008-06-03

    Smaller cuprous oxides (Cu{sub 2}O) nanocubes were synthesized by solution-phase method at 160 deg. C, using ethylene glycol reducing Cu(NO{sub 3}){sub 2}.3H{sub 2}O with poly(vinylypyrrolidone) (pvp) as capping agent. The Cu{sub 2}O nanocubes were characterized by field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), selected area electron diffraction (SAED) and X-ray powder diffraction (XRD). SEM showed that most of Cu{sub 2}O nanocubes were uniform and monodisperse, with the average edge length about 130 nm. The TEM results were consistent with the SEM results. Selected area electron diffraction (SAED) suggested that as-prepared Cu{sub 2}O nanocubes were single crystalline. The geometric shape and size of Cu{sub 2}O nanoparticles were greatly affected by the presence of PVP and its molar ratio (in repeating unit) relative to copper nitrate, temperature and the concentration of Cu(NO{sub 3}){sub 2}.3H{sub 2}O. The mechanism of Cu{sub 2}O nanocubes formation was also discussed.

  11. Solution-Phase Synthesis of a Tricyclic Pyrrole-2-Carboxamide Discovery Library Applying a Stetter-Paal-Knorr Reaction Sequence

    PubMed Central

    Iyer, Pravin S.; Fodor, Matthew D.; Coleman, Claire M.; Twining, Leslie A.; Mitasev, Branko

    2012-01-01

    The solution phase synthesis of a discovery library of 178 tricyclic pyrrole-2-carboxamides was accomplished in nine steps and seven purifications starting with three benzoyl protected amino acid methyl esters. Further diversity was introduced by two glyoxaldehydes and forty-one primary amines. The combination of Pauson-Khand, Stetter and microwave assisted Paal Knorr reactions was applied as a key sequence. The discovery library was designed with the help of QikProp 2.1 and physicochemical data are presented for all pyrroles. Library members were synthesized and purified in parallel and analyzed by LC-MS. Selected compounds were fully characterized. PMID:16677007

  12. Solution-phase automated synthesis of an α-amino aldehyde as a versatile intermediate

    PubMed Central

    Masui, Hisashi; Yosugi, Sae; Fuse, Shinichiro

    2017-01-01

    A solution-phase automated synthesis of the versatile synthetic intermediate, Garner’s aldehyde, was demonstrated. tert-Butoxycarbonyl (Boc) protection, acetal formation, and reduction of the ester to the corresponding aldehyde were performed utilizing our originally developed automated synthesizer, ChemKonzert. The developed procedure was also useful for the synthesis of Garner’s aldehyde analogues possessing fluorenylmethyloxycarbonyl (Fmoc) or benzyloxycarbonyl (Cbz) protection. PMID:28228851

  13. Fischer Indole Synthesis in the Gas Phase, the Solution Phase, and at the Electrospray Droplet Interface

    NASA Astrophysics Data System (ADS)

    Bain, Ryan M.; Ayrton, Stephen T.; Cooks, R. Graham

    2017-02-01

    Previous reports have shown that reactions occurring in the microdroplets formed during electrospray ionization can, under the right conditions, exhibit significantly greater rates than the corresponding bulk solution-phase reactions. The observed acceleration under electrospray ionization could result from a solution-phase, a gas-phase, or an interfacial reaction. This study shows that a gas-phase ion/molecule (or ion/ion) reaction is not responsible for the observed rate enhancement in the particular case of the Fischer indole synthesis. The results show that the accelerated reaction proceeds in the microdroplets, and evidence is provided that an interfacial process is involved.

  14. Parallelizing quantum circuit synthesis

    NASA Astrophysics Data System (ADS)

    Di Matteo, Olivia; Mosca, Michele

    2016-03-01

    Quantum circuit synthesis is the process in which an arbitrary unitary operation is decomposed into a sequence of gates from a universal set, typically one which a quantum computer can implement both efficiently and fault-tolerantly. As physical implementations of quantum computers improve, the need is growing for tools that can effectively synthesize components of the circuits and algorithms they will run. Existing algorithms for exact, multi-qubit circuit synthesis scale exponentially in the number of qubits and circuit depth, leaving synthesis intractable for circuits on more than a handful of qubits. Even modest improvements in circuit synthesis procedures may lead to significant advances, pushing forward the boundaries of not only the size of solvable circuit synthesis problems, but also in what can be realized physically as a result of having more efficient circuits. We present a method for quantum circuit synthesis using deterministic walks. Also termed pseudorandom walks, these are walks in which once a starting point is chosen, its path is completely determined. We apply our method to construct a parallel framework for circuit synthesis, and implement one such version performing optimal T-count synthesis over the Clifford+T gate set. We use our software to present examples where parallelization offers a significant speedup on the runtime, as well as directly confirm that the 4-qubit 1-bit full adder has optimal T-count 7 and T-depth 3.

  15. Solution-phase synthesis of metal and/or semiconductor homojunction/heterojunction nanomaterials.

    PubMed

    Feng, Xiumei; Hu, Guanqi; Hu, Jianqiang

    2011-05-01

    The design and architecture of programmable metal-semiconductor nanostructures with excellent optoelectronic properties from metal and semiconductor building blocks with nanoscale dimensions have been a key aim of material scientists due to their central roles in the fabrication of electronic, optical, and optoelectronic nanodevices. This review focuses on the latest advances in the solution-phase synthesis of metal and/or semiconductor homojunction/heterojunction nanomaterials. It begins with the simplest construction of metal/metal and semiconductor/semiconductor homojunctions, and then highlights the synthetic design of metal/metal and semiconductor/semiconductor heterojunction nanostructures with different building blocks. Special emphasis is placed on metal/semiconductor heterojunction nanomaterials, which are the most challenging and promising nanomaterials for future applications in optoelectronic nanodevices. Finally, this review concludes with personal perspectives on the directions for future research in this field.

  16. Facile room-temperature solution-phase synthesis of a spherical covalent organic framework for high-resolution chromatographic separation.

    PubMed

    Yang, Cheng-Xiong; Liu, Chang; Cao, Yi-Meng; Yan, Xiu-Ping

    2015-08-07

    A simple and facile room-temperature solution-phase synthesis was developed to fabricate a spherical covalent organic framework with large surface area, good solvent stability and high thermostability for high-resolution chromatographic separation of diverse important industrial analytes including alkanes, cyclohexane and benzene, α-pinene and β-pinene, and alcohols with high column efficiency and good precision.

  17. Solution-phase synthesis of heteroatom-substituted carbon scaffolds for hydrogen storage.

    PubMed

    Jin, Zhong; Sun, Zhengzong; Simpson, Lin J; O'Neill, Kevin J; Parilla, Philip A; Li, Yan; Stadie, Nicholas P; Ahn, Channing C; Kittrell, Carter; Tour, James M

    2010-11-03

    This paper reports a bottom-up solution-phase process for the preparation of pristine and heteroatom (boron, phosphorus, or nitrogen)-substituted carbon scaffolds that show good surface areas and enhanced hydrogen adsorption capacities and binding energies. The synthesis method involves heating chlorine-containing small organic molecules with metallic sodium at reflux in high-boiling solvents. For heteroatom incorporation, heteroatomic electrophiles are added to the reaction mixture. Under the reaction conditions, micrometer-sized graphitic sheets assembled by 3-5 nm-sized domains of graphene nanoflakes are formed, and when they are heteroatom-substituted, the heteroatoms are uniformly distributed. The substituted carbon scaffolds enriched with heteroatoms (boron ∼7.3%, phosphorus ∼8.1%, and nitrogen ∼28.1%) had surface areas as high as 900 m(2) g(-1) and enhanced reversible hydrogen physisorption capacities relative to pristine carbon scaffolds or common carbonaceous materials. In addition, the binding energies of the substituted carbon scaffolds, as measured by adsorption isotherms, were 8.6, 8.3, and 5.6 kJ mol(-1) for the boron-, phosphorus-, and nitrogen-enriched carbon scaffolds, respectively.

  18. Synthesis of stable C-linked ferrocenyl amino acids and their use in solution-phase peptide synthesis.

    PubMed

    Philip, Anijamol T; Chacko, Shibin; Ramapanicker, Ramesh

    2015-12-01

    Incorporation of ferrocenyl group to peptides is an efficient method to alter their hydrophobicity. Ferrocenyl group can also act as an electrochemical probe when incorporated onto functional peptides. Most often, ferrocene is incorporated onto peptides post-synthesis via amide, ester or triazole linkages. Stable amino acids containing ferrocene as a C-linked side chain are potentially useful building units for the synthesis of ferrocene-containing peptides. We report here an efficient route to synthesize ferrocene-containing amino acids that are stable and can be used in peptide synthesis. Coupling of 2-ferrocenyl-1,3-dithiane and iodides derived from aspartic acid or glutamic acid using n-butyllithium leads to the incorporation of a ferrocenyl unit to the δ-position or ε-position of an α-amino acid. The reduction or hydrolysis of the dithiane group yields an alkyl or an oxo derivative. The usability of the synthesized amino acids is demonstrated by incorporating one of the amino acids in both C-terminus and N-terminus of tripeptides in solution phase.

  19. An Efficient Solution-Phase Synthesis of 4,5,7-Trisubstituted Pyrrolo[3,2-d]pyrimidines

    PubMed Central

    Zhang, Weihe; Liu, Jing; Stashko, Michael A.; Wang, Xiaodong

    2013-01-01

    We have developed an efficient and robust route to synthesize 4,5,7-trisubstituted pyrrolo[3,2-d]pyrimidines as potent kinase inhibitors. This solution-phase synthesis features a SNAr substitution reaction, cross-coupling reaction, one-pot reduction/reductive amination and N-alkylation reaction. These reactions occur rapidly with high yields and have broad substrate scopes. A variety of groups can be selectively introduced into the N5 and C7 positions of 4,5,7-trisubstituted pyrrolopyrimidines at a late stage of the synthesis, thereby providing a highly efficient approach to explore the structure-activity relationships of pyrrolopyrimidine derivatives. Four synthetic analogs have been profiled against a panel of 48 kinases and a new and selective FLT3 inhibitor 9 is identified. PMID:23181516

  20. Further development of a robust workup process for solution-phase high-throughput library synthesis to address environmental and sample tracking issues.

    PubMed

    Kuroda, Noritaka; Hird, Nick; Cork, David G

    2006-01-01

    During further improvement of a high-throughput, solution-phase synthesis system, new workup tools and apparatus for parallel liquid-liquid extraction and evaporation have been developed. A combination of in-house design and collaboration with external manufacturers has been used to address (1) environmental issues concerning solvent emissions and (2) sample tracking errors arising from manual intervention. A parallel liquid-liquid extraction unit, containing miniature high-speed magnetic stirrers for efficient mixing of organic and aqueous phases, has been developed for use on a multichannel liquid handler. Separation of the phases is achieved by dispensing them into a newly patented filter tube containing a vertical hydrophobic porous membrane, which allows only the organic phase to pass into collection vials positioned below. The vertical positioning of the membrane overcomes the hitherto dependence on the use of heavier-than-water, bottom-phase, organic solvents such as dichloromethane, which are restricted due to environmental concerns. Both small (6-mL) and large (60-mL) filter tubes were developed for parallel phase separation in library and template synthesis, respectively. In addition, an apparatus for parallel solvent evaporation was developed to (1) remove solvent from the above samples with highly efficient recovery and (2) avoid the movement of individual samples between their collection on a liquid handler and registration to prevent sample identification errors. The apparatus uses a diaphragm pump to achieve a dynamic circulating closed system with a heating block for the rack of 96 sample vials and an efficient condenser to trap the solvents. Solvent recovery is typically >98%, and convenient operation and monitoring has made the apparatus the first choice for removal of volatile solvents.

  1. Fluorous Parallel Synthesis of A Hydantoin/Thiohydantoin Library

    PubMed Central

    Lu, Yimin; Zhang, Wei

    2007-01-01

    Fluorous tagging strategy is applied to solution-phase parallel synthesis of a library containing hydantoin and thiohydantoin analogs. Two perfluoroalkyl (Rf)-tagged α-amino esters each react with 6 aromatic aldehydes under reductive amination conditions. Twelve amino esters then each react with 10 isocyanates and isothiocyanates in parallel. The resulting 120 ureas and thioureas undergo spontaneous cyclization to form the corresponding hydantoins and thiohydantoins. The intermediate and final product purifications are performed with solid-phase extraction (SPE) over FluoroFlash™ cartridges, no chromatography is required. Using standard instruments and straightforward SPE technique, one chemist accomplished the 120-member library synthesis in less than 5 working days, including starting material synthesis and product analysis. PMID:15789556

  2. Got LiZnP? Solution phase synthesis of filled tetrahedral semiconductors in the nanoregime.

    PubMed

    White, Miles A; Thompson, Michelle J; Miller, Gordon J; Vela, Javier

    2016-02-28

    We report the synthesis and characterization of nanocrystalline LiZnP. The reaction proceeds through a zinc metal intermediate followed by rapid incorporation of lithium and phosphorus. We demonstrate flexibility in the selection of Li, Zn, and P precursors, as well as extension of this method to other half-Heusler phases.

  3. Solution phase synthesis of aluminum-doped silicon nanoparticles via room-temperature, solvent based chemical reduction of silicon tetrachloride

    NASA Astrophysics Data System (ADS)

    Mowbray, Andrew James

    We present a method of wet chemical synthesis of aluminum-doped silicon nanoparticles (Al-doped Si NPs), encompassing the solution-phase co-reduction of silicon tetrachloride (SiCl4) and aluminum chloride (AlCl 3) by sodium naphthalide (Na[NAP]) in 1,2-dimethoxyethane (DME). The development of this method was inspired by the work of Baldwin et al. at the University of California, Davis, and was adapted for our research through some noteworthy procedural modifications. Centrifugation and solvent-based extraction techniques were used throughout various stages of the synthesis procedure to achieve efficient and well-controlled separation of the Si NP product from the reaction media. In addition, the development of a non-aqueous, formamide-based wash solution facilitated simultaneous removal of the NaCl byproduct and Si NP surface passivation via attachment of 1-octanol to the particle surface. As synthesized, the Si NPs were typically 3-15 nm in diameter, and were mainly amorphous, as opposed to crystalline, as concluded from SAED and XRD diffraction pattern analysis. Aluminum doping at various concentrations was accomplished via the inclusion of aluminum chloride (AlCl3); which was in small quantities dissolved into the synthesis solution to be reduced alongside the SiCl4 precursor. The introduction of Al into the chemically-reduced Si NP precipitate was not found to adversely affect the formation of the Si NPs, but was found to influence aspects such as particle stability and dispersibility throughout various stages of the procedure. Analytical techniques including transmission electron microscopy (TEM), FTIR spectroscopy, and ICP-optical emission spectroscopy were used to comprehensively characterize the product NPs. These methods confirm both the presence of Al and surface-bound 1-octanol in the newly formed Si NPs.

  4. Solution-Phase Perfluoroalkylation of C60 Leads to Efficient and Selective Synthesis of Bis-Perfluoroalkylated Fullerenes

    PubMed Central

    Kuvychko, Igor V.; Strauss, Steven H.; Boltalina, Olga V.

    2012-01-01

    A solution-phase perfluoroalkylation of C60 with a series of RFI reagents was studied. The effects of molar ratio of the reagents, reaction time, and presence of copper metal promoter on fullerene conversion and product composition were evaluated. Ten aliphatic and aromatic RFI reagents were investigated (CF3I, C2F5I, n-C3F7I, i-C3F7I, n-C4F9I, (CF3)(C2F5)CFI, n-C8F17I, C6F5CF2I, C6F5I, and 1,3-(CF3)2C6F3I) and eight of them (except for C6F5I and 1,3-(CF3)2C6F3I) were found to add the respective RF groups to C60 in solution. Efficient and selective synthesis of C60(RF)2 derivatives was developed. PMID:25843973

  5. Shape-controlled synthesis of Cu2O nanocrystals by one pot solution-phase reduction process

    NASA Astrophysics Data System (ADS)

    Zhang, Meili; Yu, Jinpeng; Zhang, Jianmin; Lan, Qi; Dai, Jia; Huang, Yaohan; Li, Guangli; Fan, Qingfei; Fan, Ximei; Zhou, Zuowan

    2017-03-01

    An interesting evolution to prepare shape-controlled Cu2O nanocrystals was realized by a convenient one pot synthesis. The Cu2O nanocrystals with different shapes can be obtained simply by adjusting the composition of reaction system. And, a plausible mechanism was also proposed to explain the nanostructures formation. The surface of Cu2O spheres with thorn exhibited high photocatalytic activity on the degradation of methyl orange (MO) solution under visible light irradiation. The photodegradation efficiency of MO solution reach up to 99.67% at the first 10 min. It is still as high as 98% even at the end of the fourth cycle.

  6. Controllable synthesis and growth mechanism of {alpha}-Co(OH){sub 2} nanorods and nanoplates by a facile solution-phase route

    SciTech Connect

    Wang Wenzhong; Feng Kai; Wang Zhi; Ma Yunyan; Zhang Suyun; Liang Yujie

    2011-12-15

    A facile chemical precipitation route has been developed to control synthesis of {alpha}-cobalt hydroxide nanostructures with rod-like and plate-like morphologies. The {alpha}-Co(OH){sub 2} nanorods were achieved in large quantity when the experiments were carried out in the presence of a suitable shape-controlling reagent polyvinyl pyrrolidone (PVP), while the {alpha}-Co(OH){sub 2} nanoplates were obtained when the experiments were conducted in the absence of PVP, whilst keeping other experimental conditions constant. The chemical composition and morphologies of the as-prepared {alpha}-Co(OH){sub 2} nanoparticles were characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The effect of polymer PVP on the morphologies of {alpha}-Co(OH){sub 2} nanoparticles were discussed in detail. The results indicated that PVP played a key role for the formation of {alpha}-Co(OH){sub 2} nanorods. The growth mechanism of the as-synthesized nanorods and nanoplates were discussed in detail based on the experimental results. A possible growth mechanism has been proposed to illustrate the growth of {alpha}-Co(OH){sub 2} nanorods. - Graphical abstract: A facile solution-phase route has been developed to synthesize {alpha}-Co(OH){sub 2} nanorods and nanoplates. The possible growth mechanism of nanorods and nanoplates was proposed. Highlights: Black-Right-Pointing-Pointer A facile controllable route was described for {alpha}-Co(OH){sub 2} nanowires and nanoplates. Black-Right-Pointing-Pointer The {alpha}-Co(OH){sub 2} nanowires were achieved in the presence of shape controller PVP. Black-Right-Pointing-Pointer The {alpha}-Co(OH){sub 2} nanoplates were obtained in the absence of shape controller PVP. Black-Right-Pointing-Pointer The shape controller PVP played a key role in the formation of {alpha}-Co(OH){sub 2} nanowires.

  7. Solution-phase parallel synthesis and screening of anti-tumor activities from fenbufen and ethacrynic acid libraries.

    PubMed

    Su, Yuan-Hsiao; Chiang, Li-Wu; Jeng, Kee-Ching; Huang, Ho-Lien; Chen, Jenn-Tzong; Lin, Wuu-Jyh; Huang, Chia-Wen; Yu, Chung-Shan

    2011-03-01

    The derivatives with fenbufen and ethacrynic acid core compounds was synthesized through a facial preparation of 1-amino-4-azidobutane. The subsequent coupling with 102 members of carboxylic acids afforded amide products. The in situ screening using colorimetric assay with 3-(4.5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide showed that fenbufen but not ethacrynic acid butyl amide members displayed the cytotoxicities to tumor cells substantially, including two human cell lines (MCF7 and A549) and two murine cell lines (C26 and TRAMP-C1). Three fenbufen analogs were found to have a good anti-tumor activity comparable to cisplatin.

  8. Solution-phase synthesis of single-crystal Cu3Si nanowire arrays on diverse substrates with dual functions as high-performance field emitters and efficient anti-reflective layers

    NASA Astrophysics Data System (ADS)

    Yuan, Fang-Wei; Wang, Chiu-Yen; Li, Guo-An; Chang, Shu-Hao; Chu, Li-Wei; Chen, Lih-Juann; Tuan, Hsing-Yu

    2013-09-01

    There is strong and growing interest in applying metal silicide nanowires as building blocks for a new class of silicide-based applications, including spintronics, nano-scale interconnects, thermoelectronics, and anti-reflective coating materials. Solution-phase environments provide versatile materials chemistry as well as significantly lower production costs compared to gas-phase synthesis. However, solution-phase synthesis of silicide nanowires remains challenging due to the lack of fundamental understanding of silicidation reactions. In this study, single-crystalline Cu3Si nanowire arrays were synthesized in an organic solvent. Self-catalyzed, dense single-crystalline Cu3Si nanowire arrays were synthesized by thermal decomposition of monophenylsilane in the presence of copper films or copper substrates at 420 to 475 °C and 10.3 MPa in supercritical benzene. The solution-grown Cu3Si nanowire arrays serve dual functions as field emitters and anti-reflective layers, which are reported on copper silicide materials for the first time. Cu3Si nanowires exhibit superior field-emission properties, with a turn-on-voltage as low as 1.16 V μm-1, an emission current density of 8 mA cm-2 at 4.9 V μm-1, and a field enhancement factor (β) of 1500. Cu3Si nanowire arrays appear black with optical absorption less than 5% between 400 and 800 nm with minimal reflectance, serving as highly efficient anti-reflective layers. Moreover, the Cu3Si nanowires could be grown on either rigid or flexible substrates (PI). This study shows that solution-phase silicide reactions are adaptable for high-quality silicide nanowire growth and demonstrates their promise towards fabrication of metal silicide-based devices.There is strong and growing interest in applying metal silicide nanowires as building blocks for a new class of silicide-based applications, including spintronics, nano-scale interconnects, thermoelectronics, and anti-reflective coating materials. Solution-phase environments

  9. Solution-phase synthesis of single-crystal Cu3Si nanowire arrays on diverse substrates with dual functions as high-performance field emitters and efficient anti-reflective layers.

    PubMed

    Yuan, Fang-Wei; Wang, Chiu-Yen; Li, Guo-An; Chang, Shu-Hao; Chu, Li-Wei; Chen, Lih-Juann; Tuan, Hsing-Yu

    2013-10-21

    There is strong and growing interest in applying metal silicide nanowires as building blocks for a new class of silicide-based applications, including spintronics, nano-scale interconnects, thermoelectronics, and anti-reflective coating materials. Solution-phase environments provide versatile materials chemistry as well as significantly lower production costs compared to gas-phase synthesis. However, solution-phase synthesis of silicide nanowires remains challenging due to the lack of fundamental understanding of silicidation reactions. In this study, single-crystalline Cu3Si nanowire arrays were synthesized in an organic solvent. Self-catalyzed, dense single-crystalline Cu3Si nanowire arrays were synthesized by thermal decomposition of monophenylsilane in the presence of copper films or copper substrates at 420 to 475 °C and 10.3 MPa in supercritical benzene. The solution-grown Cu3Si nanowire arrays serve dual functions as field emitters and anti-reflective layers, which are reported on copper silicide materials for the first time. Cu3Si nanowires exhibit superior field-emission properties, with a turn-on-voltage as low as 1.16 V μm(-1), an emission current density of 8 mA cm(-2) at 4.9 V μm(-1), and a field enhancement factor (β) of 1500. Cu3Si nanowire arrays appear black with optical absorption less than 5% between 400 and 800 nm with minimal reflectance, serving as highly efficient anti-reflective layers. Moreover, the Cu3Si nanowires could be grown on either rigid or flexible substrates (PI). This study shows that solution-phase silicide reactions are adaptable for high-quality silicide nanowire growth and demonstrates their promise towards fabrication of metal silicide-based devices.

  10. Titanium(IV) isopropoxide mediated solution phase reductive amination on an automated platform: application in the generation of urea and amide libraries.

    PubMed

    Bhattacharyya, S; Fan, L; Vo, L; Labadie, J

    2000-04-01

    Amine libraries and their derivatives are important targets for high throughput synthesis because of their versatility as medicinal agents and agrochemicals. As a part of our efforts towards automated chemical library synthesis, a titanium(IV) isopropoxide mediated solution phase reductive amination protocol was successfully translated to automation on the Trident(TM) library synthesizer of Argonaut Technologies. An array of 24 secondary amines was prepared in high yield and purity from 4 primary amines and 6 carbonyl compounds. These secondary amines were further utilized in a split synthesis to generate libraries of ureas, amides and sulfonamides in solution phase on the Trident(TM). The automated runs included 192 reactions to synthesize 96 ureas in duplicate and 96 reactions to synthesize 48 amides and 48 sulfonamides. A number of polymer-assisted solution phase protocols were employed for parallel work-up and purification of the products in each step.

  11. Synthesis of Met-enkephalin by solution-phase peptide synthesis methodology utilizing para-toluene sulfonic acid as N-terminal masking of l-methionine amino acid.

    PubMed

    Khan, Riaz A

    2016-12-01

    The Met-enkephalin, Tyr-Gly-Gly-Phe-Met, was synthesized by the solution-phase synthesis (SPS) methodology employing -OBzl group as carboxyls' protection, while the t-Boc groups were employed for the N-terminal α-amines' protection for the majority of the amino acids of the pentapeptide sequence. The l-methionine (l-Met) amino acid was used as PTSA.Met-OBzl obtained from the simultaneous protection of the α-amino, and carboxyl group with para-toluene sulfonic acid (PTSA) and as-OBzl ester, respectively in a C-terminal start of the 2 + 2 + 1 fragments condensation convergent synthetic approach. The protection strategy provided a short, single-step, simultaneous, orthogonal, nearly quantitative, robust, and stable process to carry through the protected l-methionine and l-phenylalanine coupling without any structural deformities during coupling and workups. The structurally confirmed final pentapeptide product was feasibly obtained in good yields through the current approach.

  12. Automatic logic synthesis for parallel alternating latches clocking schemes

    NASA Astrophysics Data System (ADS)

    Guerrero, D.; Bellido, M.; Juan, J.; Millan, A.; Ruiz, P.; Ostua, E.; Viejo, J.

    2007-05-01

    This paper proposes a VHDL coding technique that allows for the automatic synthesis of digital circuits using the so called Parallel Alternating Latches Clocking Schemes (PALACS). The proposed method greatly improves the applicability of PALACS and its benefits. This technique is verified through design examples in three different CMOS processes and using logic level simulation, with successful results in all the cases.

  13. Building blocks for the solution phase synthesis of oligonucleotides: regioselective hydrolysis of 3',5'-Di-O-levulinylnucleosides using an enzymatic approach.

    PubMed

    García, Javier; Fernández, Susana; Ferrero, Miguel; Sanghvi, Yogesh S; Gotor, Vicente

    2002-06-28

    A short and convenient synthesis of 3'- and 5'-O-levulinyl-2'-deoxynucleosides has been developed from the corresponding 3',5'-di-O-levulinyl derivatives by regioselective enzymatic hydrolysis, avoiding several tedious chemical protection/deprotection steps. Thus, Candida antartica lipase B (CAL-B) was found to selectively hydrolyze the 5'-levulinate esters, furnishing 3'-O-levulinyl-2'-deoxynucleosides 3 in >80% isolated yields. On the other hand, immobilized Pseudomonas cepacia lipase (PSL-C) and Candida antarctica lipase A (CAL-A) exhibit the opposite selectivity toward the hydrolysis at the 3'-position, affording 5'-O-levulinyl derivatives 4 in >70% yields. A similar hydrolysis procedure was successfully extended to the synthesis of 3'- and 5'-O-levulinyl-protected 2'-O-alkylribonucleosides 7 and 8. This work demonstrates for the first time application of commercial CAL-B and PSL-C toward regioselective hydrolysis of levulinyl esters with excellent selectivity and yields. It is noteworthy that protected cytidine and adenosine base derivatives were not adequate substrates for the enzymatic hydrolysis with CAL-B, whereas PSL-C was able to accommodate protected bases during selective hydrolysis. In addition, we report an improved synthesis of dilevulinyl esters using a polymer-bound carbodiimide as a replacement for dicyclohexylcarbodiimide (DCC), thus considerably simplifying the workup for esterification reactions.

  14. Gram-scale solution-phase synthesis of selective sodium bicarbonate co-transport inhibitor S0859: in vitro efficacy studies in breast cancer cells.

    PubMed

    Larsen, Ann M; Krogsgaard-Larsen, Niels; Lauritzen, Gitte; Olesen, Christina W; Honoré Hansen, Steen; Boedtkjer, Ebbe; Pedersen, Stine F; Bunch, Lennart

    2012-10-01

    Na(+)-coupled HCO(3)(-) transporters (NBCs) mediate the transport of bicarbonate ions across cell membranes and are thus ubiquitous regulators of intracellular pH. NBC dysregulation is associated with a range of diseases; for instance, NBCn1 is strongly up-regulated in a model of ErbB2-dependent breast cancer, a malignant and widespread cancer with no targeted treatment options, and single-nucleotide polymorphisms in NBCn1 genetically link to breast cancer development and hypertension. The N-cyanosulfonamide S0859 has been shown to selectively inhibit NBCs, and its availability on the gram scale is therefore of significant interest to the scientific community. Herein we describe a short and efficient synthesis of S0859 with an overall yield of 45 % from commercially available starting materials. The inhibitory effect of S0859 on recovery of intracellular pH after an acid load was verified in human and murine cancer cell lines in Ringer solutions. However, S0859 binds very strongly to components in plasma, and accordingly, measurements on isolated murine tissues showed no effect of S0859 at concentrations up to 50 μM.

  15. Controllable synthesis and growth mechanism of α-Co(OH) 2 nanorods and nanoplates by a facile solution-phase route

    NASA Astrophysics Data System (ADS)

    Wang, Wenzhong; Feng, Kai; Wang, Zhi; Ma, Yunyan; Zhang, Suyun; Liang, Yujie

    2011-12-01

    A facile chemical precipitation route has been developed to control synthesis of α-cobalt hydroxide nanostructures with rod-like and plate-like morphologies. The α-Co(OH) 2 nanorods were achieved in large quantity when the experiments were carried out in the presence of a suitable shape-controlling reagent polyvinyl pyrrolidone (PVP), while the α-Co(OH) 2 nanoplates were obtained when the experiments were conducted in the absence of PVP, whilst keeping other experimental conditions constant. The chemical composition and morphologies of the as-prepared α-Co(OH) 2 nanoparticles were characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). The effect of polymer PVP on the morphologies of α-Co(OH) 2 nanoparticles were discussed in detail. The results indicated that PVP played a key role for the formation of α-Co(OH) 2 nanorods. The growth mechanism of the as-synthesized nanorods and nanoplates were discussed in detail based on the experimental results. A possible growth mechanism has been proposed to illustrate the growth of α-Co(OH) 2 nanorods.

  16. A Laboratory Preparation of Aspartame Analogs Using Simultaneous Multiple Parallel Synthesis Methodology

    ERIC Educational Resources Information Center

    Qvit, Nir; Barda, Yaniv; Gilon, Chaim; Shalev, Deborah E.

    2007-01-01

    This laboratory experiment provides a unique opportunity for students to synthesize three analogues of aspartame, a commonly used artificial sweetener. The students are introduced to the powerful and useful method of parallel synthesis while synthesizing three dipeptides in parallel using solid-phase peptide synthesis (SPPS) and simultaneous…

  17. A parallel synthesis demonstration library of tri-substituted indazoles containing new antimutagenic/antioxidant hits related to benzydamine.

    PubMed

    Menon, Sanjay; Vaidya, Hemin; Pillai, Segaran; Vidya, Ramdas; Mitscher, Lester A

    2003-08-01

    A solution phase strategy for the multiple parallel synthesis of a demonstration library of indazoles is described by which regio-selectivity problems inherent to previous syntheses of this nucleus are largely overcome. Synthesis of selected components proceeded satisfactorily indicating that a fully realized library of indazole analogs could readily be produced using this methodology. Simple modifications of the basic nucleophilic aromatic substitution route unambiguously produce a range of N-1 substitutions (alkyl, aryl and aralkyl) in 50-75% yields. Next a range of substituents was introduced at the C-3 position in 50-80% yields by O-alkylation. Careful choice of reagents and reaction conditions were required to prevent by-product formation due to competing alkylation at N-2 (trace to 15% yields). When present, these contaminants were readily removed by chromofiltration. A third diversity site was sketched in at C-5 in 75-90% yield by reductive alkylation or acylation. Screening of some of the demonstration library members in vitro revealed highly active antioxidants suggesting that producing a full library would be worthwhile.

  18. Alternative solvents for elevated-temperature solid-phase parallel synthesis. Application to thionation of amides.

    PubMed

    Coats, Steven J; Link, Jeffrey S; Hlasta, Dennis J

    2003-03-06

    A new class of higher-boiling solvents was investigated for elevated-temperature solid-phase parallel synthesis. Extremely low vapor pressures at high temperature and a broader range of solvent effect tuning make this new class of solvents an ideal choice for high-temperature parallel solid-phase synthesis. Benzyl benzoate is identified as a superior high-boiling solvent for parallel solid-phase Lawesson's thionation reactions.

  19. Combinatorial parallel synthesis and automated screening of a novel class of liquid crystalline materials.

    PubMed

    Deeg, Oliver; Kirsch, Peer; Pauluth, Detlef; Bäuerle, Peter

    2002-12-07

    Combinatorial parallel synthesis has led to the rapid generation of a single-compound library of novel fluorinated quaterphenyls. Subsequent automated screening revealed liquid crystalline (LC) behaviour and gave qualitative relationships of molecular structures and solid state properties.

  20. Parallel Combinatorial Synthesis of Azo Dyes: A Combinatorial Experiment Suitable for Undergraduate Laboratories

    ERIC Educational Resources Information Center

    Gung, Benjamin W.; Taylor, Richard T.

    2004-01-01

    An experiment in the parallel synthesis of azo dyes that demonstrates the concepts of structure-activity relationships and chemical diversity with vivid colors is described. It is seen that this experiment is suitable for the second-semester organic chemistry laboratory and also for the one-semester organic laboratory.

  1. One-Pot Parallel Synthesis of Alkyl Sulfides, Sulfoxides, and Sulfones.

    PubMed

    Bogolubsky, Andrey V; Moroz, Yurii S; Mykhailiuk, Pavel K; Ostapchuk, Eugeniy N; Rudnichenko, Alexander V; Dmytriv, Yurii V; Bondar, Anna N; Zaporozhets, Olga A; Pipko, Sergey E; Doroschuk, Roman A; Babichenko, Liudmyla N; Konovets, Anzhelika I; Tolmachev, Andrey

    2015-06-08

    A simple and cost-effective one-pot parallel synthesis approach to sulfides, sulfoxides, and sulfones from thiourea was elaborated. The method combines two procedures optimized to the parallel synthesis conditions: alkylation of thiourea with alkyl chlorides and mono or full oxidation of in situ generated sulfides with H2O2 or H2O2-(NH4)2MoO4. The experimental set up required commonly used lab equipment: conventional oven and ultrasonic bath; the work up includes filtration or extraction with chloroform. The method was evaluated on an 81 member library of drug-like sulfides, sulfoxides, and sulfones yielding the compounds on a 30-300 mg scale. A small-scale synthesis of 2-(benzhydrylsulfinyl)acetamide (modafinil) utilizing our approach resulted in similar efficiency to the published procedures.

  2. Solution-Phase Processes of Macromolecular Crystallization

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Minamitani, Elizabeth Forsythe

    2004-01-01

    We have proposed, for the tetragonal form of chicken egg lysozyme, that solution phase assembly processes are needed to form the growth units for crystal nucleation and growth. The starting point for the self-association process is the monomeric protein, and the final crystallographic symmetry is defined by the initial dimerization interactions of the monomers and subsequent n-mers formed, which in turn are a function of the crystallization conditions. It has been suggested that multimeric proteins generally incorporate the underlying multimers symmetry into the final crystallographic symmetry. We posed the question of what happens to a protein that is known to grow as an n-mer when it is placed in solution conditions where it is monomeric. The trypsin-treated, or cut, form of the protein canavalin (CCAN) has been shown to nucleate and grow crystals as a trimer from neutral to slightly acidic solutions. Under these conditions the solution is composed almost wholly of trimers. The insoluble protein can be readily dissolved by weakly basic solution, which results in a solution that is monomeric. There are three possible outcomes to an attempt at crystallization of the protein under monomeric (high pH) conditions: 1) we will obtain the same crystals as under trimer conditions, but at different protein concentrations governed by the self association equilibria; 2) we will obtain crystals having a different symmetry, based upon a monomeric growth unit; 3) we will not obtain crystals. Obtaining the first result would be indicative that the solution-phase self-association process is critical to the crystal nucleation and growth process. The second result would be less clear, as it may also reflect a pH-dependent shift in the trimer-trimer molecular interactions. The third result, particularly for experiments in the transition pH's between trimeric and monomeric CCAN, would indicate that the monomer does not crystallize, and that solution phase self association is not part

  3. Synthesis of spherical parallel manipulator for dexterous medical task

    NASA Astrophysics Data System (ADS)

    Chaker, Abdelbadiâ; Mlika, Abdelfattah; Laribi, Med Amine; Romdhane, Lotfi; Zeghloul, Saïd

    2012-06-01

    This paper deals with the design and the analysis of a spherical parallel manipulator (SPM) for a haptic minimally invasive surgery application. First the medical task was characterized with the help of a surgeon who performed a suture technique called anastomosis. A Vicon system was used to capture the motion of the surgeon, which yielded the volume swept by the tool during the anastomosis operation. The identified workspace can be represented by a cone with a half vertex angle of 26°. A multi objective optimization procedure based on genetic algorithms was then carried out to find the optimal SPM. Two criteria were considered, i.e., task workspace and mechanism dexterity. The optimized SPM was then analyzed to determine the error on the orientation of the end effector as a function of the manufacturing errors of the different links of the mechanism.

  4. Dimensional synthesis of a 3-DOF parallel manipulator with full circle rotation

    NASA Astrophysics Data System (ADS)

    Ni, Yanbing; Wu, Nan; Zhong, Xueyong; Zhang, Biao

    2015-07-01

    Parallel robots are widely used in the academic and industrial fields. In spite of the numerous achievements in the design and dimensional synthesis of the low-mobility parallel robots, few research efforts are directed towards the asymmetric 3-DOF parallel robots whose end-effector can realize 2 translational and 1 rotational(2T1R) motion. In order to develop a manipulator with the capability of full circle rotation to enlarge the workspace, a new 2T1R parallel mechanism is proposed. The modeling approach and kinematic analysis of this proposed mechanism are investigated. Using the method of vector analysis, the inverse kinematic equations are established. This is followed by a vigorous proof that this mechanism attains an annular workspace through its circular rotation and 2 dimensional translations. Taking the first order perturbation of the kinematic equations, the error Jacobian matrix which represents the mapping relationship between the error sources of geometric parameters and the end-effector position errors is derived. With consideration of the constraint conditions of pressure angles and feasible workspace, the dimensional synthesis is conducted with a goal to minimize the global comprehensive performance index. The dimension parameters making the mechanism to have optimal error mapping and kinematic performance are obtained through the optimization algorithm. All these research achievements lay the foundation for the prototype building of such kind of parallel robots.

  5. Pfizer Global Virtual Library (PGVL): a chemistry design tool powered by experimentally validated parallel synthesis information.

    PubMed

    Hu, Qiyue; Peng, Zhengwei; Sutton, Scott C; Na, Jim; Kostrowicki, Jaroslav; Yang, Bo; Thacher, Thomas; Kong, Xianjun; Mattaparti, Sarathy; Zhou, Joe Zhongxiang; Gonzalez, Javier; Ramirez-Weinhouse, Michele; Kuki, Atsuo

    2012-11-12

    An unprecedented amount of parallel synthesis information was accumulated within Pfizer over the past 12 years. This information was captured by an informatics tool known as PGVL (Pfizer Global Virtual Library). PGVL was used for many aspects of drug discovery including automated reactant mining and reaction product formation to build a synthetically feasible virtual compound collection. In this report, PGVL is discussed in detail. The chemistry information within PGVL has been used to extract synthesis and design information using an intuitive desktop Graphic User Interface, PGVL Hub. Several real-case examples of PGVL are also presented.

  6. Confined synthesis of graphene wrapped LiMn0.5Fe0.5PO4 composite via two step solution phase method as high performance cathode for Li-ion batteries

    NASA Astrophysics Data System (ADS)

    Xiang, Wei; Wu, Zhen-Guo; Wang, En-Hui; Chen, Ming-Zhe; Song, Yang; Zhang, Ji-Bin; Zhong, Yan-Jun; Chou, Shu-Lei; Luo, Jian-Hong; Guo, Xiao-Dong

    2016-10-01

    A novel strategy for confined synthesis of graphene wrapped nano-sized LiMn0.5Fe0.5PO4 hybrid composite has been developed, including co-precipitation and solvothermal reactions. The LiMn0.5Fe0.5PO4 nanoparticles with a constrained diameter of 20 nm are homogeneously wrapped by a continuous interconnected graphene sheets. The mechanism and composite structure evolution during the process are carefully investigated and discussed. With the shortened Li+ diffusion paths and enhanced electron conductivity, the hybrid composite shows high discharge capacity and superior rate performance with the discharge capacities of 166 mA h g-1 at 0.1 C and 90 mA h g-1 at 20 C. Excellent cycle stability is also demonstrated with only about 7.8% capacity decay after 500 cycles at 1 C.

  7. Sequence-Defined Oligomers from Hydroxyproline Building Blocks for Parallel Synthesis Applications.

    PubMed

    Kanasty, Rosemary L; Vegas, Arturo J; Ceo, Luke M; Maier, Martin; Charisse, Klaus; Nair, Jayaprakash K; Langer, Robert; Anderson, Daniel G

    2016-08-08

    The functionality of natural biopolymers has inspired significant effort to develop sequence-defined synthetic polymers for applications including molecular recognition, self-assembly, and catalysis. Conjugation of synthetic materials to biomacromolecules has played an increasingly important role in drug delivery and biomaterials. We developed a controlled synthesis of novel oligomers from hydroxyproline-based building blocks and conjugated these materials to siRNA. Hydroxyproline-based monomers enable the incorporation of broad structural diversity into defined polymer chains. Using a perfluorocarbon purification handle, we were able to purify diverse oligomers through a single solid-phase extraction method. The efficiency of synthesis was demonstrated by building 14 unique trimers and 4 hexamers from 6 diverse building blocks. We then adapted this method to the parallel synthesis of hundreds of materials in 96-well plates. This strategy provides a platform for the screening of libraries of modified biomolecules.

  8. Rapid parallel synthesis of bioactive folded cyclotides using a tea-bag approach

    PubMed Central

    Aboye, Teshome; Kuang, Yuting; Neamati, Nouri

    2015-01-01

    We report here for the first time the rapid parallel production of bioactive folded cyclotides by using Fmoc-based solid-phase peptide synthesis in combination with a tea-bag approach. Using this approach we efficiently synthesized 15 different analogs of the CXCR4 antagonist cyclotide MCo-CVX-5c. Cyclotides were cyclized using a single-pot cyclization/folding reaction in the presence of reduced glutathione. Natively folded cyclotides were quickly purified from the cyclization/folding crude by activated thiol sepharose-based chromatography. The different folded cyclotide analogs were finally tested for their ability to inhibit the CXCR4 receptor in a cell-based assay. These results indicate that this approach can be used for the efficient chemical synthesis of cyclotide-based libraries that can be easily interfaced with solution or cell-based assays for the rapid screening of novel cyclotides with improved biological properties. PMID:25663016

  9. Aliphatic polyurethane-silica nanocomposites prepared by the parallel synthesis: Morphology and mechanical characteristics

    NASA Astrophysics Data System (ADS)

    Gofman, I. V.; Sukhanova, T. E.; Vylegzhanina, M. É.; Abalov, I. V.; Stepanova, I. S.; Trofimov, A. E.; Ten'kovtsev, A. V.

    2010-03-01

    Films of aliphatic polyurethane-silica composites containing up to 27.3 mol % of SiO2 nanoparticles have been prepared by the parallel synthesis using the sol-gel technology. It has been revealed that the variations in the mechanical properties of these materials with increasing concentration of nanoparticles exhibit a nontrivial behavior: the ultimate strain gradually increases, whereas the elastic modulus and the yield stress decrease. A correlation of the changes observed in the mechanical characteristics with an increase in the free volume of the material with increasing silica concentration has been established. Atomic-force microscopy has confirmed the existence of a developed system of nanopores with characteristic sizes from 15 to 100 nm in the materials under investigation.

  10. Simple plate-based, parallel synthesis of disulfide fragments using the CuAAC click reaction.

    PubMed

    Turner, David M; Tom, Christopher T M B; Renslo, Adam R

    2014-12-08

    Disulfide exchange screening is a site-directed approach to fragment-based lead discovery that requires a bespoke library of disulfide-containing fragments. Previously, we described a simple one-pot, two-step synthesis of disulfide fragments from amine- or acid-bearing starting materials. Here, we describe the synthesis of disulfide fragments that bear a 1,4-substituted-1,2,3-triazole linkage between disulfide and molecular diversity element. This work establishes the compatibility of copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) chemistry with a one-pot, two-step reaction sequence that can be readily parallelized. We performed 96 reactions in a single deep-well microtiter plate, employing 48 alkynes and two different azide linker reagents. From this effort, a total of 81 triazole-containing disulfide fragments were obtained in useful isolated yields. Thus, CuAAC chemistry offers an experimentally convenient method to rapidly prepare disulfide fragments that are structurally distinct from fragments accessed via amide, sulfonamide, or isocyanate chemistries.

  11. Parallel Synthesis of Poly(amino ether)-Templated Plasmonic Nanoparticles for Transgene Delivery

    PubMed Central

    2015-01-01

    Plasmonic nanoparticles have been increasingly investigated for numerous applications in medicine, sensing, and catalysis. In particular, gold nanoparticles have been investigated for separations, sensing, drug/nucleic acid delivery, and bioimaging. In addition, silver nanoparticles demonstrate antibacterial activity, resulting in potential application in treatments against microbial infections, burns, diabetic skin ulcers, and medical devices. Here, we describe the facile, parallel synthesis of both gold and silver nanoparticles using a small set of poly(amino ethers), or PAEs, derived from linear polyamines, under ambient conditions and in absence of additional reagents. The kinetics of nanoparticle formation were dependent on PAE concentration and chemical composition. In addition, yields were significantly greater in case of PAEs when compared to 25 kDa poly(ethylene imine), which was used as a standard catonic polymer. Ultraviolet radiation enhanced the kinetics and the yield of both gold and silver nanoparticles, likely by means of a coreduction effect. PAE-templated gold nanoparticles demonstrated the ability to deliver plasmid DNA, resulting in transgene expression, in 22Rv1 human prostate cancer and MB49 murine bladder cancer cell lines. Taken together, our results indicate that chemically diverse poly(amino ethers) can be employed for rapidly templating the formation of metal nanoparticles under ambient conditions. The simplicity of synthesis and chemical diversity make PAE-templated nanoparticles useful tools for several applications in biotechnology, including nucleic acid delivery. PMID:25084138

  12. Parallel microfluidic synthesis of size-tunable polymeric nanoparticles using 3D flow focusing towards in vivo study

    PubMed Central

    Lim, Jong-Min; Bertrand, Nicolas; Valencia, Pedro M.; Rhee, Minsoung; Langer, Robert; Jon, Sangyong; Farokhzad, Omid C.; Karnik, Rohit

    2014-01-01

    Microfluidic synthesis of nanoparticles (NPs) can enhance the controllability and reproducibility in physicochemical properties of NPs compared to bulk synthesis methods. However, applications of microfluidic synthesis are typically limited to in vitro studies due to low production rates. Herein, we report the parallelization of NP synthesis by 3D hydrodynamic flow focusing (HFF) using a multilayer microfluidic system to enhance the production rate without losing the advantages of reproducibility, controllability, and robustness. Using parallel 3D HFF, polymeric poly(lactide-co-glycolide)-b-polyethyleneglycol (PLGA-PEG) NPs with sizes tunable in the range of 13–150 nm could be synthesized reproducibly with high production rate. As a proof of concept, we used this system to perform in vivo pharmacokinetic and biodistribution study of small (20 nm diameter) PLGA-PEG NPs that are otherwise difficult to synthesize. Microfluidic parallelization thus enables synthesis of NPs with tunable properties with production rates suitable for both in vitro and in vivo studies. PMID:23969105

  13. Fmoc-based peptide thioester synthesis with self-purifying effect: heading to native chemical ligation in parallel formats.

    PubMed

    Thomas, Franziska

    2013-03-01

    The chemical synthesis of proteins has facilitated functional studies of proteins due to the site-specific incorporation of post-translational modifications, labels, and non-proteinogenic amino acids. Moreover, native chemical ligation provides facile access to proteins by chemical means. However, the application of the native chemical ligation reaction in the synthesis of parallel formats such as protein arrays has been complicated because of the often cumbersome and time-consuming synthesis of the required peptide thioesters. An Fmoc-based peptide thioester synthesis with self-purification on the sulfonamide 'safety-catch' linker widens this bottleneck because HPLC purification can be avoided. The method is based on an on-resin cyclization-thiolysis reaction sequence. A macrocyclization via the N-terminus of the full-length peptide followed by a thiolytic C-terminal ring opening allows selective detachment of the truncation products and the full-length peptide. A brief overview of the chemical aspects of this method is provided including the optimization steps and the automation process. Furthermore, the application of the cyclization-thiolysis approach combined with the native chemical ligation reaction in the parallel synthesis of a library of 16 SH3-domain variants of SHO1 in yeast is described, demonstrating the value of this new technique for the chemical synthesis of protein arrays.

  14. Solution phase van der Waals epitaxy of ZnO wire arrays.

    PubMed

    Zhu, Yue; Zhou, Yong; Utama, Muhammad Iqbal Bakti; de la Mata, María; Zhao, Yanyuan; Zhang, Qing; Peng, Bo; Magen, Cesar; Arbiol, Jordi; Xiong, Qihua

    2013-08-21

    As an incommensurate epitaxy, van der Waals epitaxy allows defect-free crystals to grow on substrates even with a large lattice mismatch. Furthermore, van der Waals epitaxy is proposed as a universal platform where heteroepitaxy can be achieved irrespective of the nature of the overlayer material and the method of crystallization. Here we demonstrate van der Waals epitaxy in solution phase synthesis for seedless and catalyst-free growth of ZnO wire arrays on phlogopite mica at low temperature. A unique incommensurate interface is observed even with the incomplete initial wetting of ZnO onto the substrate. Interestingly, the imperfect contacting layer does not affect the crystalline and optical properties of other parts of the wires. In addition, we present patterned growth of a well-ordered array with hexagonal facets and in-plane alignment. We expect our seedless and catalyst-free solution phase van der Waals epitaxy synthesis to be widely applicable in other materials and structures.

  15. Parallel evolution of Nitric Oxide signaling: Diversity of synthesis & memory pathways

    PubMed Central

    Moroz, Leonid L.; Kohn, Andrea B.

    2014-01-01

    The origin of NO signaling can be traceable back to the origin of life with the large scale of parallel evolution of NO synthases (NOSs). Inducible-like NOSs may be the most basal prototype of all NOSs and that neuronal-like NOS might have evolved several times from this prototype. Other enzymatic and non-enzymatic pathways for NO synthesis have been discovered using reduction of nitrites, an alternative source of NO. Diverse synthetic mechanisms can co-exist within the same cell providing a complex NO-oxygen microenvironment tightly coupled with cellular energetics. The dissection of multiple sources of NO formation is crucial in analysis of complex biological processes such as neuronal integration and learning mechanisms when NO can act as a volume transmitter within memory-forming circuits. In particular, the molecular analysis of learning mechanisms (most notably in insects and gastropod molluscs) opens conceptually different perspectives to understand the logic of recruiting evolutionarily conserved pathways for novel functions. Giant uniquely identified cells from Aplysia and related species precent unuque opportunities for integrative analysis of NO signaling at the single cell level. PMID:21622160

  16. Type synthesis of two-degrees-of-freedom rotational parallel mechanism with two continuous rotational axes

    NASA Astrophysics Data System (ADS)

    Xu, Yundou; Zhang, Dongsheng; Wang, Min; Yao, Jiantao; Zhao, Yongsheng

    2016-07-01

    The two-rotational-degrees-of-freedom(2R) parallel mechanism(PM) with two continuous rotational axes(CRAs) has a simple kinematic model. It is therefore easy to implement trajectory planning, parameter calibration, and motion control, which allows for a variety of application prospects. However, no systematic analysis on structural constraints of the 2R-PM with two CRAs has been performed, and there are only a few types of 2R-PM with two CRAs. Thus, a theory regarding the type synthesis of the 2R-PM with two CRAs is systematically established. First, combining the theories of reciprocal screw and space geometry, the spatial arrangement relationships of the constraint forces applied to the moving platform by the branches are explored, which give the 2R-PM two CRAs. The different distributions of the constraint forces in each branch are also studied. On the basis of the obtained structural constraints of branches, and considering the geometric relationships of constraint forces in each branch, the appropriate kinematic chains are constructed. Through the reasonable configuration of branch kinematic chains corresponding to every structural constraint, a series of new 2R-PMs with two CRAs are finally obtained.

  17. A parallel algorithm for multi-level logic synthesis using the transduction method. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Lim, Chieng-Fai

    1991-01-01

    The Transduction Method has been shown to be a powerful tool in the optimization of multilevel networks. Many tools such as the SYLON synthesis system (X90), (CM89), (LM90) have been developed based on this method. A parallel implementation is presented of SYLON-XTRANS (XM89) on an eight processor Encore Multimax shared memory multiprocessor. It minimizes multilevel networks consisting of simple gates through parallel pruning, gate substitution, gate merging, generalized gate substitution, and gate input reduction. This implementation, called Parallel TRANSduction (PTRANS), also uses partitioning to break large circuits up and performs inter- and intra-partition dynamic load balancing. With this, good speedups and high processor efficiencies are achievable without sacrificing the resulting circuit quality.

  18. Polymer fullerene solution phase behaviour and film formation pathways.

    PubMed

    Dattani, Rajeev; Cabral, João T

    2015-04-28

    We report the phase behaviour of polymer/fullerene/solvent ternary mixtures and its consequence for the morphology of the resulting composite thin films. We focus particularly on solutions of polystyrene (PS), C60 fullerene and toluene, which are examined by static and dynamic light scattering, and films obtained from various solution ages and thermal annealing conditions, using atomic force and light microscopy. Unexpectedly, the solution phase behaviour below the polymer overlap concentration, c*, is found to be described by a simple excluded volume argument (occupied by the polymer chains) and the neat C60/solvent miscibility. Scaling consistent with full exclusion is found when the miscibility of the fullerene in the solvent is much lower than that of the polymer, giving way to partial exclusion with more soluble fullerenes (phenyl-C61-butyric acid methyl ester, PCBM) and a less asymmetric solvent (chlorobenzene), employed in photovoltaic devices. Spun cast and drop cast films were prepared from PS/C60/toluene solutions across the phase diagram to yield an identical PS/C60 composition and film thickness, resulting in qualitatively different morphologies in agreement with our measured solution phase boundaries. Our findings are relevant to the solution processing of polymer/fullerene composites (including organic photovoltaic devices), which generally require effective solubilisation of fullerene derivatives and polymer pairs in this concentration range, and the design of well-defined thin film morphologies.

  19. Resin Capsules: Permeable Containers for Parallel/Combinatorial Solid-Phase Organic Synthesis

    PubMed Central

    Bouillon, Isabelle; Soural, Miroslav; Krchňák, Viktor

    2009-01-01

    A resin capsule is a permeable container for resin beads designed for multiple/combinatorial solid-phase organic synthesis. Resin capsules consist of a high density polyethylene ring sealed with peek mesh on both sides. The cylindrical shape of resin capsules enabled space-saving packing into plastic column-like reaction vessels commonly used for solid-phase organic synthesis. Resin capsules have been evaluated for their use in combinatorial synthesis, and a set of model compounds with excellent purity was prepared. PMID:18656988

  20. Parallel synthesis of ureas and carbamates from amines and CO2 under mild conditions.

    PubMed

    Peterson, Scott L; Stucka, Sabrina M; Dinsmore, Christopher J

    2010-03-19

    A mild and efficient library synthesis technique has been developed for the synthesis of ureas and carbamates from carbamic acids derived from the DBU-catalyzed reaction of amines and gaseous carbon dioxide. Carbamic acids derived from primary amines reacted with Mitsunobu reagents to generate isocyanates in situ which were condensed with primary and secondary amines to afford the desired ureas. Similarly, carbamic acids from secondary amines reacted with alcohols activated with Mitsunobu reagents to form carbamates.

  1. Synthesis and analysis of a new class of six-degree-of-freedom parallel minimanipulators

    NASA Astrophysics Data System (ADS)

    Tsai, Lung-Wen; Tahmasebi, Farhad

    1993-07-01

    A new class of six-degree-of-freedom parallel minimanipulators capable of providing high resolution and high-stiffness for fine position and force control in a hybrid serial-parallel manipulator system is presented. Positional resolution and stiffness of minimanipulators are improved using two-degree-of-freedom planar linkages as drivers. The minimanipulators are based on only three inextensible limbs, as opposed to most of the six-limbed parallel manipulators, which makes it possible to reduce its direct kinematics to solving a polynomial in a single variable and to diminish possibility of mechanical interference between limbs. The base-mounted minimanipulator actuators are characterized by high payload capacity, small actuator size, and low power dissipitation.

  2. Synthesis and analysis of a new class of six-degree-of-freedom parallel minimanipulators

    NASA Technical Reports Server (NTRS)

    Tsai, Lung-Wen; Tahmasebi, Farhad

    1993-01-01

    A new class of six-degree-of-freedom parallel minimanipulators capable of providing high resolution and high-stiffness for fine position and force control in a hybrid serial-parallel manipulator system is presented. Positional resolution and stiffness of minimanipulators are improved using two-degree-of-freedom planar linkages as drivers. The minimanipulators are based on only three inextensible limbs, as opposed to most of the six-limbed parallel manipulators, which makes it possible to reduce its direct kinematics to solving a polynomial in a single variable and to diminish possibility of mechanical interference between limbs. The base-mounted minimanipulator actuators are characterized by high payload capacity, small actuator size, and low power dissipitation.

  3. Electric-arc synthesis of soot with high content of higher fullerenes in parallel arc

    NASA Astrophysics Data System (ADS)

    Dutlov, A. E.; Nekrasov, V. M.; Sergeev, A. G.; Bubnov, V. P.; Kareev, I. E.

    2016-12-01

    Soot with a relatively high content of higher fullerenes (C76, C78, C80, C82, C84, C86, etc.) is synthesized in a parallel arc upon evaporation of pure carbon electrodes. The content of higher fullerenes in soot extract amounts to 13.8 wt % when two electrodes are simultaneously burnt in electric-arc reactor. Such a content is comparable with the content obtained upon evaporation of composite graphite electrodes with potassium carbonate impurity.

  4. Parallel synthesis of 1,3-dihydro-1,4-benzodiazepine-2-ones employing catch and release.

    PubMed

    Laustsen, Line S; Sams, Christian K

    2007-01-01

    An efficient solid-phase method has been developed for the parallel synthesis of 1,3-dihydro-1,4-benzodiazepine-2-one derivatives. A key step in this procedure involves catching crude 2-aminobenzoimine products 4 on an amino acid Wang resin 10. Mild acidic conditions then promote a ring closure and in the same step cleavage from the resin to give pure benzodiazepine products 12. The 2-aminobenzoimines 4 can be synthesized from either 2-aminobenzonitriles 1 and Grignard reagents 2 or from iodoanilines 5 and nitriles 7 allowing a range of diversification. Further diversification can be introduced to the benzodiazepine products by N-alkylation promoted by a resin bound base and alkylating agents 13.

  5. Kinetic precipitation of solution-phase polyoxomolybdate followed by transmission electron microscopy: a window to solution-phase nanostructure.

    PubMed

    Zhu, Yan; Cammers-Goodwin, Arthur; Zhao, Bin; Dozier, Alan; Dickey, Elizabeth C

    2004-05-17

    This study aimed to elucidate the structural nature of the polydisperse, nanoscopic components in the solution and the solid states of partially reduced polyoxomolybdate derived from the [Mo132] keplerate, [(Mo)Mo5]12-[Mo2 acetate]30. Designer tripodal hexamine-tris-crown ethers and nanoscopic molybdate coprecipitated from aqueous solution. These microcrystalline solids distributed particle radii between 2-30 nm as assayed by transmission electron microscopy (TEM). The solid materials and their particle size distributions were snap shots of the solution phase. The mother liquor of the preparation of the [Mo132] keplerate after three days revealed large species (r=20-30 nm) in the coprecipitate, whereas [Mo132] keplerate redissolved in water revealed small species (3-7 nm) in the coprecipitate. Nanoparticles of coprecipitate were more stable than solids derived solely from partially reduced molybdate. The TEM features of all material analyzed lacked facets on the nanometer length scale; however, the structures diffracted electrons and appeared to be defect-free as evidenced by Moiré patterns in the TEM images. Moiré patterns and size-invariant optical densities of the features in the micrographs suggested that the molybdate nanoparticles were vesicular.

  6. Solution-Phase Epitaxial Growth of Quasi-Monocrystalline Cuprous Oxide on Metal Nanowires

    PubMed Central

    2014-01-01

    The epitaxial growth of monocrystalline semiconductors on metal nanostructures is interesting from both fundamental and applied perspectives. The realization of nanostructures with excellent interfaces and material properties that also have controlled optical resonances can be very challenging. Here we report the synthesis and characterization of metal–semiconductor core–shell nanowires. We demonstrate a solution-phase route to obtain stable core–shell metal–Cu2O nanowires with outstanding control over the resulting structure, in which the noble metal nanowire is used as the nucleation site for epitaxial growth of quasi-monocrystalline Cu2O shells at room temperature in aqueous solution. We use X-ray and electron diffraction, high-resolution transmission electron microscopy, energy dispersive X-ray spectroscopy, photoluminescence spectroscopy, and absorption spectroscopy, as well as density functional theory calculations, to characterize the core–shell nanowires and verify their structure. Metal–semiconductor core–shell nanowires offer several potential advantages over thin film and traditional nanowire architectures as building blocks for photovoltaics, including efficient carrier collection in radial nanowire junctions and strong optical resonances that can be tuned to maximize absorption. PMID:25233392

  7. Solution-phase epitaxial growth of quasi-monocrystalline cuprous oxide on metal nanowires.

    PubMed

    Sciacca, Beniamino; Mann, Sander A; Tichelaar, Frans D; Zandbergen, Henny W; van Huis, Marijn A; Garnett, Erik C

    2014-10-08

    The epitaxial growth of monocrystalline semiconductors on metal nanostructures is interesting from both fundamental and applied perspectives. The realization of nanostructures with excellent interfaces and material properties that also have controlled optical resonances can be very challenging. Here we report the synthesis and characterization of metal-semiconductor core-shell nanowires. We demonstrate a solution-phase route to obtain stable core-shell metal-Cu2O nanowires with outstanding control over the resulting structure, in which the noble metal nanowire is used as the nucleation site for epitaxial growth of quasi-monocrystalline Cu2O shells at room temperature in aqueous solution. We use X-ray and electron diffraction, high-resolution transmission electron microscopy, energy dispersive X-ray spectroscopy, photoluminescence spectroscopy, and absorption spectroscopy, as well as density functional theory calculations, to characterize the core-shell nanowires and verify their structure. Metal-semiconductor core-shell nanowires offer several potential advantages over thin film and traditional nanowire architectures as building blocks for photovoltaics, including efficient carrier collection in radial nanowire junctions and strong optical resonances that can be tuned to maximize absorption.

  8. Reactivity-dependent PCR: direct, solution-phase in vitro selection for bond formation.

    PubMed

    Gorin, David J; Kamlet, Adam S; Liu, David R

    2009-07-08

    In vitro selection is a key component of efforts to discover functional nucleic acids and small molecules from libraries of DNA, RNA, and DNA-encoded small molecules. Such selections have been widely used to evolve RNA and DNA catalysts and, more recently, to discover new reactions from DNA-encoded libraries of potential substrates. While effective, current strategies for selections of bond-forming and bond-cleaving reactivity are generally indirect, require the synthesis of biotin-linked substrates, and involve multiple solution-phase and solid-phase manipulations. In this work we report the successful development and validation of reactivity-dependent PCR (RDPCR), a new method that more directly links bond formation or bond cleavage with the amplification of desired sequences and that obviates the need for solid-phase capture, washing, and elution steps. We show that RDPCR can be used to select for bond formation in the context of reaction discovery and for bond cleavage in the context of protease activity profiling.

  9. A parallel synthesis scheme for generating libraries of DNA polymerase substrates and inhibitors.

    PubMed

    Strobel, Heike; Dugué, Laurence; Marlière, Philippe; Pochet, Sylvie

    2002-12-02

    We report a combinatorial approach aimed at producing in a single step a large family of nucleoside triphosphate derivatives that could be tested for their ability to be substrates for DNA polymerases. We propose as a unique triphosphate building block a nucleotide with a hydrazine function anchored to an imidazole ring. Condensation between the 5'-triphosphate derivative of 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-imidazole-4-hydrazide (dY(NH(2))TP) and any aldehyde or ketone, followed by reduction of the intermediate hydrazones dXmTP, resulted in the corresponding hydrazides (dXnTP). Following this scheme, a series of aldehydes having various aromatic parts yielded a number of adducts dY(NHR)TP. Vent (exo-) DNA polymerase is found to be able to catalyse the single incorporation of these bulky triphosphate derivatives. Subsequent extensions of the modified pairs with canonical triphosphates resulted mainly in abortive elongations at primer+2, except after the incorporation of dY(NHben)TP and, to a lesser extent, dY(NHphe)TP opposite C. These results illustrate the potential of this parallel synthetic scheme for generating new substrates or inhibitors of replication in a single step.

  10. Parallel synthesis and biological evaluation of 837 analogues of procaspase-activating compound 1 (PAC-1).

    PubMed

    Hsu, Danny C; Roth, Howard S; West, Diana C; Botham, Rachel C; Novotny, Chris J; Schmid, Steven C; Hergenrother, Paul J

    2012-01-09

    Procaspase-Activating Compound 1 (PAC-1) is an ortho-hydroxy N-acyl hydrazone that enhances the enzymatic activity of procaspase-3 in vitro and induces apoptosis in cancer cells. An analogue of PAC-1, called S-PAC-1, was evaluated in a veterinary clinical trial in pet dogs with lymphoma and found to have considerable potential as an anticancer agent. With the goal of identifying more potent compounds in this promising class of experimental therapeutics, a combinatorial library based on PAC-1 was created, and the compounds were evaluated for their ability to induce death of cancer cells in culture. For library construction, 31 hydrazides were condensed in parallel with 27 aldehydes to create 837 PAC-1 analogues, with an average purity of 91%. The compounds were evaluated for their ability to induce apoptosis in cancer cells, and through this work, six compounds were discovered to be substantially more potent than PAC-1 and S-PAC-1. These six hits were further evaluated for their ability to relieve zinc-mediated inhibition of procaspase-3 in vitro. In general, the newly identified hit compounds are two- to four-fold more potent than PAC-1 and S-PAC-1 in cell culture, and thus have promise as experimental therapeutics for treatment of the many cancers that have elevated expression levels of procaspase-3.

  11. Parallel solid-phase synthesis and structural characterization of a library of highly substituted chiral 1,3-oxazolidines.

    PubMed

    Tremblay, M R; Wentworth, P; Lee, G E; Janda, K D

    2000-01-01

    The rapid parallel synthesis and characterization of diverse chirally defined 1,3-oxazolidines is reported. Three diversity elements were incorporated in a 6 x 4 x 4 block approach to generate a 96-member 1,3-oxazolidine library. The synthetic route involved initial attachment of six nonracemic phenylglycidols, (2S,3S)1A-C and (2R,3R)-2A-C, to 2% cross-linked polystyrene resin via a chlorodiethylsilane linker (PS-DES), followed by regio- and stereoselective oxirane ring opening with four primary amines (3a-d). The key condensation reaction between the resulting polymer-bound beta-amino alcohols and four aldehydes (4a-d) was found to occur optimally in warm benzene (60 degrees C) in the presence of anhydrous magnesium sulfate. Cleavage of the oxazolidines from the resin support was achieved with TBAF to give the individual members (2R,4R,5R)-5Aaa-Cdd and (2S,4S,5S)-6Aaa-Cdd in good to excellent yields (51-99%) based on mass recovery. Purities of all these crude products was generally >85% (as measured by LCMS). 1H, 13C NMR, and 1D difference nOe of the library members confirmed the structural and stereochemical integrity of the substituents around the 1,3-oxazolidine core. The asymmetric induction at C-2 (cis or trans to the C-4 substituent) ratio ranged from 4 to I to 49 to 1 across the library. This report highlights the versatility of the 1,3-oxazolidine heterocycle as a scaffold for concise parallel library construction and opens the way for high-throughput screening of such compounds in the biological sphere.

  12. Structure-based Design and In-Parallel Synthesis of Inhibitors of AmpC b-lactamase

    SciTech Connect

    Tondi, D.; Powers, R.A.; Negri, M.C.; Caselli, M.C.; Blazquez, J.; Costi, M.P.; Shoichet, B.K.

    2010-03-08

    Group I {beta}-lactamases are a major cause of antibiotic resistance to {beta}-lactams such as penicillins and cephalosporins. These enzymes are only modestly affected by classic {beta}-lactam-based inhibitors, such as clavulanic acid. Conversely, small arylboronic acids inhibit these enzymes at sub-micromolar concentrations. Structural studies suggest these inhibitors bind to a well-defined cleft in the group I {beta}-lactamase AmpC; this cleft binds the ubiquitous R1 side chain of {beta}-lactams. Intriguingly, much of this cleft is left unoccupied by the small arylboronic acids. To investigate if larger boronic acids might take advantage of this cleft, structure-guided in-parallel synthesis was used to explore new inhibitors of AmpC. Twenty-eight derivatives of the lead compound, 3-aminophenylboronic acid, led to an inhibitor with 80-fold better binding (2; K{sub i} 83 nM). Molecular docking suggested orientations for this compound in the R1 cleft. Based on the docking results, 12 derivatives of 2 were synthesized, leading to inhibitors with K{sub i} values of 60 nM and with improved solubility. Several of these inhibitors reversed the resistance of nosocomial Gram-positive bacteria, though they showed little activity against Gram-negative bacteria. The X-ray crystal structure of compound 2 in complex with AmpC was subsequently determined to 2.1 {angstrom} resolution. The placement of the proximal two-thirds of the inhibitor in the experimental structure corresponds with the docked structure, but a bond rotation leads to a distinctly different placement of the distal part of the inhibitor. In the experimental structure, the inhibitor interacts with conserved residues in the R1 cleft whose role in recognition has not been previously explored. Combining structure-based design with in-parallel synthesis allowed for the rapid exploration of inhibitor functionality in the R1 cleft of AmpC. The resulting inhibitors differ considerably from {beta}-lactams but

  13. A library synthesis of 4-hydroxy-3-methyl-6-phenylbenzofuran-2-carboxylic acid ethyl ester derivatives as anti-tumor agents.

    PubMed

    Hayakawa, Ichiro; Shioya, Rieko; Agatsuma, Toshinori; Furukawa, Hidehiko; Naruto, Shunji; Sugano, Yuichi

    2004-09-06

    As a result of a hit-to-lead program using a technique of solution-phase parallel synthesis, a highly potent (2,4-dimethoxyphenyl)-[6-(3-fluorophenyl)-4-hydroxy-3-methylbenzofuran-2-yl]methanone (15b) was synthesized as an optimized derivative of 4-hydroxy-3-methyl-6-phenylbenzofuran-2-carboxylic acid ethyl ester (1), which was discovered as a screening hit from small-molecule libraries and exhibited selective cytotoxicity against a tumorigenic cell line.

  14. 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.

  15. Vertical Single-Crystalline Organic Nanowires on Graphene: Solution-Phase Epitaxy and Optical Microcavities.

    PubMed

    Zheng, Jian-Yao; Xu, Hongjun; Wang, Jing Jing; Winters, Sinéad; Motta, Carlo; Karademir, Ertuğrul; Zhu, Weigang; Varrla, Eswaraiah; Duesberg, Georg S; Sanvito, Stefano; Hu, Wenping; Donegan, John F

    2016-08-10

    Vertically aligned nanowires (NWs) of single crystal semiconductors have attracted a great deal of interest in the past few years. They have strong potential to be used in device structures with high density and with intriguing optoelectronic properties. However, fabricating such nanowire structures using organic semiconducting materials remains technically challenging. Here we report a simple procedure for the synthesis of crystalline 9,10-bis(phenylethynyl) anthracene (BPEA) NWs on a graphene surface utilizing a solution-phase van der Waals (vdW) epitaxial strategy. The wires are found to grow preferentially in a vertical direction on the surface of graphene. Structural characterization and first-principles ab initio simulations were performed to investigate the epitaxial growth and the molecular orientation of the BPEA molecules on graphene was studied, revealing the role of interactions at the graphene-BPEA interface in determining the molecular orientation. These free-standing NWs showed not only efficient optical waveguiding with low loss along the NW but also confinement of light between the two end facets of the NW forming a microcavity Fabry-Pérot resonator. From an analysis of the optical dispersion within such NW microcavities, we observed strong slowing of the waveguided light with a group velocity reduced to one-tenth the speed of light. Applications of the vertical single-crystalline organic NWs grown on graphene will benefit from a combination of the unique electronic properties and flexibility of graphene and the tunable optical and electronic properties of organic NWs. Therefore, these vertical organic NW arrays on graphene offer the potential for realizing future on-chip light sources.

  16. Divergent Synthetic Access to E‐ and Z‐Stereodefined All‐Carbon‐Substituted Olefin Scaffolds: Application to Parallel Synthesis of (E)‐ and (Z)‐Tamoxifens

    PubMed Central

    Ashida, Yuichiro; Honda, Atsushi; Sato, Yuka

    2017-01-01

    Abstract A highly substrate‐general synthesis of all‐carbon‐substituted E‐ and Z‐stereodefined olefins is performed. The method comprises two sets of parallel and stereocomplementary preparations of (E)‐ and (Z)‐α,β‐unsaturated esters involving two robust and distinctive reactions: 1) stereocomplementary enol tosylations using readily available TsCl/diamine/(LiCl) base reagents, and 2) stereoretentive Negishi cross‐coupling using the catalysts [Pd(dppe)Cl2] (for E) and [Pd(dppb)Cl2] (for Z). The present parallel approach is categorized as both type I (convergent approach: 16 examples, 56–87 % yield) and type II (divergent approach: 18 examples, 70–95 % yield). The obtained (E)‐ and (Z)‐α,β‐unsaturated ester scaffolds are successfully transformed into various E‐ and Z‐stereodefined known and novel olefins (8×2 derivatization arrays). As a demonstration, application to the parallel synthesis of both (E)‐ and (Z)‐tamoxifens, a representative motif of all‐carbon‐substituted olefins, is accomplished in a total of eight steps with an overall yield of 58 % (average 93 %) and 57 % (average 93 %), respectively. PMID:28168153

  17. Automated liquid-liquid extraction workstation for library synthesis and its use in the parallel and chromatography-free synthesis of 2-alkyl-3-alkyl-4-(3H)-quinazolinones.

    PubMed

    Carpintero, Mercedes; Cifuentes, Marta; Ferritto, Rafael; Haro, Rubén; Toledo, Miguel A

    2007-01-01

    An automated liquid-liquid extraction workstation has been developed. This module processes up to 96 samples in an automated and parallel mode avoiding the time-consuming and intensive sample manipulation during the workup process. To validate the workstation, a highly automated and chromatography-free synthesis of differentially substituted quinazolin-4(3H)-ones with two diversity points has been carried out using isatoic anhydride as starting material.

  18. Mapping the Catechol Binding Site in Dopamine D1 Receptors: Synthesis and Evaluation of Two Parallel Series of Bicyclic Dopamine Analogues

    PubMed Central

    Bonner, Lisa A.; Laban, Uros; Chemel, Benjamin R.; Juncosa, Jose I.; Lill, Markus A.; Watts, Val J.; Nichols, David E.

    2012-01-01

    A novel class of isochroman dopamine analogues, 1, originally reported by Abbott Laboratories, had greater than 100-fold selectivity for D1-like vs. D2-like receptors. We synthesized a parallel series of chroman compounds, 2, and showed that repositioning the oxygen in the heterocyclic ring reduced potency and conferred D2-like receptor selectivity to these compounds. In silico modeling supported the hypothesis that the altered pharmacology for 2 was due to potential intramolecular hydrogen bonding between the oxygen in the chroman ring and the meta-hydroxyl of the catechol moiety. This interaction realigns the catechol hydroxyl groups and disrupts key interactions between these ligands and critical serine residues in TM5 of the D1-like receptors. This hypothesis was tested by the synthesis and pharmacological evaluation of a parallel series of carbocyclic compounds, 3. Our results suggest that when the potential for intramolecular hydrogen bonding is removed, D1-like receptor potency and selectivity is restored. PMID:21538900

  19. Novel ultrasound-promoted parallel synthesis of trifluoroatrolactamide library via a one-pot Passerini/hydrolysis reaction sequence and their fungicidal activities.

    PubMed

    Yu, Shu-Jing; Zhu, Cong; Bian, Qiang; Cui, Can; Du, Xiu-Jiang; Li, Zheng-Ming; Zhao, Wei-Guang

    2014-01-13

    An ultrasound-promoted one-pot Passerini/hydrolysis reaction sequence has been developed for the synthesis of trifluoroatrolactamide derivatives using a diverse range of trifluoroacetophenones and isonitriles in acetic acid. Parallel synthesis in a centrifuge tube using a noncontact ultrasonic cell crusher was used in this study as an efficient method for the rapid generation of combinatorial trifluoroatrolactamide libraries, and subsequent biochemical evaluation of the resulting compounds indicated that they possessed excellent broad-spectrum fungicidal activities. N-(4-chlorophenyl)-2-(4-ethylphenyl)-3,3,3-trifluoro-2-hydroxypropanamide and N-(4-chlorophenyl)-3,3,3-trifluoro-2-hydroxy-2-(4-methoxyphenyl)propanamide, in particular, showed significant fungicidal activities against all of the fungal species tested in the current study.

  20. Parallel microwave-assisted synthesis of ionic liquids and screening for denitrogenation of straight-run diesel feed by liquid-liquid extraction.

    PubMed

    Ceron, Miguel A; Guzman-Lucero, Diego J; Palomeque, Jorge F; Martínez-Palou, Rafael

    2012-06-01

    Fifty-six ionic liquids were efficiently synthesized in parallel format under one-pot, solvent-free microwave-assisted synthesis. These compounds were evaluated as extracting agents of nitrogen-containing compounds from a real Diesel feed before being submitted to the hydrodesulfurization process to obtain ultralow sulfur Diesel. Our results showed that halogenated ionic liquids are an excellent alternative due to these ionic liquids are relatively inexpensive, presenting a high selectivity for the extraction of nitrogen-containing compounds and can be regenerated and recycled.

  1. Discovery of benzimidazole-diamide finger loop (Thumb Pocket I) allosteric inhibitors of HCV NS5B polymerase: Implementing parallel synthesis for rapid linker optimization.

    PubMed

    Goulet, Sylvie; Poupart, Marc-André; Gillard, James; Poirier, Martin; Kukolj, George; Beaulieu, Pierre L

    2010-01-01

    Previously described SAR of benzimidazole-based non-nucleoside finger loop (Thumb Pocket I) inhibitors of HCV NS5B polymerase was expanded. Prospecting studies using parallel synthesis techniques allowed the rapid identification of novel cinnamic acid right-hand sides that provide renewed opportunities for further optimization of these inhibitors. Novel diamide derivatives such as 44 exhibited comparable potency (enzymatic and cell-based HCV replicon) as previously described tryptophan-based inhibitors but physicochemical properties (e.g., aqueous solubility and lipophilicity) have been improved, resulting in molecules with reduced off-target liabilities (CYP inhibition) and increased metabolic stability.

  2. Doping and Alloying in the Solution-Phase Synthesis of Germanium Nanocrystals

    SciTech Connect

    Ruddy, D. A.; Neale, N. R.

    2012-01-01

    Group IV nanocrystals (NCs) are receiving increased attention as a potentially non-toxic nanomaterial for use in a number of important optoelectronic applications (e.g., solar photoconversion, photodetectors, LEDs, biological imaging). With these goals in mind, doping and alloying with Group III, IV, and V elements may play a major role in tailoring the NC properties, such as developing n-type and p-type conductivity through substitutional doping, as well as affecting the optical absorption, emission, and overall charge transport in a NC film. Here we present an extension of the mixed-valence iodide precursor methodology to incorporate Group III, IV, and V elements to produce E-GeNC materials. All main-group elements (E) that surround Ge on the periodic table (i.e., E = Al, Si, P, Ga, As, In, Sn, and Sb) can be incorporated via this methodology. The extent to which the dopant elements are included will be discussed, along with the optical absorbance, emission, and related properties of the NCs. In addition, the effect of the dopant elements on the NC growth kinetics will be discussed.

  3. Membrane-Protein Binding Measured with Solution-Phase Plasmonic Nanocube Sensors

    PubMed Central

    Wu, Hung-Jen; Henzie, Joel; Lin, Wan-Chen; Rhodes, Christopher; Li, Zhu; Sartorel, Elodie; Thorner, Jeremy; Yang, Peidong; Groves, Jay. T.

    2013-01-01

    We describe a solution-phase sensor of lipid-protein binding based on localized surface plasmon resonance (LSPR) of silver nanocubes. When silica-coated nanocubes are mixed into a suspension of lipid vesicles, supported membranes spontaneously assemble on their surfaces. Using a standard laboratory spectrophotometer, we calibrate the LSPR peak shift due to protein binding to the membrane surface and then characterize the lipid-binding specificity of a pleckstrin-homology domain protein. PMID:23085614

  4. Supramolecular chemistry: from aromatic foldamers to solution-phase supramolecular organic frameworks

    PubMed Central

    2015-01-01

    Summary This mini-review covers the growth, education, career, and research activities of the author. In particular, the developments of various folded, helical and extended secondary structures from aromatic backbones driven by different noncovalent forces (including hydrogen bonding, donor–acceptor, solvophobicity, and dimerization of conjugated radical cations) and solution-phase supramolecular organic frameworks driven by hydrophobically initiated aromatic stacking in the cavity of cucurbit[8]uril (CB[8]) are highlighted. PMID:26664626

  5. An open-source, massively parallel code for non-LTE synthesis and inversion of spectral lines and Zeeman-induced Stokes profiles

    NASA Astrophysics Data System (ADS)

    Socas-Navarro, H.; de la Cruz Rodríguez, J.; Asensio Ramos, A.; Trujillo Bueno, J.; Ruiz Cobo, B.

    2015-05-01

    With the advent of a new generation of solar telescopes and instrumentation, interpreting chromospheric observations (in particular, spectropolarimetry) requires new, suitable diagnostic tools. This paper describes a new code, NICOLE, that has been designed for Stokes non-LTE radiative transfer, for synthesis and inversion of spectral lines and Zeeman-induced polarization profiles, spanning a wide range of atmospheric heights from the photosphere to the chromosphere. The code features a number of unique features and capabilities and has been built from scratch with a powerful parallelization scheme that makes it suitable for application on massive datasets using large supercomputers. The source code is written entirely in Fortran 90/2003 and complies strictly with the ANSI standards to ensure maximum compatibility and portability. It is being publicly released, with the idea of facilitating future branching by other groups to augment its capabilities. The source code is currently hosted at the following repository: http://https://github.com/hsocasnavarro/NICOLE

  6. Palladium(0)-catalyzed coupling-cyclization reaction of polymer-supported aryl iodides with 1,2-allenyl carboxylic acids. Solid-phase parallel synthesis of butenolides.

    PubMed

    Ma, Shengming; Duan, Dehui; Wang, Yizhong

    2002-01-01

    In this contribution, we constructed a library of butenolides with 77 members by parallel synthesis strategy on Merrifield resin. Sixteen 2,3-allenoic acids and 12 polymer-bound aryl iodides were combined to react with each other, and then the polymer-supported products were cleaved to release butenolide derivatives. The reactions with alkyl-substituted 2,3-allenoic acids in acetonitrile afforded the corresponding products in high yields and high purities, whereas those with aryl-substituted acids in acetonitrile failed. After some reaction conditions were screened, the solid-phase reactions with aryl-substituted 2,3-allenoic acids were realized in toluene, and the products are of good purities albeit in slightly low yields. In the benzyl ether linkage, a new cleavage model was found. By adding 6 equiv of acetyl bromide, we can get single (5-oxo-2,5-dihydrofuran-3-yl)benzyl bromide other than the corresponding benzyl acetate. To further increase the diversities, a dihydropyran (DHP) linker was introduced into our combinatorial synthesis of butenolides. By reversing the addition sequence of 2,3-allenoic acids and organic base, we realized the solid-phase cyclization reaction of polymer-bound aryl iodides with the THP linkage in moderate yields and good purities. Now the library of butenolides includes (5-oxo-2,5-dihydrofuran-3-yl)benzoic acids, -aryl acetates, -benzyl bromides, -benzyl alcohols, and -phenols, which are difficult to synthesize with conventional solution methods.

  7. Strategies to indium nitride and gallium nitride nanoparticles: Low-temperature, solution-phase and precursor routes

    NASA Astrophysics Data System (ADS)

    Dingman, Sean Douglas

    I present new strategies to low-temperature solution-phase synthesis of indium and gallium nitride (InN and GaN) ceramic materials. The strategies include: direct conversion of precursor molecules to InN by pyrolysis, solution-phase synthesis of nanostructured InN fibers via molecular precursors and co-reactants, and synthesis of powders through reactions derived from molten-salt chemistry. Indium nitride powders are prepared by pyrolysis of the precursors R 2InN3 (R = t-Bu (1), i-Amyl(2), Et(3), i-Pr( 4)). The precursors are synthesized via azide-alkoxide exchange of R2InOMe with Me3SiN3. The precursors are coordination polymers containing five-coordinate indium centers. Pyrolysis of 1 and 2 under N2 at 400°C yields powders consisting primarily of InN with average crystal sizes of 15--35 nm. 1 yields nanocrystalline InN with average particle sizes of 7 nm at 250°C. 3 and 4 yield primarily In metal from pyrolysis. Refluxing 1 in diisopropylbenzene (203°C) in the presence of primary amines yields InN nanofibers 10--100 nm in length. InN nanofibers of up to 1 mum can be synthesized by treating 1 with 1,1-dimethylhydrazine (DMHy) The DMHy appears to control the fiber length by acting as a secondary source of active nitrogen in order to sustain fiber growth. The resulting fibers are attached to droplets of indium metal implying a solution-liquid-solid growth mechanism. Precursor 4 yields crystalline InN whiskers when reacted with DMHy. Reactions of 4 with reducing agents such as HSnBu3, yield InN nanoparticles with an average crystallite size of 16 nm. Gallium precursors R2GaN3 (R = t-Bu( 5), Me3SiCH2(6) and i-Pr( 7)), synthesized by azide-alkoxide exchange, are found to be inert toward solution decomposition and do not yield GaN. These compounds are molecular dimers and trimers unlike the indium analogs. Compound 6 displays a monomer-dimer equilibrium in benzene solution, but exists as a solid-state trimer. InN powders are also synthesized by reactions of InCl3 and

  8. Adsorption of polycations on clays: A comparative in situ study using {sup 133}Cs and {sup 23}Na solution phase NMR

    SciTech Connect

    Billingham, J.; Breen, C.; Rawson, J.O.; Yarwood, J.; Mann, B.E.

    1997-09-15

    {sup 23}Na solution phase NMR has been evaluated as an in situ probe to study the adsorption of tetramethylammonium (TMA{sup +}) and two polycations, FL17 and Magnafloc 1697, onto clays in aqueous suspensions containing 2.5 mass% low iron Texas bentonite. The NMR data shows the effectiveness of the organocations at displacing Na{sup +} from the bentonite surface. This information has been correlated with that obtained from particle-size and electrophoretic measurements in aqueous solution, together with information from adsorption isotherms. These results have been compared to those obtained in parallel studies using {sup 133}Cs solution phase NMR. FL17 and 1697 both exhibited high affinity adsorption isotherms on Na{sup +}- and Cs{sup +}-clay, whereas the adsorption of TMA{sup +}, which represents the cationic portion of the polymers was of lower affinity. Na{sup +}-bentonite adsorbed almost twice the amount of polycation required to fulfill the cation-exchange capacity (CEC) of the bentonite. The electrophoretic and particle size data indicated significant differences in the size of the polycation/clay flocs and the amount of polymer adsorbed on the external faces of the flocs in the presence of Na{sup +}- and Cs{sup +}-exchange ions. Correlation of this data with the NMR results suggests that the Na{sup +}-bentonite/polycation flocs are large, of low density, and that the polycation is concentrated in the interior while the Na{sup +}-ions occupy exchange sites on the external faces.

  9. Fluorous Mixture Synthesis of Two Libraries with Novel Hydantoin- and Benzodiazepinedione-Fused Heterocyclic Scaffolds

    PubMed Central

    Zhang, Wei; Lu, Yimin; Chen, Christine Hiu-Tung; Zeng, Lu; Kassel, Daniel B.

    2007-01-01

    Diversity-oriented synthesis (DOS) and fluorous mixture synthesis (FMS) are two aspects of combinatorial chemistry. DOS generates library scaffolds with skeletal, substitution, and stereochemistry variations, whereas FMS is a highly efficient tool for library production. The combination of these two aspects in solution-phase synthesis of two novel heterocyclic compound libraries is presented in this paper. Mixtures of different fluorous amino acids undergo [3+2] cycloadditions followed by post-condensation reactions. The mixtures are then demixed by fluorous HPLC. Fluorous tags are removed by cyclization to afford hydantoin- and benzodiazepinedione-fused heterocyclic compounds as individual, pure and structurally defined molecules. The application of MS-directed HPLC and parallel four-channel LC/MS analysis further increases the efficiency of FMS. PMID:16961407

  10. Parallel solid-phase synthesis and characterization of new sulfonamide and carboxamide proline derivatives as potential CNS agents.

    PubMed

    Zajdel, Paweł; Subra, Gilles; Bojarski, Andrzej J; Duszyńska, Beata; Pawłowski, Maciej; Martinez, Jean

    2005-04-15

    A solid-phase synthesis of the 64-member library of novel sulfonamide and carboxamide proline derivatives, focused on the 5-HT7 receptor antagonist SB-258741, was described. The final compounds were obtained in good yields and high purity upon cleavage from SynPhase Lanterns, functionalized by a BAL linker. The library representatives were screened for 5-HT7, 5-HT1A and D2 receptors to explore the impact of a tertiary amine moiety, the length of an alkylene spacer and the aryl fragment on the receptor affinity. The preliminary biological results provided data for further investigation aimed at a search for 5-HT7 receptor agents, and permitted the identification of several compounds with significant 5-HT1A receptor affinity.

  11. Parallel synthesis and biological activity of a new class of high affinity and selective delta-opioid ligand.

    PubMed

    Barn, D R; Caulfield, W L; Cottney, J; McGurk, K; Morphy, J R; Rankovic, Z; Roberts, B

    2001-10-01

    A considerable number of research papers describing the synthesis and testing of the delta opioid receptor (DOR) ligands, SNC-80 and TAN-67, and analogues of these two compounds, have been published in recent years. However, there have been few reports of the discovery of completely new structural classes of selective DOR ligand. By optimising a hit compound identified by high throughput screening, a new series of tetrahydroisoquinoline sulphonamide-based delta opioid ligands was discovered. The main challenge in this series was to simultaneously improve both affinity and physicochemical properties, notably aqueous solubility. The most active ligand had an affinity (IC(50)) of 6 nM for the cloned human DOR, representing a 15-fold improvement relative to the original hit 1 (IC(50) 98 nM). Compounds from this new series show good selectivity for the DOR over mu and kappa opioid receptors. However the most active and selective compounds had poor aqueous solubility. Improved aqueous solubility was obtained by replacing the phthalimide group in 1 by basic groups, allowing the synthesis of salt forms. A series of compounds with improved affinity and solubility relative to 1 was identified and these compounds showed activity in an in vivo model of antinociception, the formalin paw test. In the case of compound 19, this analgesic activity was shown to be mediated primarily via a DOR mechanism. The most active compound in vivo, 46, showed superior potency in this test compared to the reference DOR ligand, TAN-67 and similar potency to morphine (68% and 58% inhibition in Phases 1 and 2, respectively, at a dose of 10 mmol/kg i.v.).

  12. A Theoretical Study of Ene Reactions in Solution: A Solution-Phase Translational Entropy Model.

    PubMed

    Zhao, Liu; Li, Shi-Jun; Fang, De-Cai

    2015-12-01

    Several density functional theory (DFT) methods, such as CAM-B3LYP, M06, ωB97x, and ωB97xD, are used to characterize a range of ene reactions. The Gibbs free energy, activation enthalpy, and entropy are calculated with both the gas- and solution-phase translational entropy; the results obtained from the solution-phase translational entropies are quite close to the experimental measurements, whereas the gas-phase translational entropies do not perform well. For ene reactions between the enophile propanedioic acid (2-oxo-1,3-dimethyl ester) and π donors, the two-solvent-involved explicit+implicit model can be employed to obtain accurate activation entropies and free-energy barriers, because the interaction between the carbonyl oxygen atom and the solvent in the transition state is strengthened with the formation of C-C and O-H bonds. In contrast, an implicit solvent model is adequate to calculate activation entropies and free-energy barriers for the corresponding reactions of the enophile 4-phenyl-1,2,4-triazoline-3,5-dione.

  13. Hardware-software-co-design of parallel and distributed systems using a behavioural programming and multi-process model with high-level synthesis

    NASA Astrophysics Data System (ADS)

    Bosse, Stefan

    2011-05-01

    A new design methodology for parallel and distributed embedded systems is presented using the behavioural hardware compiler ConPro providing an imperative programming model based on concurrently communicating sequential processes (CSP) with an extensive set of interprocess-communication primitives and guarded atomic actions. The programming language and the compiler-based synthesis process enables the design of constrained power- and resourceaware embedded systems with pure Register-Transfer-Logic (RTL) efficiently mapped to FPGA and ASIC technologies. Concurrency is modelled explicitly on control- and datapath level. Additionally, concurrency on data-path level can be automatically explored and optimized by different schedulers. The CSP programming model can be synthesized to hardware (SoC) and software (C,ML) models and targets. A common source for both hardware and software implementation with identical functional behaviour is used. Processes and objects of the entire design can be distributed on different hardware and software platforms, for example, several FPGA components and software executed on several microprocessors, providing a parallel and distributed system. Intersystem-, interprocess-, and object communication is automatically implemented with serial links, not visible on programming level. The presented design methodology has the benefit of high modularity, freedom of choice of target technologies, and system architecture. Algorithms can be well matched to and distributed on different suitable execution platforms and implementation technologies, using a unique programming model, providing a balance of concurrency and resource complexity. An extended case study of a communication protocol used in high-density sensor-actuator networks should demonstrate and compare the design of a hardware and software target. The communication protocol is suited for high-density intra-and interchip networks.

  14. Accelerated exploration of multi-principal element alloys with solid solution phases.

    PubMed

    Senkov, O N; Miller, J D; Miracle, D B; Woodward, C

    2015-03-05

    Recent multi-principal element, high entropy alloy (HEA) development strategies vastly expand the number of candidate alloy systems, but also pose a new challenge--how to rapidly screen thousands of candidate alloy systems for targeted properties. Here we develop a new approach to rapidly assess structural metals by combining calculated phase diagrams with simple rules based on the phases present, their transformation temperatures and useful microstructures. We evaluate over 130,000 alloy systems, identifying promising compositions for more time-intensive experimental studies. We find the surprising result that solid solution alloys become less likely as the number of alloy elements increases. This contradicts the major premise of HEAs--that increased configurational entropy increases the stability of disordered solid solution phases. As the number of elements increases, the configurational entropy rises slowly while the probability of at least one pair of elements favouring formation of intermetallic compounds increases more rapidly, explaining this apparent contradiction.

  15. Solution-phase photochemistry of a [FeFe]hydrogenase model compound: evidence of photoinduced isomerisation.

    PubMed

    Kania, Rafal; Frederix, Pim W J M; Wright, Joseph A; Ulijn, Rein V; Pickett, Christopher J; Hunt, Neil T

    2012-01-28

    The solution-phase photochemistry of the [FeFe] hydrogenase subsite model (μ-S(CH(2))(3)S)Fe(2)(CO)(4)(PMe(3))(2) has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.

  16. Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation

    SciTech Connect

    Kania, Rafal; Hunt, Neil T.; Frederix, Pim W. J. M.; Wright, Joseph A.; Pickett, Christopher J.; Ulijn, Rein V.

    2012-01-28

    The solution-phase photochemistry of the [FeFe] hydrogenase subsite model ({mu}-S(CH{sub 2}){sub 3}S)Fe{sub 2}(CO){sub 4}(PMe{sub 3}){sub 2} has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.

  17. Accelerated exploration of multi-principal element alloys with solid solution phases

    NASA Astrophysics Data System (ADS)

    Senkov, O. N.; Miller, J. D.; Miracle, D. B.; Woodward, C.

    2015-03-01

    Recent multi-principal element, high entropy alloy (HEA) development strategies vastly expand the number of candidate alloy systems, but also pose a new challenge—how to rapidly screen thousands of candidate alloy systems for targeted properties. Here we develop a new approach to rapidly assess structural metals by combining calculated phase diagrams with simple rules based on the phases present, their transformation temperatures and useful microstructures. We evaluate over 130,000 alloy systems, identifying promising compositions for more time-intensive experimental studies. We find the surprising result that solid solution alloys become less likely as the number of alloy elements increases. This contradicts the major premise of HEAs—that increased configurational entropy increases the stability of disordered solid solution phases. As the number of elements increases, the configurational entropy rises slowly while the probability of at least one pair of elements favouring formation of intermetallic compounds increases more rapidly, explaining this apparent contradiction.

  18. Solution-phase photochemistry of a [FeFe]hydrogenase model compound: Evidence of photoinduced isomerisation

    NASA Astrophysics Data System (ADS)

    Kania, Rafal; Frederix, Pim W. J. M.; Wright, Joseph A.; Ulijn, Rein V.; Pickett, Christopher J.; Hunt, Neil T.

    2012-01-01

    The solution-phase photochemistry of the [FeFe] hydrogenase subsite model (μ-S(CH2)3S)Fe2(CO)4(PMe3)2 has been studied using ultrafast time-resolved infrared spectroscopy supported by density functional theory calculations. In three different solvents, n-heptane, methanol, and acetonitrile, relaxation of the tricarbonyl intermediate formed by UV photolysis of a carbonyl ligand leads to geminate recombination with a bias towards a thermodynamically less stable isomeric form, suggesting that facile interconversion of the ligand groups at the Fe center is possible in the unsaturated species. In a polar or hydrogen bonding solvent, this process competes with solvent substitution leading to the formation of stable solvent adduct species. The data provide further insight into the effect of incorporating non-carbonyl ligands on the dynamics and photochemistry of hydrogenase-derived biomimetic compounds.

  19. Sample-Averaged Biexciton Quantum Yield Measured by Solution-Phase Photon Correlation

    PubMed Central

    Beyler, Andrew P.; Bischof, Thomas S.; Cui, Jian; Coropceanu, Igor; Harris, Daniel K.; Bawendi, Moungi G.

    2015-01-01

    The brightness of nanoscale optical materials such as semiconductor nanocrystals is currently limited in high excitation flux applications by inefficient multiexciton fluorescence. We have devised a solution-phase photon correlation measurement that can conveniently and reliably measure the average biexciton-to-exciton quantum yield ratio of an entire sample without user selection bias. This technique can be used to investigate the multiexciton recombination dynamics of a broad scope of synthetically underdeveloped materials, including those with low exciton quantum yields and poor fluorescence stability. Here, we have applied this method to measure weak biexciton fluorescence in samples of visible-emitting InP/ZnS and InAs/ZnS core/shell nanocrystals, and to demonstrate that a rapid CdS shell growth procedure can markedly increase the biexciton fluorescence of CdSe nanocrystals. PMID:25409496

  20. Parallel rendering

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas W.

    1995-01-01

    This article provides a broad introduction to the subject of parallel rendering, encompassing both hardware and software systems. The focus is on the underlying concepts and the issues which arise in the design of parallel rendering algorithms and systems. We examine the different types of parallelism and how they can be applied in rendering applications. Concepts from parallel computing, such as data decomposition, task granularity, scalability, and load balancing, are considered in relation to the rendering problem. We also explore concepts from computer graphics, such as coherence and projection, which have a significant impact on the structure of parallel rendering algorithms. Our survey covers a number of practical considerations as well, including the choice of architectural platform, communication and memory requirements, and the problem of image assembly and display. We illustrate the discussion with numerous examples from the parallel rendering literature, representing most of the principal rendering methods currently used in computer graphics.

  1. Dynamics of organic and inorganic arsenic in the solution phase of an acidic fen in Germany

    NASA Astrophysics Data System (ADS)

    Huang, J.-H.; Matzner, E.

    2006-04-01

    Wetland soils play a key role for the transformation of heavy metals in forested watersheds, influencing their mobility, and ecotoxicity. Our goal was to investigate the mechanisms of release from solid to solution phase, the mobility, and the transformation of arsenic species in a fen soil. In methanol-water extracts, monomethylarsonic acid, dimethylarsinic acid, trimethylarsine oxide, arsenobetaine, and two unknown organic arsenic species were found with concentrations up to 14 ng As g -1 at the surface horizon. Arsenate is the dominant species at the 0-30 cm depth, whereas arsenite predominated at the 30-70 cm depth. Only up to 2.2% of total arsenic in fen was extractable with methanol-water. In porewaters, depth gradient spatial variation of arsenic species, pH, redox potentials, and the other chemical parameters along the profile was observed in June together with high proportion of organic arsenic species (up to 1.2 μg As L -1, 70% of total arsenic). Tetramethylarsonium ion and an unknown organic arsenic species were additionally detected in porewaters at deeper horizons. In comparison, the arsenic speciation in porewaters in April was homogeneous with depth and no organic arsenic species were found. Thus, the occurrence of microbial methylation of arsenic in fen was demonstrated for the first time. The 10 times elevated total arsenic concentrations in porewaters in June compared to April were accompanied by elevated concentrations of total iron, lower concentrations of sulfate and the presence of ammonium and phosphate. The low proportion of methanol-water extractable total arsenic suggests a generally low mobility of arsenic in fen soils. The release of arsenic from solid to solution phases in fen is dominantly controlled by dissolution of iron oxides, redox transformation, and methylation of arsenic, driven by microbial activity in the growing season. As a result, increased concentrations of total arsenic and potentially toxic arsenic species in fen

  2. Perfect polar stacking of parallel beloamphiphile layers. Synthesis, structure and solid-state optical properties of the unsymmetrical acetophenone azine DCA.

    PubMed

    Glaser, Rainer; Knotts, Nathan; Yu, Ping; Li, Linghui; Chandrasekhar, Meera; Martin, Christopher; Barnes, Charles L

    2006-06-21

    Extraordinary high degrees of polar order can be achieved by a rational design that involves the polar stacking of parallel beloamphiphile monolayers (PBAM). This strategy is exemplified by the acetophenone azines MCA (4-methoxy-4'-chloroacetophenone azine) and DCA (4-decoxy-4'-chloroacetophenone azine). The beloamphiphile design aims to achieve strong lateral interactions by way of arene-arene, azine-azine, arene-azine and halogen-bonding interactions. Dipole-induced interactions and halogen bonding dominate interlayer interactions and halogen bonding is shown to effect the layer stacking. Crystals of DCA contain PBAMs with perfect polar order and perfect polar layer stacking, while crystals of MCA features perfect polar order only in one of two layers and layer stacking is polar but not entirely perfect. We report the synthesis of the beloamphiphile DCA, its crystal structure, and we present a comparative discussion of the structures and intermolecular interactions of MCA and DCA. Absorbance and photoluminescence measurements have been carried out for solutions of DCA and for DCA crystals. DCA exhibits a broad emission centered at 2.5 eV when excited with UV radiation. The nonlinear optical response was studied by measuring second harmonic generation (SHG). Strong SHG signals have been observed due to the polar alignment and the DCA crystal's NLO response is 34 times larger than that of urea. Optimization of the beloamphiphile and systematic SAR studies of the polar organic crystals, which are now possible for the very first time, will further improve the performance of this new class of functional organic materials. The materials are organic semiconductors and show promise as blue emitters, as nonlinear optical materials and as OLED materials.

  3. Scalable solution-phase epitaxial growth of symmetry-mismatched heterostructures on two-dimensional crystal soft template

    PubMed Central

    Lin, Zhaoyang; Yin, Anxiang; Mao, Jun; Xia, Yi; Kempf, Nicholas; He, Qiyuan; Wang, Yiliu; Chen, Chih-Yen; Zhang, Yanliang; Ozolins, Vidvuds; Ren, Zhifeng; Huang, Yu; Duan, Xiangfeng

    2016-01-01

    Epitaxial heterostructures with precisely controlled composition and electronic modulation are of central importance for electronics, optoelectronics, thermoelectrics, and catalysis. In general, epitaxial material growth requires identical or nearly identical crystal structures with small misfit in lattice symmetry and parameters and is typically achieved by vapor-phase depositions in vacuum. We report a scalable solution-phase growth of symmetry-mismatched PbSe/Bi2Se3 epitaxial heterostructures by using two-dimensional (2D) Bi2Se3 nanoplates as soft templates. The dangling bond–free surface of 2D Bi2Se3 nanoplates guides the growth of PbSe crystal without requiring a one-to-one match in the atomic structure, which exerts minimal restriction on the epitaxial layer. With a layered structure and weak van der Waals interlayer interaction, the interface layer in the 2D Bi2Se3 nanoplates can deform to accommodate incoming layer, thus functioning as a soft template for symmetry-mismatched epitaxial growth of cubic PbSe crystal on rhombohedral Bi2Se3 nanoplates. We show that a solution chemistry approach can be readily used for the synthesis of gram-scale PbSe/Bi2Se3 epitaxial heterostructures, in which the square PbSe (001) layer forms on the trigonal/hexagonal (0001) plane of Bi2Se3 nanoplates. We further show that the resulted PbSe/Bi2Se3 heterostructures can be readily processed into bulk pellet with considerably suppressed thermal conductivity (0.30 W/m·K at room temperature) while retaining respectable electrical conductivity, together delivering a thermoelectric figure of merit ZT three times higher than that of the pristine Bi2Se3 nanoplates at 575 K. Our study demonstrates a unique epitaxy mode enabled by the 2D nanocrystal soft template via an affordable and scalable solution chemistry approach. It opens up new opportunities for the creation of diverse epitaxial heterostructures with highly disparate structures and functions. PMID:27730211

  4. Magnesium-solution phase catholyte semi-fuel cell for undersea vehicles

    NASA Astrophysics Data System (ADS)

    Medeiros, Maria G.; Bessette, Russell R.; Deschenes, Craig M.; Patrissi, Charles J.; Carreiro, Louis G.; Tucker, Steven P.; Atwater, Delmas W.

    A magnesium-solution phase catholyte semi-fuel cell (SFC) is under development at the Naval Undersea Warfare Center (NUWC) as an energetic electrochemical system for low rate, long endurance undersea vehicle applications. This electrochemical system consists of a magnesium anode, a sodium chloride anolyte, a conductive membrane, a catalyzed carbon current collector, and a catholyte of sodium chloride, sulfuric acid and hydrogen peroxide. Bipolar electrode fabrication to minimize cell stack volume, long duration testing, and scale-up of electrodes from 77 to 1000 cm 2 have been the objectives of this project. Single cell and multi-cell testing at the 77 cm 2 configuration have been utilized to optimize all testing parameters including start-up conditions, flow rates, temperatures, and electrolyte concentrations while maintaining high voltages and efficiencies. The fabrication and testing of bipolar electrodes and operating parameter optimization for large electrode area cells will be presented. Designs for 1000 cm 2 electrodes, electrolyte flow patterns and current/voltage distribution across these large area cells will also be discussed.

  5. Nanomaterial-based biosensors using dual transducing elements for solution phase detection.

    PubMed

    Li, Ning; Su, Xiaodi; Lu, Yi

    2015-05-07

    Biosensors incorporating nanomaterials have demonstrated superior performance compared to their conventional counterparts. Most reported sensors use nanomaterials as a single transducer of signals, while biosensor designs using dual transducing elements have emerged as new approaches to further improve overall sensing performance. This review focuses on recent developments in nanomaterial-based biosensors using dual transducing elements for solution phase detection. The review begins with a brief introduction of the commonly used nanomaterial transducers suitable for designing dual element sensors, including quantum dots, metal nanoparticles, upconversion nanoparticles, graphene, graphene oxide, carbon nanotubes, and carbon nanodots. This is followed by the presentation of the four basic design principles, namely Förster Resonance Energy Transfer (FRET), Amplified Fluorescence Polarization (AFP), Bio-barcode Assay (BCA) and Chemiluminescence (CL), involving either two kinds of nanomaterials, or one nanomaterial and an organic luminescent agent (e.g. organic dyes, luminescent polymers) as dual transducers. Biomolecular and chemical analytes or biological interactions are detected by their control of the assembly and disassembly of the two transducing elements that change the distance between them, the size of the fluorophore-containing composite, or the catalytic properties of the nanomaterial transducers, among other property changes. Comparative discussions on their respective design rules and overall performances are presented afterwards. Compared with the single transducer biosensor design, such a dual-transducer configuration exhibits much enhanced flexibility and design versatility, allowing biosensors to be more specifically devised for various purposes. The review ends by highlighting some of the further development opportunities in this field.

  6. Promoting solution phase discharge in Li-O2 batteries containing weakly solvating electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Gao, Xiangwen; Chen, Yuhui; Johnson, Lee; Bruce, Peter G.

    2016-08-01

    On discharge, the Li-O2 battery can form a Li2O2 film on the cathode surface, leading to low capacities, low rates and early cell death, or it can form Li2O2 particles in solution, leading to high capacities at relatively high rates and avoiding early cell death. Achieving discharge in solution is important and may be encouraged by the use of high donor or acceptor number solvents or salts that dissolve the LiO2 intermediate involved in the formation of Li2O2. However, the characteristics that make high donor or acceptor number solvents good (for example, high polarity) result in them being unstable towards LiO2 or Li2O2. Here we demonstrate that introduction of the additive 2,5-di-tert-butyl-1,4-benzoquinone (DBBQ) promotes solution phase formation of Li2O2 in low-polarity and weakly solvating electrolyte solutions. Importantly, it does so while simultaneously suppressing direct reduction to Li2O2 on the cathode surface, which would otherwise lead to Li2O2 film growth and premature cell death. It also halves the overpotential during discharge, increases the capacity 80- to 100-fold and enables rates >1 mA cmareal-2 for cathodes with capacities of >4 mAh cmareal-2. The DBBQ additive operates by a new mechanism that avoids the reactive LiO2 intermediate in solution.

  7. Parallel machines: Parallel machine languages

    SciTech Connect

    Iannucci, R.A. )

    1990-01-01

    This book presents a framework for understanding the tradeoffs between the conventional view and the dataflow view with the objective of discovering the critical hardware structures which must be present in any scalable, general-purpose parallel computer to effectively tolerate latency and synchronization costs. The author presents an approach to scalable general purpose parallel computation. Linguistic Concerns, Compiling Issues, Intermediate Language Issues, and hardware/technological constraints are presented as a combined approach to architectural Develoement. This book presents the notion of a parallel machine language.

  8. A liquid flatjet system for solution phase soft-x-ray spectroscopy

    PubMed Central

    Ekimova, Maria; Quevedo, Wilson; Faubel, Manfred; Wernet, Philippe; Nibbering, Erik T. J.

    2015-01-01

    We present a liquid flatjet system for solution phase soft-x-ray spectroscopy. The flatjet set-up utilises the phenomenon of formation of stable liquid sheets upon collision of two identical laminar jets. Colliding the two single water jets, coming out of the nozzles with 50 μm orifices, under an impact angle of 48° leads to double sheet formation, of which the first sheet is 4.6 mm long and 1.0 mm wide. The liquid flatjet operates fully functional under vacuum conditions (<10−3 mbar), allowing soft-x-ray spectroscopy of aqueous solutions in transmission mode. We analyse the liquid water flatjet thickness under atmospheric pressure using interferomeric or mid-infrared transmission measurements and under vacuum conditions by measuring the absorbance of the O K-edge of water in transmission, and comparing our results with previously published data obtained with standing cells with Si3N4 membrane windows. The thickness of the first liquid sheet is found to vary between 1.4–3 μm, depending on the transverse and longitudinal position in the liquid sheet. We observe that the derived thickness is of similar magnitude under 1 bar and under vacuum conditions. A catcher unit facilitates the recycling of the solutions, allowing measurements on small sample volumes (∼10 ml). We demonstrate the applicability of this approach by presenting measurements on the N K-edge of aqueous NH4+. Our results suggest the high potential of using liquid flatjets in steady-state and time-resolved studies in the soft-x-ray regime. PMID:26798824

  9. Parallel pipelining

    SciTech Connect

    Joseph, D.D.; Bai, R.; Liao, T.Y.; Huang, A.; Hu, H.H.

    1995-09-01

    In this paper the authors introduce the idea of parallel pipelining for water lubricated transportation of oil (or other viscous material). A parallel system can have major advantages over a single pipe with respect to the cost of maintenance and continuous operation of the system, to the pressure gradients required to restart a stopped system and to the reduction and even elimination of the fouling of pipe walls in continuous operation. The authors show that the action of capillarity in small pipes is more favorable for restart than in large pipes. In a parallel pipeline system, they estimate the number of small pipes needed to deliver the same oil flux as in one larger pipe as N = (R/r){sup {alpha}}, where r and R are the radii of the small and large pipes, respectively, and {alpha} = 4 or 19/7 when the lubricating water flow is laminar or turbulent.

  10. Solid- and solution phase transformations in novel hybrid iodoplumbate derivatives templated by solvated yttrium complexes.

    PubMed

    Mishra, Shashank; Jeanneau, Erwann; Daniele, Stéphane; Ledoux, Gilles; Swamy, Prakash N

    2008-10-20

    Solvated yttrium iodide precursors [Y(L)8]I3 [L = dimethylformamide (DMF) or dimethylsulfoxide (DMSO)], prepared in situ by stirring YI3(Pr(i)OH)4 in DMF/DMSO, react with 3 equiv of PbI2 in the presence of NH4I to give novel hybrid derivatives based on either a one-dimensional (1D) straight chain, [Y(DMF)8][Pb3(mu-I)9](1infinity) x DMF (1), or discrete pentanuclear iodoplumbates, [Y(DMSO)8]2[(DMSO)2Pb5(mu3-I)2(mu-I)8I6] (2a). The complex 2a and a closely related [Y(DMSO)8][Y(DMSO)7(DMF)][(DMSO)2Pb5(mu3-I)2(mu-I)8I6] (2b) were obtained in good yield by solution phase transformation of 1 in DMSO under slight different conditions. Derivatives 1 and 2 also undergo unique solid-state transformation in a confined environment of paratone to give 1D polymers based on zigzag iodoplumbate chains; crystals of 1 transform into [Y(DMF)6(H2O)2][Pb3(mu3-I)(mu-I)7I](1infinity) (3) via an exchange reaction, whereas those of 2a and 2b are converted into [Y(DMSO)7][Pb3(mu3-I)(mu-I)7I](1infinity) (4) via a decomposition pathway. The trifurcate H-bonding between water ligands on yttrium cation and iodide of the iodoplumbate anion plays a pivotal role in transforming the straight 1D polymeric Pb-I chain of 1 into a zigzag chain in 3. The thermogravimetry-differential thermal analysis studies indicate that complexes with DMF ligands are thermally more stable than those with DMSO ones, the mixed DMF-H2O ligand complex 3 being the most stable one because of the presence of strong H-bonding. Diffuse-reflectance UV-visible spectral analyses of 1-4 show an optical band gap in the 1.86-2.54 eV range, indicating these derivatives as potential semiconductors. In contrast to non-emissive 3 and 4, derivatives 1, 2a, and 2b show remarkable luminescent emission with peak maxima at 703 nm, assigned as an iodine 5p-lead 6s to lead 6p charge transfer (XM-M-CT).

  11. Hybrid vapor phase-solution phase growth techniques for improved CZT(S,Se) photovoltaic device performance

    DOEpatents

    Chang, Liang-Yi; Gershon, Talia S.; Haight, Richard A.; Lee, Yun Seog

    2016-12-27

    A hybrid vapor phase-solution phase CZT(S,Se) growth technique is provided. In one aspect, a method of forming a kesterite absorber material on a substrate includes the steps of: depositing a layer of a first kesterite material on the substrate using a vapor phase deposition process, wherein the first kesterite material includes Cu, Zn, Sn, and at least one of S and Se; annealing the first kesterite material to crystallize the first kesterite material; and depositing a layer of a second kesterite material on a side of the first kesterite material opposite the substrate using a solution phase deposition process, wherein the second kesterite material includes Cu, Zn, Sn, and at least one of S and Se, wherein the first kesterite material and the second kesterite material form a multi-layer stack of the absorber material on the substrate. A photovoltaic device and method of formation thereof are also provided.

  12. Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species?

    PubMed Central

    Balthasart, Françoise; Plavec, Janez; Gabelica, Valérie

    2013-01-01

    G-quadruplex nucleic acids can bind ammonium ions in solution and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG4T4G4)2, (dG4T3G4)2 and (dG3T4G4)2, and the intramolecular G-quadruplexes dG4(T4G4)3 and dG2T2G2TGTG2T2G2 (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure travelling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between G-quartets, but also additional ammonium ions bound at specific sites outside the external G-quartets can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the G-quadruplex fold in the gas phase. Ion mobility experiments therefore help assigning the number of inner ammonium ions in the solution phase structure. PMID:23132414

  13. Quantum chemical and solution phase evaluation of metallocenes as reducing agents for the prospective atomic layer deposition of copper.

    PubMed

    Dey, Gangotri; Wrench, Jacqueline S; Hagen, Dirk J; Keeney, Lynette; Elliott, Simon D

    2015-06-14

    We propose and evaluate the use of metallocene compounds as reducing agents for the chemical vapour deposition (and specifically atomic layer deposition, ALD) of the transition metal Cu from metalorganic precursors. Ten different transition metal cyclopentadienyl compounds are screened for their utility in the reduction of Cu from five different Cu precursors by evaluating model reaction energies with density functional theory (DFT) and solution phase chemistry.

  14. Application of parallel liquid chromatography/mass spectrometry for high throughput microsomal stability screening of compound libraries.

    PubMed

    Xu, Rongda; Nemes, Csaba; Jenkins, Kelly M; Rourick, Robyn A; Kassel, Daniel B; Liu, Charles Z C

    2002-02-01

    Solution-phase and solid-phase parallel synthesis and high throughput screening have enabled biologically active and selective compounds to be identified at an unprecedented rate. The challenge has been to convert these hits into viable development candidates. To accelerate the conversion of these hits into lead development candidates, early assessment of the physicochemical and pharmacological properties of these compounds is being made. In particular, in vitro absorption, distribution, metabolism, and elimination (ADME) assays are being conducted at earlier and earlier stages of discovery with the goal of reducing the attrition rate of these potential drug candidates as they progress through development. In this report, we present an eight-channel parallel liquid chromatography/mass spectrometry (LC/MS) system in combination with custom Visual Basic and Applescript automated data processing applications for high throughput early ADME. The parallel LC/MS system was configured with one set of gradient LC pumps and an eight-channel multiple probe autosampler. The flow was split equivalently into eight streams before the multiple probe autosampler and recombined after the eight columns and just prior to the mass spectrometer ion source. The system was tested for column-to-column variation and for reproducibility over a 17 h period (approximately 500 injections per column). The variations in retention time and peak area were determined to be less than 2 and 10%, respectively, in both tests. The parallel LC/MS system described permits time-course microsomal incubations (t(o), t5, t15, t30) to be measured in triplicate and enables estimations of t 1/2 microsomal stability. The parallel LC/MS system is capable of analyzing up to 240 samples per hour and permits the complete profiling up to two microtiter plates of compounds per day (i.e., 176 test substrate compounds + sixteen controls).

  15. Solution-phase monitoring of the structural evolution of a Molybdenum Blue nanoring.

    PubMed

    Miras, Haralampos N; Richmond, Craig J; Long, De-Liang; Cronin, Leroy

    2012-02-29

    The inorganic host-guest complex Na(22){[Mo(VI)(36)O(112)(H(2)O)(16)]⊂[Mo(VI)(130)Mo(V)(20)O(442)(OH)(10)(H(2)O)(61)]}·180H(2)O ≡ {Mo(36)}⊂{Mo(150)}, compound 1, has been isolated in its solid crystalline state via unconventional synthesis in a custom flow reactor. Carrying out the reaction under controlled flow conditions selected for the generation of {Mo(36)}⊂{Mo(150)} as the major product, allowing it to be reproducibly isolated in a moderate yield, as opposed to traditional "one-pot" batch syntheses that typically lead to crystallization of the {Mo(36)} and {Mo(150)} species separately. Structural and spectroscopic studies of compound 1 and the archetypal Molybdenum Blue (MB) wheel, {Mo(150)}, identified compound 1 as a likely intermediate in the {Mo(36)} templated synthesis of MB wheels. Further evidence illustrating the template effect of {Mo(36)} to MB wheel synthesis was indicated by an increase in the yield and rate of production of {Mo(150)} as a direct result of the addition of preformed {Mo(36)} to the reaction mixture. Dynamic light scattering (DLS) techniques were also used to corroborate the mechanism of formation of the MB wheels through observation of the individual cluster species in solution. DLS measurement of the reaction solutions from which {Mo(36)} and {Mo(150)} crystallized gave particle size distribution curves averaging 1.9 and 3.9 nm, consistent with the dimensions of the discrete clusters, which allowed the use of size as a possible distinguishing feature of these key species in the reduced acidified molybdate solutions and to observe the templation of the MB wheel by {Mo(36)} directly.

  16. Synthesis of Chemiluminescent Esters: A Combinatorial Synthesis Experiment for Organic Chemistry Students

    ERIC Educational Resources Information Center

    Duarte, Robert; Nielson, Janne T.; Dragojlovic, Veljko

    2004-01-01

    A group of techniques aimed at synthesizing a large number of structurally diverse compounds is called combinatorial synthesis. Synthesis of chemiluminescence esters using parallel combinatorial synthesis and mix-and-split combinatorial synthesis is experimented.

  17. Large-scale solution-phase growth of Cu-doped ZnO nanowire networks.

    PubMed

    Xu, Chunju; Koo, Tae-Woong; Kim, Byung-Sung; Lee, Jae-Hyun; Hwang, Sung Woo; Whang, Dongmok

    2011-07-01

    Film-like networks of Cu-doped (0.8-2.5 at.%) ZnO nanowires were successfully synthesized through a facile solution process at a low temperature (<100 degrees C). The pH value of solution plays a key role in controlling the density and quality of the Cu-doped ZnO nanowires and the dopant concentration of ZnO nanowires was controlled by adjusting the Cu2+/Zn2+ concentration ratio during the synthesis. The structural study showed that the as-prepared Cu-doped ZnO nanowires with a narrow diameter range of 20-30 nm were single crystal and grew along [0001] direction. Photoluminescence and electrical conductivity measurements showed that Cu doping can lead to a redshift in bandgap energy and an increase in the resistivity of ZnO. The thermal annealing of the as-grown nanowires at a low temperature (300 degrees C) decreased the defect-related emission within the visible range and increased the electrical conductivity. The high-quality ZnO nanowire network with controlled doping will enable further application to flexible and transparent electronics.

  18. Importance of Solvation in Understanding the Chiroptical Spectra of Natural Products in Solution Phase: Garcinia Acid Dimethyl Ester

    PubMed Central

    Polavarapu, Prasad L.; Scalmani, Giovanni; Hawkins, Edward K.; Rizzo, Carmelo; Jeirath, Neha; Ibnusaud, Ibrahim; Habel, Deenamma; Nair, Divya Sadasivan; Haleema, Simimole

    2013-01-01

    The optical rotatory dispersion (ORD), electronic circular dichroism (ECD), and vibrational circular dichroism (VCD) spectra of (+)-garcinia acid dimethyl ester have been measured and analyzed by comparison with the corresponding spectra predicted by quantum chemical methods for (2S,3S)-garcinia acid dimethyl ester. For solution-phase calculations the recently developed continuous surface charge polarizable continuum model (PCM) has been used. It is found that gas-phase predictions and PCM predictions at the B3LYP/aug-cc-pVDZ level yield nearly mirror-image ECD spectra in the 190–250 nm region for the same absolute configuration and that gas-phase ECD predictions lead to incorrect absolute configuration. At the CAM-B3LYP/aug-cc-pVDZ level, however, gas-phase predictions and PCM predictions of ECD in the 190–250 nm region are not so different, but PCM predictions provide better agreement with the experimental observations. For carbonyl stretching vibrations, the vibrational band positions predicted at the B3LYP/aug-cc-pVDZ level in gas-phase calculations differ significantly from the corresponding experimentally observed band positions, and this discrepancy has also been corrected by the use of PCM. In addition, the solution-phase VCD predictions provided better agreement (with experimental VCD observations) than gas-phase VCD predictions. These observations underscore the importance of including solvent effects in quantum chemical calculations of chiroptical spectroscopic properties. PMID:21114277

  19. Understanding the solution phase chemistry and solid state thermodynamic behavior of pharmaceutical cocrystals

    NASA Astrophysics Data System (ADS)

    Maheshwari, Chinmay

    Cocrystals have drawn a lot of research interest in the last decade due to their potential to favorably alter the physicochemical and biopharmaceutical properties of active pharmaceutical ingredients. This dissertation focuses on the thermodynamic stability and solubility of pharmaceutical cocrystals. Specifically, the objectives are to; (i) investigate the influence of coformer properties such as solubility and ionization characteristics on cocrystal solubility and stability as a function of pH, (ii) to measure the thermodynamic solubility of metastable cocrystals, and study the solubility differences measured by kinetic and equilibrium methods, (iii) investigate the role of surfactants on the solubility and synthesis of cocrystals, (iv) investigate the solid state phase transformation of reactants to cocrystals and the factors that influence the reaction kinetics and, (v) provide models that enable the prediction of cocrystal formation by calculating the free energy of formation for a solid to solid transformation of reactants to cocrystals. Cocrystal solubilities were measured directly when cocrystals were thermodynamically stable, while solubilities were calculated from eutectic concentration measurements when cocrystals were of higher solubility than its components. Cocrystal solubility was highly dependent on coformer solubilities for gabapentin-lactam and lamotrigine cocrystals. It was found that melting point is not a good indicator of cocrystal solubility as solute-solvent interactions quantified by the activity coefficient play a huge role in the observed solubility. Similar to salts, cocrystals also exhibit pHmax, however the salts and cocrystals have different dependencies on the parameters that govern the value of pHmax. It is also shown that cocrystals could provide solubility advantage over salts as lamotrigine-nicotinamide cocrystal hydrate has about 6 fold higher solubility relative to lamotrigine-saccharin salt. In the case of mixtures of solid

  20. Fast and Facile Synthesis of 4-Nitrophenyl 2-Azidoethylcarbamate Derivatives from N-Fmoc-Protected α-Amino Acids as Activated Building Blocks for Urea Moiety-Containing Compound Library.

    PubMed

    Chen, Ying-Ying; Chang, Li-Te; Chen, Hung-Wei; Yang, Chia-Ying; Hsin, Ling-Wei

    2017-03-13

    A fast and facile synthesis of a series of 4-nitrophenyl 2-azidoethylcarbamate derivatives as activated urea building blocks was developed. The N-Fmoc-protected 2-aminoethyl mesylates derived from various commercially available N-Fmoc-protected α-amino acids, including those having functionalized side chains with acid-labile protective groups, were directly transformed into 4-nitrophenyl 2-azidoethylcarbamate derivatives in 1 h via a one-pot two-step reaction. These urea building blocks were utilized for the preparation of a series of urea moiety-containing mitoxantrone-amino acid conjugates in 75-92% yields and parallel solution-phase synthesis of a urea compound library consisted of 30 members in 38-70% total yields.

  1. Parallel pivoting combined with parallel reduction

    NASA Technical Reports Server (NTRS)

    Alaghband, Gita

    1987-01-01

    Parallel algorithms for triangularization of large, sparse, and unsymmetric matrices are presented. The method combines the parallel reduction with a new parallel pivoting technique, control over generations of fill-ins and a check for numerical stability, all done in parallel with the work being distributed over the active processes. The parallel technique uses the compatibility relation between pivots to identify parallel pivot candidates and uses the Markowitz number of pivots to minimize fill-in. This technique is not a preordering of the sparse matrix and is applied dynamically as the decomposition proceeds.

  2. High resolution ion mobility measurements for gas phase proteins: correlation between solution phase and gas phase conformations

    NASA Astrophysics Data System (ADS)

    Hudgins, Robert R.; Woenckhaus, Jürgen; Jarrold, Martin F.

    1997-11-01

    Our high resolution ion mobility apparatus has been modified by attaching an electrospray source to perform measurements for biological molecules. While the greater resolving power permits the resolution of more conformations for BPTI and cytochrome c, the resolved features are generally much broader than expected for a single rigid conformation. A major advantage of the new experimental configuration is the much gentler introduction of ions into the drift tube, so that the observed gas phase conformations appear to more closely reflect those present in solution. For example, it is possible to distinguish between the native state of cytochrome c and the methanol-denatured form on the basis of the ion mobility measurements; the mass spectra alone are not sensitive enough to detect this change. Thus this approach may provide a quick and sensitive tool for probing the solution phase conformations of biological molecules.

  3. Stability and spinodal decomposition of the solid-solution phase in the ruthenium-cerium-oxide electro-catalyst.

    PubMed

    Li, Yanmei; Wang, Xin; Shao, Yanqun; Tang, Dian; Wu, Bo; Tang, Zhongzhi; Lin, Wei

    2015-01-14

    The phase diagram of Ru-Ce-O was calculated by a combination of ab initio density functional theory and thermodynamic calculations. The phase diagram indicates that the solubility between ruthenium oxide and cerium oxide is very low at temperatures below 1100 K. Solid solution phases, if existing under normal experimental conditions, are metastable and subject to a quasi-spinodal decomposition to form a mixture of a Ru-rich rutile oxide phase and a Ce-rich fluorite oxide phase. To study the spinodal decomposition of Ru-Ce-O, Ru0.6Ce0.4O2 samples were prepared at 280 °C and 450 °C. XRD and in situ TEM characterization provide proof of the quasi-spinodal decomposition of Ru0.6Ce0.4O2. The present study provides a fundamental reference for the phase design of the Ru-Ce-O electro-catalyst.

  4. Diversity-oriented synthesis of 1-substituted 4-aryl-6-oxo-1,6-dihydropyridine-3-carboxamides.

    PubMed

    Baškovč, Jernej; Dahmann, Georg; Golobič, Amalija; Grošelj, Uroš; Kočar, Drago; Stanovnik, Branko; Svete, Jurij

    2012-09-10

    A simple five-step diversity-oriented synthesis of 1-substituted 4-aryl-6-oxo-1,6-dihydropyridine-3-carboxamides was developed. Treatment of dimethyl 2-((dimethylamino)methylidene)-3-oxopentanedioate with twenty primary amines gave 1-substituted methyl 4-hydroxy-6-oxo-1,6-dihydropyridine-3-carboxylates. Transformation into the corresponding 4-tosyloxy and 4-chloro derivatives, followed by Suzuki-Miyaura arylations gave a series of eleven N-substituted methyl 4-aryl-6-oxo-1,6-dihydropyridine-3-carboxylates. Combinatorial screening was employed to establish suitable reaction conditions for Suzuki-Miyaura arylation of N-alkylpyridones. Hydrolysis of the esters followed by parallel solution-phase amidation of the corresponding carboxylic acids with primary and secondary amines furnished a library of seventeen final products.

  5. A nanofluidic system for massively parallel PCR

    NASA Astrophysics Data System (ADS)

    Brenan, Colin; Morrison, Tom; Roberts, Douglas; Hurley, James

    2008-02-01

    Massively parallel nanofluidic systems are lab-on-a-chip devices where solution phase biochemical and biological analyses are implemented in high density arrays of nanoliter holes micro-machined in a thin platen. Polymer coatings make the interior surfaces of the holes hydrophilic and the exterior surface of the platen hydrophobic for precise and accurate self-metered loading of liquids into each hole without cross-contamination. We have created a "nanoplate" based on this concept, equivalent in performance to standard microtiter plates, having 3072 thirty-three nanoliter holes in a stainless steel platen the dimensions of a microscope slide. We report on the performance of this device for PCR-based single nucleotide polymorphism (SNP) genotyping or quantitative measurement of gene expression by real-time PCR in applications ranging from plant and animal diagnostics, agricultural genetics and human disease research.

  6. Special parallel processing workshop

    SciTech Connect

    1994-12-01

    This report contains viewgraphs from the Special Parallel Processing Workshop. These viewgraphs deal with topics such as parallel processing performance, message passing, queue structure, and other basic concept detailing with parallel processing.

  7. Easy parallel screening of reagent stability, quality control, and metrology in solid phase peptide synthesis (SPPS) and peptide couplings for microarrays.

    PubMed

    Achyuthan, Komandoor E; Wheeler, David R

    2015-10-01

    Evaluating the stability of coupling reagents, quality control (QC), and surface functionalization metrology are all critical to the production of high quality peptide microarrays. We describe a broadly applicable screening technique for evaluating the fidelity of solid phase peptide synthesis (SPPS), the stability of activation/coupling reagents, and a microarray surface metrology tool. This technique was used to assess the stability of the activation reagent 1-{[1-(Cyano-2-ethoxy-2-oxo-ethylidenaminooxy)dimethylamino-morpholinomethylene]}methaneaminiumHexafluorophosphate (COMU) (Sigma-Aldrich, St. Louis, MO, USA) by SPPS of Leu-Enkephalin (YGGFL) or the coupling of commercially synthesized YGGFL peptides to (3-aminopropyl)triethyoxysilane-modified glass surfaces. Coupling efficiency was quantitated by fluorescence signaling based on immunoreactivity of the YGGFL motif. It was concluded that COMU solutions should be prepared fresh and used within 5 h when stored at ~23 °C and not beyond 24 h if stored refrigerated, both in closed containers. Caveats to gauging COMU stability by absorption spectroscopy are discussed. Commercial YGGFL peptides needed independent QC, due to immunoreactivity variations for the same sequence synthesized by different vendors. This technique is useful in evaluating the stability of other activation/coupling reagents besides COMU and as a metrology tool for SPPS and peptide microarrays.

  8. Parallel rendering techniques for massively parallel visualization

    SciTech Connect

    Hansen, C.; Krogh, M.; Painter, J.

    1995-07-01

    As the resolution of simulation models increases, scientific visualization algorithms which take advantage of the large memory. and parallelism of Massively Parallel Processors (MPPs) are becoming increasingly important. For large applications rendering on the MPP tends to be preferable to rendering on a graphics workstation due to the MPP`s abundant resources: memory, disk, and numerous processors. The challenge becomes developing algorithms that can exploit these resources while minimizing overhead, typically communication costs. This paper will describe recent efforts in parallel rendering for polygonal primitives as well as parallel volumetric techniques. This paper presents rendering algorithms, developed for massively parallel processors (MPPs), for polygonal, spheres, and volumetric data. The polygon algorithm uses a data parallel approach whereas the sphere and volume render use a MIMD approach. Implementations for these algorithms are presented for the Thinking Ma.chines Corporation CM-5 MPP.

  9. Comparative study of solution-phase and vapor-phase deposition of aminosilanes on silicon dioxide surfaces.

    PubMed

    Yadav, Amrita R; Sriram, Rashmi; Carter, Jared A; Miller, Benjamin L

    2014-02-01

    The uniformity of aminosilane layers typically used for the modification of hydroxyl bearing surfaces such as silicon dioxide is critical for a wide variety of applications, including biosensors. However, in spite of many studies that have been undertaken on surface silanization, there remains a paucity of easy-to-implement deposition methods reproducibly yielding smooth aminosilane monolayers. In this study, solution- and vapor-phase deposition methods for three aminoalkoxysilanes differing in the number of reactive groups (3-aminopropyl triethoxysilane (APTES), 3-aminopropyl methyl diethoxysilane (APMDES) and 3-aminopropyl dimethyl ethoxysilane (APDMES)) were assessed with the aim of identifying methods that yield highly uniform and reproducible silane layers that are resistant to minor procedural variations. Silane film quality was characterized based on measured thickness, hydrophilicity and surface roughness. Additionally, hydrolytic stability of the films was assessed via these thickness and contact angle values following desorption in water. We found that two simple solution-phase methods, an aqueous deposition of APTES and a toluene based deposition of APDMES, yielded high quality silane layers that exhibit comparable characteristics to those deposited via vapor-phase methods.

  10. Discovery of a thermally persistent h.c.p. solid-solution phase in the Ni-W system

    SciTech Connect

    Kurz, S. J. B. Leineweber, A.; Maisel, S. B.; Höfler, M.; Müller, S.; Mittemeijer, E. J.

    2014-08-28

    Although the accepted Ni-W phase diagram does not reveal the existence of h.c.p.-based phases, h.c.p.-like stacking sequences were observed in magnetron-co-sputtered Ni-W thin films at W contents of 20 to 25 at. %, by using transmission electron microscopy and X-ray diffraction. The occurrence of this h.c.p.-like solid-solution phase could be rationalized by first-principles calculations, showing that the vicinity of the system's ground-state line is populated with metastable h.c.p.-based superstructures in the intermediate concentration range from 20 to 50 at. % W. The h.c.p.-like stacking in Ni-W films was observed to be thermally persistent, up to temperatures as high as at least 850 K, as evidenced by extensive X-ray diffraction analyses on specimens before and after annealing treatments. The tendency of Ni-W for excessive planar faulting is discussed in the light of these new findings.

  11. Quinic acid derivatives as sialyl Lewis(x)-mimicking selectin inhibitors: design, synthesis, and crystal structure in complex with E-selectin.

    PubMed

    Kaila, Neelu; Somers, William S; Thomas, Bert E; Thakker, Paresh; Janz, Kristin; DeBernardo, Silvano; Tam, Steve; Moore, William J; Yang, Ruiyang; Wrona, Wojciech; Bedard, Patricia W; Crommie, Deidre; Keith, James C; Tsao, Desiree H H; Alvarez, Juan C; Ni, Heyu; Marchese, Erik; Patton, John T; Magnani, John L; Camphausen, Raymond T

    2005-06-30

    A search for noncarbohydrate sLe(x) mimics led to the development of quinic acid derivatives as selectin inhibitors. At Wyeth we solved the first cocrystal structure of a small molecule, quinic acid, with E-selectin. In the cocomplex two hydroxyls of quinic acid mimic the calcium-bound fucose of the tetrasaccharide sLe(x). The X-ray structure, together with structure based computational methods, was used to design quinic acid based libraries that were synthesized and evaluated for their ability to block the interaction of sLex with P-selectin. A large number of analogues were prepared using solution-phase parallel synthesis. Selected compounds showed decrease in leukocyte rolling in the IVM mouse model. Compound 2 inhibited neutrophil influx in the murine TIP model and demonstrated good plasma exposure.

  12. Side-chain effects on the solution-phase conformations and charge photogeneration dynamics of low-bandgap copolymers

    NASA Astrophysics Data System (ADS)

    Huo, Ming-Ming; Liang, Ran; Xing, Ya-Dong; Hu, Rong; Zhao, Ning-Jiu; Zhang, Wei; Fu, Li-Min; Ai, Xi-Cheng; Zhang, Jian-Ping; Hou, Jian-Hui

    2013-09-01

    Solution-phase conformations and charge photogeneration dynamics of a pair of low-bandgap copolymers based on benzo[1,2-b:4,5-b']dithiophene (BDT) and thieno[3,4-b]thiophene (TT), differed by the respective carbonyl (-C) and ester (-E) substituents at the TT units, were comparatively investigated by using near-infrared time-resolved absorption (TA) spectroscopy at 25 °C and 120 °C. Steady-state and TA spectroscopic results corroborated by quantum chemical analyses prove that both PBDTTT-C and PBDTTT-E in chlorobenzene solutions are self-aggregated; however, the former bears a relatively higher packing order. Specifically, PBDTTT-C aggregates with more π-π stacked domains, whereas PBDTTT-E does with more random coils interacting strongly at the chain intersections. At 25 °C, the copolymers exhibit comparable exciton lifetimes (˜1 ns) and fluorescence quantum yields (˜2%), but distinctly different charge photogeneration dynamics: PBDTTT-C on photoexcitation gives rise to a branching ratio of charge separated (CS) over charge transfer (CT) states more than 20% higher than PBDTTT-E does, correlating with their photovoltaic performance. Temperature and excitation-wavelength dependent exciton/charge dynamics suggest that the CT states localize at the chain intersections that are survivable up to 120 °C, and that the excitons and the CS states inhabit the stretched strands and the also thermally robust orderly stacked domains. The stable self-aggregation structures and the associated primary charge dynamics of the PBDTTT copolymers in solutions are suggested to impact intimately on the morphologies and the charge photogeneration efficiency of the solid-state photoactive layers.

  13. Parallel flow diffusion battery

    DOEpatents

    Yeh, Hsu-Chi; Cheng, Yung-Sung

    1984-08-07

    A parallel flow diffusion battery for determining the mass distribution of an aerosol has a plurality of diffusion cells mounted in parallel to an aerosol stream, each diffusion cell including a stack of mesh wire screens of different density.

  14. Parallel flow diffusion battery

    DOEpatents

    Yeh, H.C.; Cheng, Y.S.

    1984-01-01

    A parallel flow diffusion battery for determining the mass distribution of an aerosol has a plurality of diffusion cells mounted in parallel to an aerosol stream, each diffusion cell including a stack of mesh wire screens of different density.

  15. Parallel processing ITS

    SciTech Connect

    Fan, W.C.; Halbleib, J.A. Sr.

    1996-09-01

    This report provides a users` guide for parallel processing ITS on a UNIX workstation network, a shared-memory multiprocessor or a massively-parallel processor. The parallelized version of ITS is based on a master/slave model with message passing. Parallel issues such as random number generation, load balancing, and communication software are briefly discussed. Timing results for example problems are presented for demonstration purposes.

  16. 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.

  17. Parallel simulation today

    NASA Technical Reports Server (NTRS)

    Nicol, David; Fujimoto, Richard

    1992-01-01

    This paper surveys topics that presently define the state of the art in parallel simulation. Included in the tutorial are discussions on new protocols, mathematical performance analysis, time parallelism, hardware support for parallel simulation, load balancing algorithms, and dynamic memory management for optimistic synchronization.

  18. FPGA-Based Filterbank Implementation for Parallel Digital Signal Processing

    NASA Technical Reports Server (NTRS)

    Berner, Stephan; DeLeon, Phillip

    1999-01-01

    One approach to parallel digital signal processing decomposes a high bandwidth signal into multiple lower bandwidth (rate) signals by an analysis bank. After processing, the subband signals are recombined into a fullband output signal by a synthesis bank. This paper describes an implementation of the analysis and synthesis banks using (Field Programmable Gate Arrays) FPGAs.

  19. Solution-Phase Crosstalk and Regulatory Interactions Between Multipotent Adult Progenitor Cells and Peripheral Blood Mononuclear Cells

    PubMed Central

    van’t Hof, Wouter; Reddy, Ashok P.; Wilmarth, Phillip A.; David, Larry L.; Raber, Amy; Bogaerts, Annelies; Timmerman, Lien; Pinxteren, Jef; Roobrouck, Valerie D.; Deans, Robert J.; Maziarz, Richard T.

    2015-01-01

    Multipotent adult progenitor cells (MAPCs) are adult adherent stromal stem cells currently being assessed in clinical trials for acute graft versus host disease with demonstrated immunomodulatory capabilities and the potential to ameliorate detrimental autoimmune and inflammation-related processes. Anti-CD3/anti-CD28 (3/28) activation of T cells within the peripheral blood mononuclear cell (PBMC) compartment was performed in the presence or absence of MAPCs. Liquid chromatography-coupled tandem mass spectrometry was used to characterize the differential secretion of proteins, and transcriptional profiling was used to monitor mRNA expression changes in both cell populations. Overall, 239 secreted and/or ectodomain-shed proteins were detected in the secretomes of PBMCs and MAPCs. In addition, 3/28 activation of PBMCs induced differential expression of 2,925 genes, and 22% of these transcripts were differentially expressed on exposure to MAPCs in Transwell. MAPCs exposed to 3/28-activated PBMCs showed differential expression of 1,247 MAPC genes. Crosstalk was demonstrated by reciprocal transcriptional regulation. Secretome proteins and transcriptional signatures were used to predict molecular activities by which MAPCs could dampen local and systemic inflammatory responses. These data support the hypothesis that MAPCs block PBMC proliferation via cell cycle arrest coupled to metabolic stress in the form of tryptophan depletion, resulting in GCN2 kinase activation, downstream signaling, and inhibition of cyclin D1 translation. These data also provide a plausible explanation for the immune privilege reported with administration of donor MAPCs. Although most components of the major histocompatibility complex class II antigen presentation pathway were markedly transcriptionally upregulated, cell surface expression of human leukocyte antigen-DR is minimal on MAPCs exposed to 3/28-activated PBMCs. Significance This study documents experiments quantifying solution-phase

  20. Parallel algorithm development

    SciTech Connect

    Adams, T.F.

    1996-06-01

    Rapid changes in parallel computing technology are causing significant changes in the strategies being used for parallel algorithm development. One approach is simply to write computer code in a standard language like FORTRAN 77 or with the expectation that the compiler will produce executable code that will run in parallel. The alternatives are: (1) to build explicit message passing directly into the source code; or (2) to write source code without explicit reference to message passing or parallelism, but use a general communications library to provide efficient parallel execution. Application of these strategies is illustrated with examples of codes currently under development.

  1. Sonochemical Synthesis of Molybdenum Disilicide (MoSi2).

    DTIC Science & Technology

    2007-11-02

    Two successful solution phase synthesis methods were developed for the preparation of Nanocrystalline MoSi particles. The first method consisted of...ignition at approximately 500 deg C that resulted in the evolution of SiCl4 and the formation of MoSi crystallites. Nanoparticles were compacted using a

  2. Parallel Atomistic Simulations

    SciTech Connect

    HEFFELFINGER,GRANT S.

    2000-01-18

    Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.

  3. Parallel digital forensics infrastructure.

    SciTech Connect

    Liebrock, Lorie M.; Duggan, David Patrick

    2009-10-01

    This report documents the architecture and implementation of a Parallel Digital Forensics infrastructure. This infrastructure is necessary for supporting the design, implementation, and testing of new classes of parallel digital forensics tools. Digital Forensics has become extremely difficult with data sets of one terabyte and larger. The only way to overcome the processing time of these large sets is to identify and develop new parallel algorithms for performing the analysis. To support algorithm research, a flexible base infrastructure is required. A candidate architecture for this base infrastructure was designed, instantiated, and tested by this project, in collaboration with New Mexico Tech. Previous infrastructures were not designed and built specifically for the development and testing of parallel algorithms. With the size of forensics data sets only expected to increase significantly, this type of infrastructure support is necessary for continued research in parallel digital forensics. This report documents the implementation of the parallel digital forensics (PDF) infrastructure architecture and implementation.

  4. Introduction to Parallel Computing

    DTIC Science & Technology

    1992-05-01

    Topology C, Ada, C++, Data-parallel FORTRAN, 2D mesh of node boards, each node FORTRAN-90 (late 1992) board has 1 application processor Devopment Tools ...parallel machines become the wave of the present, tools are increasingly needed to assist programmers in creating parallel tasks and coordinating...their activities. Linda was designed to be such a tool . Linda was designed with three important goals in mind: to be portable, efficient, and easy to use

  5. Parallel Wolff Cluster Algorithms

    NASA Astrophysics Data System (ADS)

    Bae, S.; Ko, S. H.; Coddington, P. D.

    The Wolff single-cluster algorithm is the most efficient method known for Monte Carlo simulation of many spin models. Due to the irregular size, shape and position of the Wolff clusters, this method does not easily lend itself to efficient parallel implementation, so that simulations using this method have thus far been confined to workstations and vector machines. Here we present two parallel implementations of this algorithm, and show that one gives fairly good performance on a MIMD parallel computer.

  6. PCLIPS: Parallel CLIPS

    NASA Technical Reports Server (NTRS)

    Hall, Lawrence O.; Bennett, Bonnie H.; Tello, Ivan

    1994-01-01

    A parallel version of CLIPS 5.1 has been developed to run on Intel Hypercubes. The user interface is the same as that for CLIPS with some added commands to allow for parallel calls. A complete version of CLIPS runs on each node of the hypercube. The system has been instrumented to display the time spent in the match, recognize, and act cycles on each node. Only rule-level parallelism is supported. Parallel commands enable the assertion and retraction of facts to/from remote nodes working memory. Parallel CLIPS was used to implement a knowledge-based command, control, communications, and intelligence (C(sup 3)I) system to demonstrate the fusion of high-level, disparate sources. We discuss the nature of the information fusion problem, our approach, and implementation. Parallel CLIPS has also be used to run several benchmark parallel knowledge bases such as one to set up a cafeteria. Results show from running Parallel CLIPS with parallel knowledge base partitions indicate that significant speed increases, including superlinear in some cases, are possible.

  7. Application Portable Parallel Library

    NASA Technical Reports Server (NTRS)

    Cole, Gary L.; Blech, Richard A.; Quealy, Angela; Townsend, Scott

    1995-01-01

    Application Portable Parallel Library (APPL) computer program is subroutine-based message-passing software library intended to provide consistent interface to variety of multiprocessor computers on market today. Minimizes effort needed to move application program from one computer to another. User develops application program once and then easily moves application program from parallel computer on which created to another parallel computer. ("Parallel computer" also include heterogeneous collection of networked computers). Written in C language with one FORTRAN 77 subroutine for UNIX-based computers and callable from application programs written in C language or FORTRAN 77.

  8. Parallel Algorithms and Patterns

    SciTech Connect

    Robey, Robert W.

    2016-06-16

    This is a powerpoint presentation on parallel algorithms and patterns. A parallel algorithm is a well-defined, step-by-step computational procedure that emphasizes concurrency to solve a problem. Examples of problems include: Sorting, searching, optimization, matrix operations. A parallel pattern is a computational step in a sequence of independent, potentially concurrent operations that occurs in diverse scenarios with some frequency. Examples are: Reductions, prefix scans, ghost cell updates. We only touch on parallel patterns in this presentation. It really deserves its own detailed discussion which Gabe Rockefeller would like to develop.

  9. Parallel Lisp simulator

    SciTech Connect

    Weening, J.S.

    1988-05-01

    CSIM is a simulator for parallel Lisp, based on a continuation passing interpreter. It models a shared-memory multiprocessor executing programs written in Common Lisp, extended with several primitives for creating and controlling processes. This paper describes the structure of the simulator, measures its performance, and gives an example of its use with a parallel Lisp program.

  10. Parallel and Distributed Computing.

    DTIC Science & Technology

    1986-12-12

    program was devoted to parallel and distributed computing . Support for this part of the program was obtained from the present Army contract and a...Umesh Vazirani. A workshop on parallel and distributed computing was held from May 19 to May 23, 1986 and drew 141 participants. Keywords: Mathematical programming; Protocols; Randomized algorithms. (Author)

  11. Massively parallel mathematical sieves

    SciTech Connect

    Montry, G.R.

    1989-01-01

    The Sieve of Eratosthenes is a well-known algorithm for finding all prime numbers in a given subset of integers. A parallel version of the Sieve is described that produces computational speedups over 800 on a hypercube with 1,024 processing elements for problems of fixed size. Computational speedups as high as 980 are achieved when the problem size per processor is fixed. The method of parallelization generalizes to other sieves and will be efficient on any ensemble architecture. We investigate two highly parallel sieves using scattered decomposition and compare their performance on a hypercube multiprocessor. A comparison of different parallelization techniques for the sieve illustrates the trade-offs necessary in the design and implementation of massively parallel algorithms for large ensemble computers.

  12. Totally parallel multilevel algorithms

    NASA Technical Reports Server (NTRS)

    Frederickson, Paul O.

    1988-01-01

    Four totally parallel algorithms for the solution of a sparse linear system have common characteristics which become quite apparent when they are implemented on a highly parallel hypercube such as the CM2. These four algorithms are Parallel Superconvergent Multigrid (PSMG) of Frederickson and McBryan, Robust Multigrid (RMG) of Hackbusch, the FFT based Spectral Algorithm, and Parallel Cyclic Reduction. In fact, all four can be formulated as particular cases of the same totally parallel multilevel algorithm, which are referred to as TPMA. In certain cases the spectral radius of TPMA is zero, and it is recognized to be a direct algorithm. In many other cases the spectral radius, although not zero, is small enough that a single iteration per timestep keeps the local error within the required tolerance.

  13. Parallel computing works

    SciTech Connect

    Not Available

    1991-10-23

    An account of the Caltech Concurrent Computation Program (C{sup 3}P), a five year project that focused on answering the question: Can parallel computers be used to do large-scale scientific computations '' As the title indicates, the question is answered in the affirmative, by implementing numerous scientific applications on real parallel computers and doing computations that produced new scientific results. In the process of doing so, C{sup 3}P helped design and build several new computers, designed and implemented basic system software, developed algorithms for frequently used mathematical computations on massively parallel machines, devised performance models and measured the performance of many computers, and created a high performance computing facility based exclusively on parallel computers. While the initial focus of C{sup 3}P was the hypercube architecture developed by C. Seitz, many of the methods developed and lessons learned have been applied successfully on other massively parallel architectures.

  14. Parallel tetrahedral mesh adaptation with dynamic load balancing

    SciTech Connect

    Oliker, Leonid; Biswas, Rupak; Gabow, Harold N.

    2000-06-28

    The ability to dynamically adapt an unstructured grid is a powerful tool for efficiently solving computational problems with evolving physical features. In this paper, we report on our experience parallelizing an edge-based adaptation scheme, called 3D-TAG, using message passing. Results show excellent speedup when a realistic helicopter rotor mesh is randomly refined. However, performance deteriorates when the mesh is refined using a solution-based error indicator since mesh adaptation for practical problems occurs in a localized region, creating a severe load imbalance. To address this problem, we have developed PLUM, a global dynamic load balancing framework for adaptive numerical computations. Even though PLUM primarily balances processor workloads for the solution phase, it reduces the load imbalance problem within mesh adaptation by repartitioning the mesh after targeting edges for refinement but before the actual subdivision. This dramatically improves the performance of parallel 3D-TAG since refinement occurs in a more load balanced fashion. We also present optimal and heuristic algorithms that, when applied to the default mapping of a parallel repartitioner, significantly reduce the data redistribution overhead. Finally, portability is examined by comparing performance on three state-of-the-art parallel machines.

  15. Parallel Tetrahedral Mesh Adaptation with Dynamic Load Balancing

    NASA Technical Reports Server (NTRS)

    Oliker, Leonid; Biswas, Rupak; Gabow, Harold N.

    1999-01-01

    The ability to dynamically adapt an unstructured grid is a powerful tool for efficiently solving computational problems with evolving physical features. In this paper, we report on our experience parallelizing an edge-based adaptation scheme, called 3D_TAG. using message passing. Results show excellent speedup when a realistic helicopter rotor mesh is randomly refined. However. performance deteriorates when the mesh is refined using a solution-based error indicator since mesh adaptation for practical problems occurs in a localized region., creating a severe load imbalance. To address this problem, we have developed PLUM, a global dynamic load balancing framework for adaptive numerical computations. Even though PLUM primarily balances processor workloads for the solution phase, it reduces the load imbalance problem within mesh adaptation by repartitioning the mesh after targeting edges for refinement but before the actual subdivision. This dramatically improves the performance of parallel 3D_TAG since refinement occurs in a more load balanced fashion. We also present optimal and heuristic algorithms that, when applied to the default mapping of a parallel repartitioner, significantly reduce the data redistribution overhead. Finally, portability is examined by comparing performance on three state-of-the-art parallel machines.

  16. The synthesis and evaluation of a solution phase indexed combinatorial library of non-natural polyenes for reversal of P-glycoprotein mediated multidrug resistance.

    PubMed

    Andrus, M B; Turner, T M; Sauna, Z E; Ambudkar, S V

    2000-08-11

    A combinatorial library of polyenes, based on (-)-stipiamide, has been constructed and evaluated for the discovery of new multidrug resistance reversal agents. A palladium coupling was used to react each individual vinyl iodide with a mixture of the seven acetylenes at near 1:1 stoichiometry. The coupling was also used to react each individual acetylene with the mixture of six vinyl iodides to create 13 pools indexed in two dimensions for a total of 42 compounds. Individual compounds were detected at equimolar concentration. The vinyl iodides, made initially using a crotylborane addition to generate the anti1,2-hydroxylmethyl products, were now made using a more efficient norephedrine propionate boron enolate aldol reaction. The indexed approach, ideally suited for cellular assays that involve membrane-bound targets, allowed for the rapid identification of reversal agents using assays with drug-resistant human breast cancer MCF7-adrR cells. Intersections of potent pools identified new compounds with promising activity. Aryl dimension pools showed R = ph and naphthyl as the most potent. The acetylene dimension had R' = phenylalaninol and alaninol as the most potent. Isolated individual compounds, both active and nonpotent, were assayed to confirm the library results. The most potent new compound was 4ek (R = naphthyl, R' = phenylaninol) at 1.45 microM. Other nonnatural individual naphthyl-amide compounds showed potent MDR reversal including the morpholino-amide 4ej (1.69 microM). Synergistic activities attributed to the two ends of the molecule were also identified. Direct interaction with Pgp was established by ATPase and photoaffinity displacement assays. The results indicate that both ends of the polyene reversal agent are involved in Pgp interaction and can be further modified for increased potency.

  17. 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.

  18. Parallel programming with PCN

    SciTech Connect

    Foster, I.; Tuecke, S.

    1991-12-01

    PCN is a system for developing and executing parallel programs. It comprises a high-level programming language, tools for developing and debugging programs in this language, and interfaces to Fortran and C that allow the reuse of existing code in multilingual parallel programs. Programs developed using PCN are portable across many different workstations, networks, and parallel computers. This document provides all the information required to develop parallel programs with the PCN programming system. In includes both tutorial and reference material. It also presents the basic concepts that underly PCN, particularly where these are likely to be unfamiliar to the reader, and provides pointers to other documentation on the PCN language, programming techniques, and tools. PCN is in the public domain. The latest version of both the software and this manual can be obtained by anonymous FTP from Argonne National Laboratory in the directory pub/pcn at info.mcs.anl.gov (c.f. Appendix A).

  19. Parallel programming with PCN

    SciTech Connect

    Foster, I.; Tuecke, S.

    1991-09-01

    PCN is a system for developing and executing parallel programs. It comprises a high-level programming language, a set of tools for developing and debugging programs in this language, and interfaces to Fortran and C that allow the reuse of existing code in multilingual parallel programs. Programs developed using PCN are portable across many different workstations, networks, and parallel computers. This document provides all the information required to develop parallel programs with the PCN programming system. It includes both tutorial and reference material. It also presents the basic concepts that underlie PCN, particularly where these are likely to be unfamiliar to the reader, and provides pointers to other documentation on the PCN language, programming techniques, and tools. PCN is in the public domain. The latest version of both the software and this manual can be obtained by anonymous FTP from Argonne National Laboratory at info.mcs.anl.gov.

  20. The Parallel Axiom

    ERIC Educational Resources Information Center

    Rogers, Pat

    1972-01-01

    Criteria for a reasonable axiomatic system are discussed. A discussion of the historical attempts to prove the independence of Euclids parallel postulate introduces non-Euclidean geometries. Poincare's model for a non-Euclidean geometry is defined and analyzed. (LS)

  1. Scalable parallel communications

    NASA Technical Reports Server (NTRS)

    Maly, K.; Khanna, S.; Overstreet, C. M.; Mukkamala, R.; Zubair, M.; Sekhar, Y. S.; Foudriat, E. C.

    1992-01-01

    Coarse-grain parallelism in networking (that is, the use of multiple protocol processors running replicated software sending over several physical channels) can be used to provide gigabit communications for a single application. Since parallel network performance is highly dependent on real issues such as hardware properties (e.g., memory speeds and cache hit rates), operating system overhead (e.g., interrupt handling), and protocol performance (e.g., effect of timeouts), we have performed detailed simulations studies of both a bus-based multiprocessor workstation node (based on the Sun Galaxy MP multiprocessor) and a distributed-memory parallel computer node (based on the Touchstone DELTA) to evaluate the behavior of coarse-grain parallelism. Our results indicate: (1) coarse-grain parallelism can deliver multiple 100 Mbps with currently available hardware platforms and existing networking protocols (such as Transmission Control Protocol/Internet Protocol (TCP/IP) and parallel Fiber Distributed Data Interface (FDDI) rings); (2) scale-up is near linear in n, the number of protocol processors, and channels (for small n and up to a few hundred Mbps); and (3) since these results are based on existing hardware without specialized devices (except perhaps for some simple modifications of the FDDI boards), this is a low cost solution to providing multiple 100 Mbps on current machines. In addition, from both the performance analysis and the properties of these architectures, we conclude: (1) multiple processors providing identical services and the use of space division multiplexing for the physical channels can provide better reliability than monolithic approaches (it also provides graceful degradation and low-cost load balancing); (2) coarse-grain parallelism supports running several transport protocols in parallel to provide different types of service (for example, one TCP handles small messages for many users, other TCP's running in parallel provide high bandwidth

  2. Parallel image compression

    NASA Technical Reports Server (NTRS)

    Reif, John H.

    1987-01-01

    A parallel compression algorithm for the 16,384 processor MPP machine was developed. The serial version of the algorithm can be viewed as a combination of on-line dynamic lossless test compression techniques (which employ simple learning strategies) and vector quantization. These concepts are described. How these concepts are combined to form a new strategy for performing dynamic on-line lossy compression is discussed. Finally, the implementation of this algorithm in a massively parallel fashion on the MPP is discussed.

  3. Revisiting and parallelizing SHAKE

    NASA Astrophysics Data System (ADS)

    Weinbach, Yael; Elber, Ron

    2005-10-01

    An algorithm is presented for running SHAKE in parallel. SHAKE is a widely used approach to compute molecular dynamics trajectories with constraints. An essential step in SHAKE is the solution of a sparse linear problem of the type Ax = b, where x is a vector of unknowns. Conjugate gradient minimization (that can be done in parallel) replaces the widely used iteration process that is inherently serial. Numerical examples present good load balancing and are limited only by communication time.

  4. Parallel architectures for vision

    SciTech Connect

    Maresca, M. ); Lavin, M.A. ); Li, H. )

    1988-08-01

    Vision computing involves the execution of a large number of operations on large sets of structured data. Sequential computers cannot achieve the speed required by most of the current applications and therefore parallel architectural solutions have to be explored. In this paper the authors examine the options that drive the design of a vision oriented computer, starting with the analysis of the basic vision computation and communication requirements. They briefly review the classical taxonomy for parallel computers, based on the multiplicity of the instruction and data stream, and apply a recently proposed criterion, the degree of autonomy of each processor, to further classify fine-grain SIMD massively parallel computers. They identify three types of processor autonomy, namely operation autonomy, addressing autonomy, and connection autonomy. For each type they give the basic definitions and show some examples. They focus on the concept of connection autonomy, which they believe is a key point in the development of massively parallel architectures for vision. They show two examples of parallel computers featuring different types of connection autonomy - the Connection Machine and the Polymorphic-Torus - and compare their cost and benefit.

  5. Sublattice parallel replica dynamics

    NASA Astrophysics Data System (ADS)

    Martínez, Enrique; Uberuaga, Blas P.; Voter, Arthur F.

    2014-06-01

    Exascale computing presents a challenge for the scientific community as new algorithms must be developed to take full advantage of the new computing paradigm. Atomistic simulation methods that offer full fidelity to the underlying potential, i.e., molecular dynamics (MD) and parallel replica dynamics, fail to use the whole machine speedup, leaving a region in time and sample size space that is unattainable with current algorithms. In this paper, we present an extension of the parallel replica dynamics algorithm [A. F. Voter, Phys. Rev. B 57, R13985 (1998), 10.1103/PhysRevB.57.R13985] by combining it with the synchronous sublattice approach of Shim and Amar [Y. Shim and J. G. Amar, Phys. Rev. B 71, 125432 (2005), 10.1103/PhysRevB.71.125432], thereby exploiting event locality to improve the algorithm scalability. This algorithm is based on a domain decomposition in which events happen independently in different regions in the sample. We develop an analytical expression for the speedup given by this sublattice parallel replica dynamics algorithm and compare it with parallel MD and traditional parallel replica dynamics. We demonstrate how this algorithm, which introduces a slight additional approximation of event locality, enables the study of physical systems unreachable with traditional methodologies and promises to better utilize the resources of current high performance and future exascale computers.

  6. Parallel Stitching of Two-Dimensional Materials

    NASA Astrophysics Data System (ADS)

    Ling, Xi; Lin, Yuxuan; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing; Department of Electrical Engineering; Computer Science, Massachusetts Institute of Technology Team

    Large scale integration of atomically thin metals (e.g. graphene), semiconductors (e.g. transition metal dichalcogenides (TMDs)), and insulators (e.g. hexagonal boron nitride) is critical for constructing the building blocks for future nanoelectronics and nanophotonics. However, the construction of in-plane heterostructures, especially between two atomic layers with large lattice mismatch, could be extremely difficult due to the strict requirement of spatial precision and the lack of a selective etching method. Here, we developed a general synthesis methodology to achieve both vertical and in-plane ``parallel stitched'' heterostructures between a two-dimensional (2D) and TMD materials, which enables both multifunctional electronic/optoelectronic devices and their large scale integration. This is achieved via selective ``sowing'' of aromatic molecule seeds during the chemical vapor deposition growth. MoS2 is used as a model system to form heterostructures with diverse other 2D materials. Direct and controllable synthesis of large-scale parallel stitched graphene-MoS2 heterostructures was further investigated. Unique nanometer overlapped junctions were obtained at the parallel stitched interface, which are highly desirable both as metal-semiconductor contact and functional devices/systems, such as for use in logical integrated circuits (ICs) and broadband photodetectors.

  7. Parallel optical sampler

    DOEpatents

    Tauke-Pedretti, Anna; Skogen, Erik J; Vawter, Gregory A

    2014-05-20

    An optical sampler includes a first and second 1.times.n optical beam splitters splitting an input optical sampling signal and an optical analog input signal into n parallel channels, respectively, a plurality of optical delay elements providing n parallel delayed input optical sampling signals, n photodiodes converting the n parallel optical analog input signals into n respective electrical output signals, and n optical modulators modulating the input optical sampling signal or the optical analog input signal by the respective electrical output signals, and providing n successive optical samples of the optical analog input signal. A plurality of output photodiodes and eADCs convert the n successive optical samples to n successive digital samples. The optical modulator may be a photodiode interconnected Mach-Zehnder Modulator. A method of sampling the optical analog input signal is disclosed.

  8. CRUNCH_PARALLEL

    SciTech Connect

    Shumaker, Dana E.; Steefel, Carl I.

    2016-06-21

    The code CRUNCH_PARALLEL is a parallel version of the CRUNCH code. CRUNCH code version 2.0 was previously released by LLNL, (UCRL-CODE-200063). Crunch is a general purpose reactive transport code developed by Carl Steefel and Yabusake (Steefel Yabsaki 1996). The code handles non-isothermal transport and reaction in one, two, and three dimensions. The reaction algorithm is generic in form, handling an arbitrary number of aqueous and surface complexation as well as mineral dissolution/precipitation. A standardized database is used containing thermodynamic and kinetic data. The code includes advective, dispersive, and diffusive transport.

  9. The NAS Parallel Benchmarks

    SciTech Connect

    Bailey, David H.

    2009-11-15

    The NAS Parallel Benchmarks (NPB) are a suite of parallel computer performance benchmarks. They were originally developed at the NASA Ames Research Center in 1991 to assess high-end parallel supercomputers. Although they are no longer used as widely as they once were for comparing high-end system performance, they continue to be studied and analyzed a great deal in the high-performance computing community. The acronym 'NAS' originally stood for the Numerical Aeronautical Simulation Program at NASA Ames. The name of this organization was subsequently changed to the Numerical Aerospace Simulation Program, and more recently to the NASA Advanced Supercomputing Center, although the acronym remains 'NAS.' The developers of the original NPB suite were David H. Bailey, Eric Barszcz, John Barton, David Browning, Russell Carter, LeoDagum, Rod Fatoohi, Samuel Fineberg, Paul Frederickson, Thomas Lasinski, Rob Schreiber, Horst Simon, V. Venkatakrishnan and Sisira Weeratunga. The original NAS Parallel Benchmarks consisted of eight individual benchmark problems, each of which focused on some aspect of scientific computing. The principal focus was in computational aerophysics, although most of these benchmarks have much broader relevance, since in a much larger sense they are typical of many real-world scientific computing applications. The NPB suite grew out of the need for a more rational procedure to select new supercomputers for acquisition by NASA. The emergence of commercially available highly parallel computer systems in the late 1980s offered an attractive alternative to parallel vector supercomputers that had been the mainstay of high-end scientific computing. However, the introduction of highly parallel systems was accompanied by a regrettable level of hype, not only on the part of the commercial vendors but even, in some cases, by scientists using the systems. As a result, it was difficult to discern whether the new systems offered any fundamental performance advantage

  10. Highly parallel computation

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.; Tichy, Walter F.

    1990-01-01

    Among the highly parallel computing architectures required for advanced scientific computation, those designated 'MIMD' and 'SIMD' have yielded the best results to date. The present development status evaluation of such architectures shown neither to have attained a decisive advantage in most near-homogeneous problems' treatment; in the cases of problems involving numerous dissimilar parts, however, such currently speculative architectures as 'neural networks' or 'data flow' machines may be entailed. Data flow computers are the most practical form of MIMD fine-grained parallel computers yet conceived; they automatically solve the problem of assigning virtual processors to the real processors in the machine.

  11. Adaptive parallel logic networks

    NASA Technical Reports Server (NTRS)

    Martinez, Tony R.; Vidal, Jacques J.

    1988-01-01

    Adaptive, self-organizing concurrent systems (ASOCS) that combine self-organization with massive parallelism for such applications as adaptive logic devices, robotics, process control, and system malfunction management, are presently discussed. In ASOCS, an adaptive network composed of many simple computing elements operating in combinational and asynchronous fashion is used and problems are specified by presenting if-then rules to the system in the form of Boolean conjunctions. During data processing, which is a different operational phase from adaptation, the network acts as a parallel hardware circuit.

  12. Matching Solid-State to Solution-Phase Photoluminescence for Near-Unity Down-Conversion Efficiency Using Giant Quantum Dots.

    PubMed

    Hanson, Christina J; Buck, Matthew R; Acharya, Krishna; Torres, Joseph A; Kundu, Janardan; Ma, Xuedan; Bouquin, Sarah; Hamilton, Christopher E; Htoon, Han; Hollingsworth, Jennifer A

    2015-06-24

    Efficient, stable, and narrowband red-emitting fluorophores are needed as down-conversion materials for next-generation solid-state lighting that is both efficient and of high color quality. Semiconductor quantum dots (QDs) are nearly ideal color-shifting phosphors, but solution-phase efficiencies have not traditionally extended to the solid-state, with losses from both intrinsic and environmental effects. Here, we assess the impacts of temperature and flux on QD phosphor performance. By controlling QD core/shell structure, we realize near-unity down-conversion efficiency and enhanced operational stability. Furthermore, we show that a simple modification of the phosphor-coated light-emitting diode device-incorporation of a thin spacer layer-can afford reduced thermal or photon-flux quenching at high driving currents (>200 mA).

  13. The Influence of the Linker Geometry in Bis(3-hydroxy-N-methyl-pyridin-2-one) Ligands on Solution-Phase Uranyl Affinity

    SciTech Connect

    Szigethy, Geza; Raymond, Kenneth

    2010-08-12

    Seven water-soluble, tetradentate bis(3-hydroxy-N-methyl-pyridin-2-one) (bis-Me-3,2-HOPO) ligands were synthesized that vary only in linker geometry and rigidity. Solution phase thermodynamic measurements were conducted between pH 1.6 and pH 9.0 to determine the effects of these variations on proton and uranyl cation affinity. Proton affinity decreases by introduction of the solubilizing triethylene glycol group as compared to un-substituted reference ligands. Uranyl affinity was found to follow no discernable trends with incremental geometric modification. The butyl-linked 4Li-Me-3,2-HOPO ligand exhibited the highest uranyl affinity, consistent with prior in vivo decorporation results. Of the rigidly-linked ligands, the o-phenylene linker imparted the best uranyl affinity to the bis-Me-3,2-HOPO ligand platform.

  14. Rapid Screening for Potential Epitopes Reactive with a Polycolonal Antibody by Solution-Phase H/D Exchange Monitored by FT-ICR Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zhang, Qian; Noble, Kyle A.; Mao, Yuan; Young, Nicolas L.; Sathe, Shridhar K.; Roux, Kenneth H.; Marshall, Alan G.

    2013-07-01

    The potential epitopes of a recombinant food allergen protein, cashew Ana o 2, reactive to polyclonal antibodies, were mapped by solution-phase amide backbone H/D exchange (HDX) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Ana o 2 polyclonal antibodies were purified in the serum from a goat immunized with cashew nut extract. Antibodies were incubated with recombinant Ana o 2 (rAna o 2) to form antigen:polyclonal antibody (Ag:pAb) complexes. Complexed and uncomplexed (free) rAna o 2 were then subjected to HDX-MS analysis. Four regions protected from H/D exchange upon pAb binding are identified as potential epitopes and mapped onto a homologous model.

  15. Parallel Coordinate Axes.

    ERIC Educational Resources Information Center

    Friedlander, Alex; And Others

    1982-01-01

    Several methods of numerical mappings other than the usual cartesian coordinate system are considered. Some examples using parallel axes representation, which are seen to lead to aesthetically pleasing or interesting configurations, are presented. Exercises with alternative representations can stimulate pupil imagination and exploration in…

  16. Parallel programming with PCN

    SciTech Connect

    Foster, I.; Tuecke, S.

    1993-01-01

    PCN is a system for developing and executing parallel programs. It comprises a high-level programming language, tools for developing and debugging programs in this language, and interfaces to Fortran and Cthat allow the reuse of existing code in multilingual parallel programs. Programs developed using PCN are portable across many different workstations, networks, and parallel computers. This document provides all the information required to develop parallel programs with the PCN programming system. It includes both tutorial and reference material. It also presents the basic concepts that underlie PCN, particularly where these are likely to be unfamiliar to the reader, and provides pointers to other documentation on the PCN language, programming techniques, and tools. PCN is in the public domain. The latest version of both the software and this manual can be obtained by anonymous ftp from Argonne National Laboratory in the directory pub/pcn at info.mcs. ani.gov (cf. Appendix A). This version of this document describes PCN version 2.0, a major revision of the PCN programming system. It supersedes earlier versions of this report.

  17. Parallel Dislocation Simulator

    SciTech Connect

    2006-10-30

    ParaDiS is software capable of simulating the motion, evolution, and interaction of dislocation networks in single crystals using massively parallel computer architectures. The software is capable of outputting the stress-strain response of a single crystal whose plastic deformation is controlled by the dislocation processes.

  18. Massively parallel processor computer

    NASA Technical Reports Server (NTRS)

    Fung, L. W. (Inventor)

    1983-01-01

    An apparatus for processing multidimensional data with strong spatial characteristics, such as raw image data, characterized by a large number of parallel data streams in an ordered array is described. It comprises a large number (e.g., 16,384 in a 128 x 128 array) of parallel processing elements operating simultaneously and independently on single bit slices of a corresponding array of incoming data streams under control of a single set of instructions. Each of the processing elements comprises a bidirectional data bus in communication with a register for storing single bit slices together with a random access memory unit and associated circuitry, including a binary counter/shift register device, for performing logical and arithmetical computations on the bit slices, and an I/O unit for interfacing the bidirectional data bus with the data stream source. The massively parallel processor architecture enables very high speed processing of large amounts of ordered parallel data, including spatial translation by shifting or sliding of bits vertically or horizontally to neighboring processing elements.

  19. High performance parallel architectures

    SciTech Connect

    Anderson, R.E. )

    1989-09-01

    In this paper the author describes current high performance parallel computer architectures. A taxonomy is presented to show computer architecture from the user programmer's point-of-view. The effects of the taxonomy upon the programming model are described. Some current architectures are described with respect to the taxonomy. Finally, some predictions about future systems are presented. 5 refs., 1 fig.

  20. Parallel fast gauss transform

    SciTech Connect

    Sampath, Rahul S; Sundar, Hari; Veerapaneni, Shravan

    2010-01-01

    We present fast adaptive parallel algorithms to compute the sum of N Gaussians at N points. Direct sequential computation of this sum would take O(N{sup 2}) time. The parallel time complexity estimates for our algorithms are O(N/n{sub p}) for uniform point distributions and O( (N/n{sub p}) log (N/n{sub p}) + n{sub p}log n{sub p}) for non-uniform distributions using n{sub p} CPUs. We incorporate a plane-wave representation of the Gaussian kernel which permits 'diagonal translation'. We use parallel octrees and a new scheme for translating the plane-waves to efficiently handle non-uniform distributions. Computing the transform to six-digit accuracy at 120 billion points took approximately 140 seconds using 4096 cores on the Jaguar supercomputer. Our implementation is 'kernel-independent' and can handle other 'Gaussian-type' kernels even when explicit analytic expression for the kernel is not known. These algorithms form a new class of core computational machinery for solving parabolic PDEs on massively parallel architectures.

  1. Parallel hierarchical radiosity rendering

    SciTech Connect

    Carter, M.

    1993-07-01

    In this dissertation, the step-by-step development of a scalable parallel hierarchical radiosity renderer is documented. First, a new look is taken at the traditional radiosity equation, and a new form is presented in which the matrix of linear system coefficients is transformed into a symmetric matrix, thereby simplifying the problem and enabling a new solution technique to be applied. Next, the state-of-the-art hierarchical radiosity methods are examined for their suitability to parallel implementation, and scalability. Significant enhancements are also discovered which both improve their theoretical foundations and improve the images they generate. The resultant hierarchical radiosity algorithm is then examined for sources of parallelism, and for an architectural mapping. Several architectural mappings are discussed. A few key algorithmic changes are suggested during the process of making the algorithm parallel. Next, the performance, efficiency, and scalability of the algorithm are analyzed. The dissertation closes with a discussion of several ideas which have the potential to further enhance the hierarchical radiosity method, or provide an entirely new forum for the application of hierarchical methods.

  2. Parallel hierarchical global illumination

    SciTech Connect

    Snell, Quinn O.

    1997-10-08

    Solving the global illumination problem is equivalent to determining the intensity of every wavelength of light in all directions at every point in a given scene. The complexity of the problem has led researchers to use approximation methods for solving the problem on serial computers. Rather than using an approximation method, such as backward ray tracing or radiosity, the authors have chosen to solve the Rendering Equation by direct simulation of light transport from the light sources. This paper presents an algorithm that solves the Rendering Equation to any desired accuracy, and can be run in parallel on distributed memory or shared memory computer systems with excellent scaling properties. It appears superior in both speed and physical correctness to recent published methods involving bidirectional ray tracing or hybrid treatments of diffuse and specular surfaces. Like progressive radiosity methods, it dynamically refines the geometry decomposition where required, but does so without the excessive storage requirements for ray histories. The algorithm, called Photon, produces a scene which converges to the global illumination solution. This amounts to a huge task for a 1997-vintage serial computer, but using the power of a parallel supercomputer significantly reduces the time required to generate a solution. Currently, Photon can be run on most parallel environments from a shared memory multiprocessor to a parallel supercomputer, as well as on clusters of heterogeneous workstations.

  3. Parallel Multigrid Equation Solver

    SciTech Connect

    Adams, Mark

    2001-09-07

    Prometheus is a fully parallel multigrid equation solver for matrices that arise in unstructured grid finite element applications. It includes a geometric and an algebraic multigrid method and has solved problems of up to 76 mullion degrees of feedom, problems in linear elasticity on the ASCI blue pacific and ASCI red machines.

  4. Serial multiplier arrays for parallel computation

    NASA Technical Reports Server (NTRS)

    Winters, Kel

    1990-01-01

    Arrays of systolic serial-parallel multiplier elements are proposed as an alternative to conventional SIMD mesh serial adder arrays for applications that are multiplication intensive and require few stored operands. The design and operation of a number of multiplier and array configurations featuring locality of connection, modularity, and regularity of structure are discussed. A design methodology combining top-down and bottom-up techniques is described to facilitate development of custom high-performance CMOS multiplier element arrays as well as rapid synthesis of simulation models and semicustom prototype CMOS components. Finally, a differential version of NORA dynamic circuits requiring a single-phase uncomplemented clock signal introduced for this application.

  5. Parallel grid population

    DOEpatents

    Wald, Ingo; Ize, Santiago

    2015-07-28

    Parallel population of a grid with a plurality of objects using a plurality of processors. One example embodiment is a method for parallel population of a grid with a plurality of objects using a plurality of processors. The method includes a first act of dividing a grid into n distinct grid portions, where n is the number of processors available for populating the grid. The method also includes acts of dividing a plurality of objects into n distinct sets of objects, assigning a distinct set of objects to each processor such that each processor determines by which distinct grid portion(s) each object in its distinct set of objects is at least partially bounded, and assigning a distinct grid portion to each processor such that each processor populates its distinct grid portion with any objects that were previously determined to be at least partially bounded by its distinct grid portion.

  6. Parallel Anisotropic Tetrahedral Adaptation

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Darmofal, David L.

    2008-01-01

    An adaptive method that robustly produces high aspect ratio tetrahedra to a general 3D metric specification without introducing hybrid semi-structured regions is presented. The elemental operators and higher-level logic is described with their respective domain-decomposed parallelizations. An anisotropic tetrahedral grid adaptation scheme is demonstrated for 1000-1 stretching for a simple cube geometry. This form of adaptation is applicable to more complex domain boundaries via a cut-cell approach as demonstrated by a parallel 3D supersonic simulation of a complex fighter aircraft. To avoid the assumptions and approximations required to form a metric to specify adaptation, an approach is introduced that directly evaluates interpolation error. The grid is adapted to reduce and equidistribute this interpolation error calculation without the use of an intervening anisotropic metric. Direct interpolation error adaptation is illustrated for 1D and 3D domains.

  7. Parallel Subconvolution Filtering Architectures

    NASA Technical Reports Server (NTRS)

    Gray, Andrew A.

    2003-01-01

    These architectures are based on methods of vector processing and the discrete-Fourier-transform/inverse-discrete- Fourier-transform (DFT-IDFT) overlap-and-save method, combined with time-block separation of digital filters into frequency-domain subfilters implemented by use of sub-convolutions. The parallel-processing method implemented in these architectures enables the use of relatively small DFT-IDFT pairs, while filter tap lengths are theoretically unlimited. The size of a DFT-IDFT pair is determined by the desired reduction in processing rate, rather than on the order of the filter that one seeks to implement. The emphasis in this report is on those aspects of the underlying theory and design rules that promote computational efficiency, parallel processing at reduced data rates, and simplification of the designs of very-large-scale integrated (VLSI) circuits needed to implement high-order filters and correlators.

  8. Parallel multilevel preconditioners

    SciTech Connect

    Bramble, J.H.; Pasciak, J.E.; Xu, Jinchao.

    1989-01-01

    In this paper, we shall report on some techniques for the development of preconditioners for the discrete systems which arise in the approximation of solutions to elliptic boundary value problems. Here we shall only state the resulting theorems. It has been demonstrated that preconditioned iteration techniques often lead to the most computationally effective algorithms for the solution of the large algebraic systems corresponding to boundary value problems in two and three dimensional Euclidean space. The use of preconditioned iteration will become even more important on computers with parallel architecture. This paper discusses an approach for developing completely parallel multilevel preconditioners. In order to illustrate the resulting algorithms, we shall describe the simplest application of the technique to a model elliptic problem.

  9. Ultrascalable petaflop parallel supercomputer

    DOEpatents

    Blumrich, Matthias A.; Chen, Dong; Chiu, George; Cipolla, Thomas M.; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Hall, Shawn; Haring, Rudolf A.; Heidelberger, Philip; Kopcsay, Gerard V.; Ohmacht, Martin; Salapura, Valentina; Sugavanam, Krishnan; Takken, Todd

    2010-07-20

    A massively parallel supercomputer of petaOPS-scale includes node architectures based upon System-On-a-Chip technology, where each processing node comprises a single Application Specific Integrated Circuit (ASIC) having up to four processing elements. The ASIC nodes are interconnected by multiple independent networks that optimally maximize the throughput of packet communications between nodes with minimal latency. The multiple networks may include three high-speed networks for parallel algorithm message passing including a Torus, collective network, and a Global Asynchronous network that provides global barrier and notification functions. These multiple independent networks may be collaboratively or independently utilized according to the needs or phases of an algorithm for optimizing algorithm processing performance. The use of a DMA engine is provided to facilitate message passing among the nodes without the expenditure of processing resources at the node.

  10. Homology, convergence and parallelism

    PubMed Central

    Ghiselin, Michael T.

    2016-01-01

    Homology is a relation of correspondence between parts of parts of larger wholes. It is used when tracking objects of interest through space and time and in the context of explanatory historical narratives. Homologues can be traced through a genealogical nexus back to a common ancestral precursor. Homology being a transitive relation, homologues remain homologous however much they may come to differ. Analogy is a relationship of correspondence between parts of members of classes having no relationship of common ancestry. Although homology is often treated as an alternative to convergence, the latter is not a kind of correspondence: rather, it is one of a class of processes that also includes divergence and parallelism. These often give rise to misleading appearances (homoplasies). Parallelism can be particularly hard to detect, especially when not accompanied by divergences in some parts of the body. PMID:26598721

  11. Parallel unstructured grid generation

    NASA Technical Reports Server (NTRS)

    Loehner, Rainald; Camberos, Jose; Merriam, Marshal

    1991-01-01

    A parallel unstructured grid generation algorithm is presented and implemented on the Hypercube. Different processor hierarchies are discussed, and the appropraite hierarchies for mesh generation and mesh smoothing are selected. A domain-splitting algorithm for unstructured grids which tries to minimize the surface-to-volume ratio of each subdomain is described. This splitting algorithm is employed both for grid generation and grid smoothing. Results obtained on the Hypercube demonstrate the effectiveness of the algorithms developed.

  12. Development of Parallel GSSHA

    DTIC Science & Technology

    2013-09-01

    C en te r Paul R. Eller , Jing-Ru C. Cheng, Aaron R. Byrd, Charles W. Downer, and Nawa Pradhan September 2013 Approved for public release...Program ERDC TR-13-8 September 2013 Development of Parallel GSSHA Paul R. Eller and Jing-Ru C. Cheng Information Technology Laboratory US Army Engineer...5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Paul Eller , Ruth Cheng, Aaron Byrd, Chuck Downer, and Nawa Pradhan 5d. PROJECT NUMBER

  13. Xyce parallel electronic simulator.

    SciTech Connect

    Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Rankin, Eric Lamont; Schiek, Richard Louis; Thornquist, Heidi K.; Fixel, Deborah A.; Coffey, Todd S; Pawlowski, Roger P; Santarelli, Keith R.

    2010-05-01

    This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide.

  14. Massively Parallel Genetics.

    PubMed

    Shendure, Jay; Fields, Stanley

    2016-06-01

    Human genetics has historically depended on the identification of individuals whose natural genetic variation underlies an observable trait or disease risk. Here we argue that new technologies now augment this historical approach by allowing the use of massively parallel assays in model systems to measure the functional effects of genetic variation in many human genes. These studies will help establish the disease risk of both observed and potential genetic variants and to overcome the problem of "variants of uncertain significance."

  15. Parallel sphere rendering

    SciTech Connect

    Krogh, M.; Painter, J.; Hansen, C.

    1996-10-01

    Sphere rendering is an important method for visualizing molecular dynamics data. This paper presents a parallel algorithm that is almost 90 times faster than current graphics workstations. To render extremely large data sets and large images, the algorithm uses the MIMD features of the supercomputers to divide up the data, render independent partial images, and then finally composite the multiple partial images using an optimal method. The algorithm and performance results are presented for the CM-5 and the M.

  16. Implementation of Parallel Algorithms

    DTIC Science & Technology

    1993-06-30

    their socia ’ relations or to achieve some goals. For example, we define a pair-wise force law of i epulsion and attraction for a group of identical...quantization based compression schemes. Photo-refractive crystals, which provide high density recording in real time, are used as our holographic media . The...of Parallel Algorithms (J. Reif, ed.). Kluwer Academic Pu’ ishers, 1993. (4) "A Dynamic Separator Algorithm", D. Armon and J. Reif. To appear in

  17. Trajectory optimization using parallel shooting method on parallel computer

    SciTech Connect

    Wirthman, D.J.; Park, S.Y.; Vadali, S.R.

    1995-03-01

    The efficiency of a parallel shooting method on a parallel computer for solving a variety of optimal control guidance problems is studied. Several examples are considered to demonstrate that a speedup of nearly 7 to 1 is achieved with the use of 16 processors. It is suggested that further improvements in performance can be achieved by parallelizing in the state domain. 10 refs.

  18. The Galley Parallel File System

    NASA Technical Reports Server (NTRS)

    Nieuwejaar, Nils; Kotz, David

    1996-01-01

    As the I/O needs of parallel scientific applications increase, file systems for multiprocessors are being designed to provide applications with parallel access to multiple disks. Many parallel file systems present applications with a conventional Unix-like interface that allows the application to access multiple disks transparently. The interface conceals the parallelism within the file system, which increases the ease of programmability, but makes it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. Furthermore, most current parallel file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic parallel workloads. We discuss Galley's file structure and application interface, as well as an application that has been implemented using that interface.

  19. Asynchronous interpretation of parallel microprograms

    SciTech Connect

    Bandman, O.L.

    1984-03-01

    In this article, the authors demonstrate how to pass from a given synchronous interpretation of a parallel microprogram to an equivalent asynchronous interpretation, and investigate the cost associated with the rejection of external synchronization in parallel microprogram structures.

  20. Status of TRANSP Parallel Services

    NASA Astrophysics Data System (ADS)

    Indireshkumar, K.; Andre, Robert; McCune, Douglas; Randerson, Lewis

    2006-10-01

    The PPPL TRANSP code suite has been used successfully over many years to carry out time dependent simulations of tokamak plasmas. However, accurately modeling certain phenomena such as RF heating and fast ion behavior using TRANSP requires extensive computational power and will benefit from parallelization. Parallelizing all of TRANSP is not required and parts will run sequentially while other parts run parallelized. To efficiently use a site's parallel services, the parallelized TRANSP modules are deployed to a shared ``parallel service'' on a separate cluster. The PPPL Monte Carlo fast ion module NUBEAM and the MIT RF module TORIC are the first TRANSP modules to be so deployed. This poster will show the performance scaling of these modules within the parallel server. Communications between the serial client and the parallel server will be described in detail, and measurements of startup and communications overhead will be shown. Physics modeling benefits for TRANSP users will be assessed.

  1. Resistor Combinations for Parallel Circuits.

    ERIC Educational Resources Information Center

    McTernan, James P.

    1978-01-01

    To help simplify both teaching and learning of parallel circuits, a high school electricity/electronics teacher presents and illustrates the use of tables of values for parallel resistive circuits in which total resistances are whole numbers. (MF)

  2. Parallel Debugging Using Graphical Views

    DTIC Science & Technology

    1988-03-01

    Voyeur , a prototype system for creating graphical views of parallel programs, provid(s a cost-effective way to construct such views for any parallel...programming system. We illustrate Voyeur by discussing four views created for debugging Poker programs. One is a vteneral trace facility for any Poker...Graphical views are essential for debugging parallel programs because of the large quan- tity of state information contained in parallel programs. Voyeur

  3. Parallel Pascal - An extended Pascal for parallel computers

    NASA Technical Reports Server (NTRS)

    Reeves, A. P.

    1984-01-01

    Parallel Pascal is an extended version of the conventional serial Pascal programming language which includes a convenient syntax for specifying array operations. It is upward compatible with standard Pascal and involves only a small number of carefully chosen new features. Parallel Pascal was developed to reduce the semantic gap between standard Pascal and a large range of highly parallel computers. Two important design goals of Parallel Pascal were efficiency and portability. Portability is particularly difficult to achieve since different parallel computers frequently have very different capabilities.

  4. Impact of solution phase behaviour and external fields on thin film morphology: PCBM and RRa-P3HT model system.

    PubMed

    Guilbert, A A Y; Cabral, J T

    2017-01-25

    We report the impact of the ternary solution phase behaviour on the film morphology and crystallization of a model polymer:fullerene system. We employ UV-Vis absorption spectroscopy, combined with sequential filtration and dilution, to establish the phase diagram for regio-random poly(3-hexylthiophene-2,5-diyl) and phenyl-C61-butyric acid methyl ester (PCBM) in chlorobenzene. Films are systematically cast from one- and two-phase regions decoupling homogeneous and heterogenous nucleation, and the role of pre-formed aggregates from solutions. Increasing annealing temperature from 120 to 200 °C reveals a highly non-monotonic nucleation profile with a maximum at 170 °C, while the crystal growth rate increases monotonically. UV ozonolysis is employed to vary substrate energy, and found to increase nucleation rate and to promote a binary crystallization process. As previously found, exposure to light, under an inert atmosphere, effectively suppresses homogeneous nucleation; however, it has a considerably smaller effect on heterogeneous nucleation, either from solution aggregates or substrate-driven. Our results establish a quantitative link between solution thermodynamics, crystallization and provide insight into morphological design based on processing parameters in a proxy organic photovoltaic system.

  5. CSM parallel structural methods research

    NASA Technical Reports Server (NTRS)

    Storaasli, Olaf O.

    1989-01-01

    Parallel structural methods, research team activities, advanced architecture computers for parallel computational structural mechanics (CSM) research, the FLEX/32 multicomputer, a parallel structural analyses testbed, blade-stiffened aluminum panel with a circular cutout and the dynamic characteristics of a 60 meter, 54-bay, 3-longeron deployable truss beam are among the topics discussed.

  6. Roo: A parallel theorem prover

    SciTech Connect

    Lusk, E.L.; McCune, W.W.; Slaney, J.K.

    1991-11-01

    We describe a parallel theorem prover based on the Argonne theorem-proving system OTTER. The parallel system, called Roo, runs on shared-memory multiprocessors such as the Sequent Symmetry. We explain the parallel algorithm used and give performance results that demonstrate near-linear speedups on large problems.

  7. Parallel Eclipse Project Checkout

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Powell, Mark W.; Bachmann, Andrew G.

    2011-01-01

    Parallel Eclipse Project Checkout (PEPC) is a program written to leverage parallelism and to automate the checkout process of plug-ins created in Eclipse RCP (Rich Client Platform). Eclipse plug-ins can be aggregated in a feature project. This innovation digests a feature description (xml file) and automatically checks out all of the plug-ins listed in the feature. This resolves the issue of manually checking out each plug-in required to work on the project. To minimize the amount of time necessary to checkout the plug-ins, this program makes the plug-in checkouts parallel. After parsing the feature, a request to checkout for each plug-in in the feature has been inserted. These requests are handled by a thread pool with a configurable number of threads. By checking out the plug-ins in parallel, the checkout process is streamlined before getting started on the project. For instance, projects that took 30 minutes to checkout now take less than 5 minutes. The effect is especially clear on a Mac, which has a network monitor displaying the bandwidth use. When running the client from a developer s home, the checkout process now saturates the bandwidth in order to get all the plug-ins checked out as fast as possible. For comparison, a checkout process that ranged from 8-200 Kbps from a developer s home is now able to saturate a pipe of 1.3 Mbps, resulting in significantly faster checkouts. Eclipse IDE (integrated development environment) tries to build a project as soon as it is downloaded. As part of another optimization, this innovation programmatically tells Eclipse to stop building while checkouts are happening, which dramatically reduces lock contention and enables plug-ins to continue downloading until all of them finish. Furthermore, the software re-enables automatic building, and forces Eclipse to do a clean build once it finishes checking out all of the plug-ins. This software is fully generic and does not contain any NASA-specific code. It can be applied to any

  8. Parallel sphere rendering

    SciTech Connect

    Krogh, M.; Hansen, C.; Painter, J.; de Verdiere, G.C.

    1995-05-01

    Sphere rendering is an important method for visualizing molecular dynamics data. This paper presents a parallel divide-and-conquer algorithm that is almost 90 times faster than current graphics workstations. To render extremely large data sets and large images, the algorithm uses the MIMD features of the supercomputers to divide up the data, render independent partial images, and then finally composite the multiple partial images using an optimal method. The algorithm and performance results are presented for the CM-5 and the T3D.

  9. Parallelized direct execution simulation of message-passing parallel programs

    NASA Technical Reports Server (NTRS)

    Dickens, Phillip M.; Heidelberger, Philip; Nicol, David M.

    1994-01-01

    As massively parallel computers proliferate, there is growing interest in findings ways by which performance of massively parallel codes can be efficiently predicted. This problem arises in diverse contexts such as parallelizing computers, parallel performance monitoring, and parallel algorithm development. In this paper we describe one solution where one directly executes the application code, but uses a discrete-event simulator to model details of the presumed parallel machine such as operating system and communication network behavior. Because this approach is computationally expensive, we are interested in its own parallelization specifically the parallelization of the discrete-event simulator. We describe methods suitable for parallelized direct execution simulation of message-passing parallel programs, and report on the performance of such a system, Large Application Parallel Simulation Environment (LAPSE), we have built on the Intel Paragon. On all codes measured to date, LAPSE predicts performance well typically within 10 percent relative error. Depending on the nature of the application code, we have observed low slowdowns (relative to natively executing code) and high relative speedups using up to 64 processors.

  10. Parallel ptychographic reconstruction

    PubMed Central

    Nashed, Youssef S. G.; Vine, David J.; Peterka, Tom; Deng, Junjing; Ross, Rob; Jacobsen, Chris

    2014-01-01

    Ptychography is an imaging method whereby a coherent beam is scanned across an object, and an image is obtained by iterative phasing of the set of diffraction patterns. It is able to be used to image extended objects at a resolution limited by scattering strength of the object and detector geometry, rather than at an optics-imposed limit. As technical advances allow larger fields to be imaged, computational challenges arise for reconstructing the correspondingly larger data volumes, yet at the same time there is also a need to deliver reconstructed images immediately so that one can evaluate the next steps to take in an experiment. Here we present a parallel method for real-time ptychographic phase retrieval. It uses a hybrid parallel strategy to divide the computation between multiple graphics processing units (GPUs) and then employs novel techniques to merge sub-datasets into a single complex phase and amplitude image. Results are shown on a simulated specimen and a real dataset from an X-ray experiment conducted at a synchrotron light source. PMID:25607174

  11. Tolerant (parallel) Programming

    NASA Technical Reports Server (NTRS)

    DiNucci, David C.; Bailey, David H. (Technical Monitor)

    1997-01-01

    In order to be truly portable, a program must be tolerant of a wide range of development and execution environments, and a parallel program is just one which must be tolerant of a very wide range. This paper first defines the term "tolerant programming", then describes many layers of tools to accomplish it. The primary focus is on F-Nets, a formal model for expressing computation as a folded partial-ordering of operations, thereby providing an architecture-independent expression of tolerant parallel algorithms. For implementing F-Nets, Cooperative Data Sharing (CDS) is a subroutine package for implementing communication efficiently in a large number of environments (e.g. shared memory and message passing). Software Cabling (SC), a very-high-level graphical programming language for building large F-Nets, possesses many of the features normally expected from today's computer languages (e.g. data abstraction, array operations). Finally, L2(sup 3) is a CASE tool which facilitates the construction, compilation, execution, and debugging of SC programs.

  12. Applied Parallel Metadata Indexing

    SciTech Connect

    Jacobi, Michael R

    2012-08-01

    The GPFS Archive is parallel archive is a parallel archive used by hundreds of users in the Turquoise collaboration network. It houses 4+ petabytes of data in more than 170 million files. Currently, users must navigate the file system to retrieve their data, requiring them to remember file paths and names. A better solution might allow users to tag data with meaningful labels and searach the archive using standard and user-defined metadata, while maintaining security. last summer, I developed the backend to a tool that adheres to these design goals. The backend works by importing GPFS metadata into a MongoDB cluster, which is then indexed on each attribute. This summer, the author implemented security and developed the user interfae for the search tool. To meet security requirements, each database table is associated with a single user, which only stores records that the user may read, and requires a set of credentials to access. The interface to the search tool is implemented using FUSE (Filesystem in USErspace). FUSE is an intermediate layer that intercepts file system calls and allows the developer to redefine how those calls behave. In the case of this tool, FUSE interfaces with MongoDB to issue queries and populate output. A FUSE implementation is desirable because it allows users to interact with the search tool using commands they are already familiar with. These security and interface additions are essential for a usable product.

  13. A systolic array parallelizing compiler

    SciTech Connect

    Tseng, P.S. )

    1990-01-01

    This book presents a completely new approach to the problem of systolic array parallelizing compiler. It describes the AL parallelizing compiler for the Warp systolic array, the first working systolic array parallelizing compiler which can generate efficient parallel code for complete LINPACK routines. This book begins by analyzing the architectural strength of the Warp systolic array. It proposes a model for mapping programs onto the machine and introduces the notion of data relations for optimizing the program mapping. Also presented are successful applications of the AL compiler in matrix computation and image processing. A complete listing of the source program and compiler-generated parallel code are given to clarify the overall picture of the compiler. The book concludes that systolic array parallelizing compiler can produce efficient parallel code, almost identical to what the user would have written by hand.

  14. Parallel kinetic resolution of tert-butyl (RS)-3-oxy-substituted cyclopent-1-ene-carboxylates for the asymmetric synthesis of 3-oxy-substituted cispentacin and transpentacin derivatives.

    PubMed

    Aye, Yimon; Davies, Stephen G; Garner, A Christopher; Roberts, Paul M; Smith, Andrew D; Thomson, James E

    2008-06-21

    tert-Butyl (RS)-3-methoxy- and (RS)-3-tert-butyldiphenylsilyloxy-cyclopent-1-ene-carboxylates display excellent levels of enantiorecognition in mutual kinetic resolutions with both lithium (RS)-N-benzyl-N-(alpha-methylbenzyl)amide and lithium (RS)-N-3,4-dimethoxybenzyl-N-(alpha-methylbenzyl)amide. A 50 : 50 pseudoenantiomeric mixture of lithium (S)-N-benzyl-N-(alpha-methylbenzyl)amide and lithium (R)-N-3,4-dimethoxybenzyl-N-(alpha-methylbenzyl)amide allows for the efficient parallel kinetic resolution of the tert-butyl (RS)-3-oxy-substituted cyclopent-1-ene-carboxylates, affording differentially protected 3-oxy-substituted cispentacin derivatives in high yield and >98% de. Subsequent N-deprotection and hydrolysis provides access to 3-oxy-substituted cispentacin derivatives in good yield, and in >98% de and >98% ee, while stereoselective epimerisation and subsequent deprotection affords the corresponding transpentacin analogues in good yield, and in >98% de and >98% ee.

  15. Parallel Computing in SCALE

    SciTech Connect

    DeHart, Mark D; Williams, Mark L; Bowman, Stephen M

    2010-01-01

    The SCALE computational architecture has remained basically the same since its inception 30 years ago, although constituent modules and capabilities have changed significantly. This SCALE concept was intended to provide a framework whereby independent codes can be linked to provide a more comprehensive capability than possible with the individual programs - allowing flexibility to address a wide variety of applications. However, the current system was designed originally for mainframe computers with a single CPU and with significantly less memory than today's personal computers. It has been recognized that the present SCALE computation system could be restructured to take advantage of modern hardware and software capabilities, while retaining many of the modular features of the present system. Preliminary work is being done to define specifications and capabilities for a more advanced computational architecture. This paper describes the state of current SCALE development activities and plans for future development. With the release of SCALE 6.1 in 2010, a new phase of evolutionary development will be available to SCALE users within the TRITON and NEWT modules. The SCALE (Standardized Computer Analyses for Licensing Evaluation) code system developed by Oak Ridge National Laboratory (ORNL) provides a comprehensive and integrated package of codes and nuclear data for a wide range of applications in criticality safety, reactor physics, shielding, isotopic depletion and decay, and sensitivity/uncertainty (S/U) analysis. Over the last three years, since the release of version 5.1 in 2006, several important new codes have been introduced within SCALE, and significant advances applied to existing codes. Many of these new features became available with the release of SCALE 6.0 in early 2009. However, beginning with SCALE 6.1, a first generation of parallel computing is being introduced. In addition to near-term improvements, a plan for longer term SCALE enhancement

  16. Toward Parallel Document Clustering

    SciTech Connect

    Mogill, Jace A.; Haglin, David J.

    2011-09-01

    A key challenge to automated clustering of documents in large text corpora is the high cost of comparing documents in a multimillion dimensional document space. The Anchors Hierarchy is a fast data structure and algorithm for localizing data based on a triangle inequality obeying distance metric, the algorithm strives to minimize the number of distance calculations needed to cluster the documents into “anchors” around reference documents called “pivots”. We extend the original algorithm to increase the amount of available parallelism and consider two implementations: a complex data structure which affords efficient searching, and a simple data structure which requires repeated sorting. The sorting implementation is integrated with a text corpora “Bag of Words” program and initial performance results of end-to-end a document processing workflow are reported.

  17. Parallel Polarization State Generation

    NASA Astrophysics Data System (ADS)

    She, Alan; Capasso, Federico

    2016-05-01

    The control of polarization, an essential property of light, is of wide scientific and technological interest. The general problem of generating arbitrary time-varying states of polarization (SOP) has always been mathematically formulated by a series of linear transformations, i.e. a product of matrices, imposing a serial architecture. Here we show a parallel architecture described by a sum of matrices. The theory is experimentally demonstrated by modulating spatially-separated polarization components of a laser using a digital micromirror device that are subsequently beam combined. This method greatly expands the parameter space for engineering devices that control polarization. Consequently, performance characteristics, such as speed, stability, and spectral range, are entirely dictated by the technologies of optical intensity modulation, including absorption, reflection, emission, and scattering. This opens up important prospects for polarization state generation (PSG) with unique performance characteristics with applications in spectroscopic ellipsometry, spectropolarimetry, communications, imaging, and security.

  18. Parallel Polarization State Generation

    PubMed Central

    She, Alan; Capasso, Federico

    2016-01-01

    The control of polarization, an essential property of light, is of wide scientific and technological interest. The general problem of generating arbitrary time-varying states of polarization (SOP) has always been mathematically formulated by a series of linear transformations, i.e. a product of matrices, imposing a serial architecture. Here we show a parallel architecture described by a sum of matrices. The theory is experimentally demonstrated by modulating spatially-separated polarization components of a laser using a digital micromirror device that are subsequently beam combined. This method greatly expands the parameter space for engineering devices that control polarization. Consequently, performance characteristics, such as speed, stability, and spectral range, are entirely dictated by the technologies of optical intensity modulation, including absorption, reflection, emission, and scattering. This opens up important prospects for polarization state generation (PSG) with unique performance characteristics with applications in spectroscopic ellipsometry, spectropolarimetry, communications, imaging, and security. PMID:27184813

  19. A parallel programming environment supporting multiple data-parallel modules

    SciTech Connect

    Seevers, B.K.; Quinn, M.J. ); Hatcher, P.J. )

    1992-10-01

    We describe a system that allows programmers to take advantage of both control and data parallelism through multiple intercommunicating data-parallel modules. This programming environment extends C-type stream I/O to include intermodule communication channels. The progammer writes each module as a separate data-parallel program, then develops a channel linker specification describing how to connect the modules together. A channel linker we have developed loads the separate modules on the parallel machine and binds the communication channels together as specified. We present performance data that demonstrates a mixed control- and data-parallel solution can yield better performance than a strictly data-parallel solution. The system described currently runs on the Intel iWarp multicomputer.

  20. Parallel imaging microfluidic cytometer.

    PubMed

    Ehrlich, Daniel J; McKenna, Brian K; Evans, James G; Belkina, Anna C; Denis, Gerald V; Sherr, David H; Cheung, Man Ching

    2011-01-01

    By adding an additional degree of freedom from multichannel flow, the parallel microfluidic cytometer (PMC) combines some of the best features of fluorescence-activated flow cytometry (FCM) and microscope-based high-content screening (HCS). The PMC (i) lends itself to fast processing of large numbers of samples, (ii) adds a 1D imaging capability for intracellular localization assays (HCS), (iii) has a high rare-cell sensitivity, and (iv) has an unusual capability for time-synchronized sampling. An inability to practically handle large sample numbers has restricted applications of conventional flow cytometers and microscopes in combinatorial cell assays, network biology, and drug discovery. The PMC promises to relieve a bottleneck in these previously constrained applications. The PMC may also be a powerful tool for finding rare primary cells in the clinic. The multichannel architecture of current PMC prototypes allows 384 unique samples for a cell-based screen to be read out in ∼6-10 min, about 30 times the speed of most current FCM systems. In 1D intracellular imaging, the PMC can obtain protein localization using HCS marker strategies at many times for the sample throughput of charge-coupled device (CCD)-based microscopes or CCD-based single-channel flow cytometers. The PMC also permits the signal integration time to be varied over a larger range than is practical in conventional flow cytometers. The signal-to-noise advantages are useful, for example, in counting rare positive cells in the most difficult early stages of genome-wide screening. We review the status of parallel microfluidic cytometry and discuss some of the directions the new technology may take.

  1. Applications of polarizable continuum models to determine accurate solution-phase thermochemical values across a broad range of cation charge - the case of U(III-VI).

    PubMed

    Parmar, Payal; Samuels, Alex; Clark, Aurora E

    2015-01-13

    Contributing factors to the solution-phase correction to the free energy of the molecular clusters U(H2O)n(3+/4+) and UO2(H2O)m(1+/2+) (n = 8, 9, 30, 41, 77; m = 4, 5, 30, 41, 77) have been examined as a function of cavity type in the integrated-equation-formalism-protocol (IEF) and SMD polarizable continuum models (PCMs). It is observed that the free energy correction, Gcorr, does not smoothly converge to zero as the number of explicitly solvating water molecules approaches the bulk limit, and the convergence behavior varies significantly with cavity and model. The rates of convergence of the gas-phase hydration energy, ΔGhyd, wherein the bare metal ion is inserted into a molecular water cluster and ΔGcorr for the reaction exhibit wide variations as a function of ion charge, cavity, and model. This is the likely source of previously reported discrepancies in predicted free energies of solvation for metal ions when using different PCM cavities and/or models. The cancellation of errors in ΔGhyd and ΔGcorr is optimal for clusters consisting of only a second solvation shell of explicit water molecules (n = m = 30). The UFF cavity within IEF, in particular, exhibits the most consistent cancellation of errors when using a molecular cluster consisting of a second shell of solvating water for all oxidation states of uranium, leading to accurate free energies of solvation ΔGsolv for these species.

  2. Development of hydrogel TentaGel shell-core beads for ultrahigh throughput solution-phase screening of encoded OBOC combinatorial small molecule libraries.

    PubMed

    Baek, Hyoung Gee; Liu, Ruiwu; Lam, Kit S

    2009-01-01

    The one-bead one-compound (OBOC) combinatorial library method enables the rapid generation and screening of millions of discrete chemical compounds on beads. Most of the OBOC screening methods require the library compounds to remain tethered to the bead during screening process. Methods have also been developed to release library compounds from immobilized beads for in situ solution phase or "lawn" assays. However, this latter approach, while extremely powerful, is severely limited by the lack of suitable solid supports for such assays. Here, we report on the development of a novel hydrogel TentaGel shell-core (HTSC) bead in which hydrogel is grafted onto the polystyrene-based TentaGel (TG) bead as an outer shell (5-80 mum thick) via free radical surface-initiated polymerization. This novel shell-core bilayer resin enables the preparation of encoded OBOC combinatorial small molecule libraries, such that the library compounds reside on the highly hydrophilic outer layer and the coding tags reside in the polystyrene-based TG core. Using fluorescein as a model small molecule compound, we have demonstrated that fluorescein molecules that have been linked covalently to the hydrogel shell via a disulfide bond could readily diffuse out of the hydrogel layer into the bead surrounding after reduction with dithiothreitol. In contrast, under identical condition, the released fluorescein molecules remained bound to unmodified TG bead. We have prepared an encoded OBOC small molecule library on the novel shell-core beads and demonstrated that the beads can be readily decoded.

  3. Approximation algorithms for scheduling unrelated parallel machines with release dates

    NASA Astrophysics Data System (ADS)

    Avdeenko, T. V.; Mesentsev, Y. A.; Estraykh, I. V.

    2017-01-01

    In this paper we propose approaches to optimal scheduling of unrelated parallel machines with release dates. One approach is based on the scheme of dynamic programming modified with adaptive narrowing of search domain ensuring its computational effectiveness. We discussed complexity of the exact schedules synthesis and compared it with approximate, close to optimal, solutions. Also we explain how the algorithm works for the example of two unrelated parallel machines and five jobs with release dates. Performance results that show the efficiency of the proposed approach have been given.

  4. Parallel Monte Carlo Simulation for control system design

    NASA Technical Reports Server (NTRS)

    Schubert, Wolfgang M.

    1995-01-01

    The research during the 1993/94 academic year addressed the design of parallel algorithms for stochastic robustness synthesis (SRS). SRS uses Monte Carlo simulation to compute probabilities of system instability and other design-metric violations. The probabilities form a cost function which is used by a genetic algorithm (GA). The GA searches for the stochastic optimal controller. The existing sequential algorithm was analyzed and modified to execute in a distributed environment. For this, parallel approaches to Monte Carlo simulation and genetic algorithms were investigated. Initial empirical results are available for the KSR1.

  5. Flow-based solution-liquid-solid nanowire synthesis

    NASA Astrophysics Data System (ADS)

    Laocharoensuk, Rawiwan; Palaniappan, Kumaranand; Smith, Nickolaus A.; Dickerson, Robert M.; Werder, Donald J.; Baldwin, Jon K.; Hollingsworth, Jennifer A.

    2013-09-01

    Discovered almost two decades ago, the solution-liquid-solid (SLS) method for semiconductor nanowire synthesis has proven to be an important route to high-quality, single-crystalline anisotropic nanomaterials. In execution, the SLS technique is similar to colloidal quantum-dot synthesis in that it entails the injection of chemical precursors into a hot surfactant solution, but mechanistically it is considered the solution-phase analogue to vapour-liquid-solid (VLS) growth. Both SLS and VLS methods make use of molten metal nanoparticles to catalyse the nucleation and elongation of single-crystalline nanowires. Significantly, however, the methods differ in how chemical precursors are introduced to the metal catalysts. In SLS, precursors are added in a one-off fashion in a flask, whereas in VLS they are carried by a flow of gas through the reaction chamber, and by-products are removed similarly. The ability to dynamically control the introduction of reactants and removal of by-products in VLS synthesis has enabled a degree of synthetic control not possible with SLS growth. We show here that SLS synthesis can be transformed into a continuous technique using a microfluidic reactor. The resulting flow-based SLS (`flow-SLS') platform allows us to slow down the synthesis of nanowires and capture mechanistic details concerning their growth in the solution phase, as well as synthesize technologically relevant axially heterostructured semiconductor nanowires, while maintaining the propensity of SLS for accessing ultrasmall diameters below 10 nm.

  6. Parallel processor engine model program

    NASA Technical Reports Server (NTRS)

    Mclaughlin, P.

    1984-01-01

    The Parallel Processor Engine Model Program is a generalized engineering tool intended to aid in the design of parallel processing real-time simulations of turbofan engines. It is written in the FORTRAN programming language and executes as a subset of the SOAPP simulation system. Input/output and execution control are provided by SOAPP; however, the analysis, emulation and simulation functions are completely self-contained. A framework in which a wide variety of parallel processing architectures could be evaluated and tools with which the parallel implementation of a real-time simulation technique could be assessed are provided.

  7. Parallel processing and expert systems

    NASA Technical Reports Server (NTRS)

    Yan, Jerry C.; Lau, Sonie

    1991-01-01

    Whether it be monitoring the thermal subsystem of Space Station Freedom, or controlling the navigation of the autonomous rover on Mars, NASA missions in the 90's cannot enjoy an increased level of autonomy without the efficient use of expert systems. Merely increasing the computational speed of uniprocessors may not be able to guarantee that real time demands are met for large expert systems. Speed-up via parallel processing must be pursued alongside the optimization of sequential implementations. Prototypes of parallel expert systems have been built at universities and industrial labs in the U.S. and Japan. The state-of-the-art research in progress related to parallel execution of expert systems was surveyed. The survey is divided into three major sections: (1) multiprocessors for parallel expert systems; (2) parallel languages for symbolic computations; and (3) measurements of parallelism of expert system. Results to date indicate that the parallelism achieved for these systems is small. In order to obtain greater speed-ups, data parallelism and application parallelism must be exploited.

  8. Parallel Programming in the Age of Ubiquitous Parallelism

    NASA Astrophysics Data System (ADS)

    Pingali, Keshav

    2014-04-01

    Multicore and manycore processors are now ubiquitous, but parallel programming remains as difficult as it was 30-40 years ago. During this time, our community has explored many promising approaches including functional and dataflow languages, logic programming, and automatic parallelization using program analysis and restructuring, but none of these approaches has succeeded except in a few niche application areas. In this talk, I will argue that these problems arise largely from the computation-centric foundations and abstractions that we currently use to think about parallelism. In their place, I will propose a novel data-centric foundation for parallel programming called the operator formulation in which algorithms are described in terms of actions on data. The operator formulation shows that a generalized form of data-parallelism called amorphous data-parallelism is ubiquitous even in complex, irregular graph applications such as mesh generation/refinement/partitioning and SAT solvers. Regular algorithms emerge as a special case of irregular ones, and many application-specific optimization techniques can be generalized to a broader context. The operator formulation also leads to a structural analysis of algorithms called TAO-analysis that provides implementation guidelines for exploiting parallelism efficiently. Finally, I will describe a system called Galois based on these ideas for exploiting amorphous data-parallelism on multicores and GPUs

  9. Trajectories in parallel optics.

    PubMed

    Klapp, Iftach; Sochen, Nir; Mendlovic, David

    2011-10-01

    In our previous work we showed the ability to improve the optical system's matrix condition by optical design, thereby improving its robustness to noise. It was shown that by using singular value decomposition, a target point-spread function (PSF) matrix can be defined for an auxiliary optical system, which works parallel to the original system to achieve such an improvement. In this paper, after briefly introducing the all optics implementation of the auxiliary system, we show a method to decompose the target PSF matrix. This is done through a series of shifted responses of auxiliary optics (named trajectories), where a complicated hardware filter is replaced by postprocessing. This process manipulates the pixel confined PSF response of simple auxiliary optics, which in turn creates an auxiliary system with the required PSF matrix. This method is simulated on two space variant systems and reduces their system condition number from 18,598 to 197 and from 87,640 to 5.75, respectively. We perform a study of the latter result and show significant improvement in image restoration performance, in comparison to a system without auxiliary optics and to other previously suggested hybrid solutions. Image restoration results show that in a range of low signal-to-noise ratio values, the trajectories method gives a significant advantage over alternative approaches. A third space invariant study case is explored only briefly, and we present a significant improvement in the matrix condition number from 1.9160e+013 to 34,526.

  10. High Performance Parallel Architectures

    NASA Technical Reports Server (NTRS)

    El-Ghazawi, Tarek; Kaewpijit, Sinthop

    1998-01-01

    Traditional remote sensing instruments are multispectral, where observations are collected at a few different spectral bands. Recently, many hyperspectral instruments, that can collect observations at hundreds of bands, have been operational. Furthermore, there have been ongoing research efforts on ultraspectral instruments that can produce observations at thousands of spectral bands. While these remote sensing technology developments hold great promise for new findings in the area of Earth and space science, they present many challenges. These include the need for faster processing of such increased data volumes, and methods for data reduction. Dimension Reduction is a spectral transformation, aimed at concentrating the vital information and discarding redundant data. One such transformation, which is widely used in remote sensing, is the Principal Components Analysis (PCA). This report summarizes our progress on the development of a parallel PCA and its implementation on two Beowulf cluster configuration; one with fast Ethernet switch and the other with a Myrinet interconnection. Details of the implementation and performance results, for typical sets of multispectral and hyperspectral NASA remote sensing data, are presented and analyzed based on the algorithm requirements and the underlying machine configuration. It will be shown that the PCA application is quite challenging and hard to scale on Ethernet-based clusters. However, the measurements also show that a high- performance interconnection network, such as Myrinet, better matches the high communication demand of PCA and can lead to a more efficient PCA execution.

  11. Synthesis of epoxybenzo[d]isothiazole 1,1-dioxides via a reductive-Heck, metathesis-sequestration protocol†‡

    PubMed Central

    Asad, Naeem; Hanson, Paul R.; Long, Toby R.; Rayabarapu, Dinesh K.; Rolfe, Alan

    2011-01-01

    An atom-economical purification protocol, using solution phase processing via ring-opening metathesis polymerization (ROMP) has been developed for the synthesis of tricyclic sultams. This chromatography-free method allows for convenient isolation of reductive-Heck products and reclamation of excess starting material via sequestration involving metathesis catalysts and a catalyst-armed Si-surface. PMID:21727956

  12. Peptide synthesis beyond DMF: THF and ACN as excellent and friendlier alternatives.

    PubMed

    Jad, Yahya E; Acosta, Gerardo A; Khattab, Sherine N; de la Torre, Beatriz G; Govender, Thavendran; Kruger, Hendrik G; El-Faham, Ayman; Albericio, Fernando

    2015-02-28

    To date, DMF has been considered as the only solvent suitable for peptide synthesis. Here we demonstrate the capacity of THF and ACN, which are friendlier solvents than DMF, to yield the product in higher purity than DMF. Using various peptide models, both THF and ACN reduced racemization in solution-phase and solid-phase synthesis when compared with DMF. Moreover, the use of ACN and THF in the solid-phase peptide synthesis of hindered peptides, such as Aib-enkephalin pentapeptide and Aib-ACP decapeptide, in combination with a complete polyethylene glycol resin (ChemMatrix), gave a better coupling efficiency than DMF.

  13. Parallels in lignin biosynthesis

    PubMed Central

    Weng, Jing-Ke; Banks, Jo Ann

    2008-01-01

    A hallmark of vascular plants is the development of a complex water-conducting system, which is physically reinforced by the heterogeneous aromatic polymer lignin. Syringyl lignin, a major building block of lignin, is often thought to be uniquely characteristic of angiosperms; however, it was demonstrated over fifty years ago that that syringyl lignin is found in another group of plants, known as the lycophytes, the ancestors of which diverged from all the other vascular plant lineages 400 million years ago.1 To determine the biochemical basis for this common biosynthetic ability, we isolated and characterized cytochrome P450-dependent monooxygenases (P450s) from the lycophyte Selaginella moellendorffii and compared them to the enzyme that is required for syringyl lignin synthesis in angiosperms. Our results showed that one of these P450s encodes an enzyme that is functionally analogous to but phylogenetically independent from its angiosperm counterpart. Here, we discuss the evolution of lignin biosynthesis in vascular plants and the role of Selaginella moellendorffii in plant comparative biology and genomics. PMID:19704782

  14. GEMAS: prediction of solid-solution phase partitioning coefficients (Kd) for oxoanions and boric acid in soils using mid-infrared diffuse reflectance spectroscopy.

    PubMed

    Janik, Leslie J; Forrester, Sean T; Soriano-Disla, José M; Kirby, Jason K; McLaughlin, Michael J; Reimann, Clemens

    2015-02-01

    The authors' aim was to develop rapid and inexpensive regression models for the prediction of partitioning coefficients (Kd), defined as the ratio of the total or surface-bound metal/metalloid concentration of the solid phase to the total concentration in the solution phase. Values of Kd were measured for boric acid (B[OH]3(0)) and selected added soluble oxoanions: molybdate (MoO4(2-)), antimonate (Sb[OH](6-)), selenate (SeO4(2-)), tellurate (TeO4(2-)) and vanadate (VO4(3-)). Models were developed using approximately 500 spectrally representative soils of the Geochemical Mapping of Agricultural Soils of Europe (GEMAS) program. These calibration soils represented the major properties of the entire 4813 soils of the GEMAS project. Multiple linear regression (MLR) from soil properties, partial least-squares regression (PLSR) using mid-infrared diffuse reflectance Fourier-transformed (DRIFT) spectra, and models using DRIFT spectra plus analytical pH values (DRIFT + pH), were compared with predicted log K(d + 1) values. Apart from selenate (R(2)  = 0.43), the DRIFT + pH calibrations resulted in marginally better models to predict log K(d + 1) values (R(2)  = 0.62-0.79), compared with those from PSLR-DRIFT (R(2)  = 0.61-0.72) and MLR (R(2)  = 0.54-0.79). The DRIFT + pH calibrations were applied to the prediction of log K(d + 1) values in the remaining 4313 soils. An example map of predicted log K(d + 1) values for added soluble MoO4(2-) in soils across Europe is presented. The DRIFT + pH PLSR models provided a rapid and inexpensive tool to assess the risk of mobility and potential availability of boric acid and selected oxoanions in European soils. For these models to be used in the prediction of log K(d + 1) values in soils globally, additional research will be needed to determine if soil variability is accounted on the calibration.

  15. Parallel Computational Protein Design

    PubMed Central

    Zhou, Yichao; Donald, Bruce R.; Zeng, Jianyang

    2016-01-01

    Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process. To address this issue, we extend and add a new module to the OSPREY program that was previously developed in the Donald lab [1] to implement a GPU-based massively parallel A* algorithm for improving protein design pipeline. By exploiting the modern GPU computational framework and optimizing the computation of the heuristic function for A* search, our new program, called gOSPREY, can provide up to four orders of magnitude speedups in large protein design cases with a small memory overhead comparing to the traditional A* search algorithm implementation, while still guaranteeing the optimality. In addition, gOSPREY can be configured to run in a bounded-memory mode to tackle the problems in which the conformation space is too large and the global optimal solution cannot be computed previously. Furthermore, the GPU-based A* algorithm implemented in the gOSPREY program can be combined with the state-of-the-art rotamer pruning algorithms such as iMinDEE [2] and DEEPer [3] to also consider continuous backbone and side-chain flexibility. PMID:27914056

  16. Parallel Adaptive Mesh Refinement

    SciTech Connect

    Diachin, L; Hornung, R; Plassmann, P; WIssink, A

    2005-03-04

    As large-scale, parallel computers have become more widely available and numerical models and algorithms have advanced, the range of physical phenomena that can be simulated has expanded dramatically. Many important science and engineering problems exhibit solutions with localized behavior where highly-detailed salient features or large gradients appear in certain regions which are separated by much larger regions where the solution is smooth. Examples include chemically-reacting flows with radiative heat transfer, high Reynolds number flows interacting with solid objects, and combustion problems where the flame front is essentially a two-dimensional sheet occupying a small part of a three-dimensional domain. Modeling such problems numerically requires approximating the governing partial differential equations on a discrete domain, or grid. Grid spacing is an important factor in determining the accuracy and cost of a computation. A fine grid may be needed to resolve key local features while a much coarser grid may suffice elsewhere. Employing a fine grid everywhere may be inefficient at best and, at worst, may make an adequately resolved simulation impractical. Moreover, the location and resolution of fine grid required for an accurate solution is a dynamic property of a problem's transient features and may not be known a priori. Adaptive mesh refinement (AMR) is a technique that can be used with both structured and unstructured meshes to adjust local grid spacing dynamically to capture solution features with an appropriate degree of resolution. Thus, computational resources can be focused where and when they are needed most to efficiently achieve an accurate solution without incurring the cost of a globally-fine grid. Figure 1.1 shows two example computations using AMR; on the left is a structured mesh calculation of a impulsively-sheared contact surface and on the right is the fuselage and volume discretization of an RAH-66 Comanche helicopter [35]. Note the

  17. A Parallel Particle Swarm Optimizer

    DTIC Science & Technology

    2003-01-01

    by a computationally demanding biomechanical system identification problem, we introduce a parallel implementation of a stochastic population based...concurrent computation. The parallelization of the Particle Swarm Optimization (PSO) algorithm is detailed and its performance and characteristics demonstrated for the biomechanical system identification problem as example.

  18. The Galley Parallel File System

    NASA Technical Reports Server (NTRS)

    Nieuwejaar, Nils; Kotz, David

    1996-01-01

    Most current multiprocessor file systems are designed to use multiple disks in parallel, using the high aggregate bandwidth to meet the growing I/0 requirements of parallel scientific applications. Many multiprocessor file systems provide applications with a conventional Unix-like interface, allowing the application to access multiple disks transparently. This interface conceals the parallelism within the file system, increasing the ease of programmability, but making it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. In addition to providing an insufficient interface, most current multiprocessor file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic scientific multiprocessor workloads. We discuss Galley's file structure and application interface, as well as the performance advantages offered by that interface.

  19. Parallel contingency statistics with Titan.

    SciTech Connect

    Thompson, David C.; Pebay, Philippe Pierre

    2009-09-01

    This report summarizes existing statistical engines in VTK/Titan and presents the recently parallelized contingency statistics engine. It is a sequel to [PT08] and [BPRT09] which studied the parallel descriptive, correlative, multi-correlative, and principal component analysis engines. The ease of use of this new parallel engines is illustrated by the means of C++ code snippets. Furthermore, this report justifies the design of these engines with parallel scalability in mind; however, the very nature of contingency tables prevent this new engine from exhibiting optimal parallel speed-up as the aforementioned engines do. This report therefore discusses the design trade-offs we made and study performance with up to 200 processors.

  20. Parallel algorithm of VLBI software correlator under multiprocessor environment

    NASA Astrophysics Data System (ADS)

    Zheng, Weimin; Zhang, Dong

    2007-11-01

    The correlator is the key signal processing equipment of a Very Lone Baseline Interferometry (VLBI) synthetic aperture telescope. It receives the mass data collected by the VLBI observatories and produces the visibility function of the target, which can be used to spacecraft position, baseline length measurement, synthesis imaging, and other scientific applications. VLBI data correlation is a task of data intensive and computation intensive. This paper presents the algorithms of two parallel software correlators under multiprocessor environments. A near real-time correlator for spacecraft tracking adopts the pipelining and thread-parallel technology, and runs on the SMP (Symmetric Multiple Processor) servers. Another high speed prototype correlator using the mixed Pthreads and MPI (Massage Passing Interface) parallel algorithm is realized on a small Beowulf cluster platform. Both correlators have the characteristic of flexible structure, scalability, and with 10-station data correlating abilities.

  1. Effects of an omega-3 fatty acid-enriched lipid emulsion on eicosanoid synthesis in acute respiratory distress syndrome (ARDS): A prospective, randomized, double-blind, parallel group study

    PubMed Central

    2011-01-01

    Background The use of lipid emulsions has been associated with changes in lung function and gas exchange which may be mediated by biologically active metabolites derived from arachidonic acid. The type and quantity of the lipid emulsions used could modulate this response, which is mediated by the eicosanoids. This study investigates the use of omega-3 fatty acid-enriched lipid emulsions in ARDS patients and their effects on eicosanoid values. Methods Prospective, randomized, double-blind, parallel group study carried out at the Intensive Medicine Department of Vall d'Hebron University Hospital (Barcelona-Spain). We studied 16 consecutive patients with ARDS and intolerance to enteral nutrition (14 men; age: 58 ± 13 years; APACHE II score 17.8 ± 2.3; Lung Injury Score: 3.1 ± 0.5; baseline PaO2/FiO2 ratio: 149 ± 40). Patients were randomized into two groups: Group A (n = 8) received the study emulsion Lipoplus® 20%, B. Braun Medical (50% MCT, 40% LCT, 10% fish oil (FO)); Group B (n = 8) received the control emulsion Intralipid® Fresenius Kabi (100% LCT). Lipid emulsions were administered for 12 h at a dose of 0.12 g/kg/h. We measured LTB4, TXB2, and 6-keto prostaglandin F1α values at baseline [immediately before the administration of the lipid emulsions (T-0)], at the end of the administration (T-12) and 24 hours after the beginning of the infusion (T 24) in arterial and mixed venous blood samples. Results In group A (FO) LTB4, TXB2, 6-keto prostaglandin F1α levels fell during omega-3 administration (T12). After discontinuation (T24), levels of inflammatory markers (both systemic and pulmonary) behaved erratically. In group B (LCT) all systemic and pulmonary mediators increased during lipid administration and returned to baseline levels after discontinuation, but the differences did not reach statistical significance. There was a clear interaction between the treatment in group A (fish oil) and changes in LTB4 over time. Conclusions Infusion of lipids enriched

  2. Synthesis of a library of 2-alkyl-3-alkyloxy-2H-indazole-6-carboxamides.

    PubMed

    Mills, Aaron D; Maloney, Patrick; Hassanein, Elsayed; Haddadin, Makhluf J; Kurth, Mark J

    2007-01-01

    A library of 200 2-alkyl-3-alkyloxy-2H-indazole-6-carboxamides was synthesized using parallel solution-phase methods. The indazole cyclization reaction was optimized for library production with the best yields resulting from controlled alcohol/water solvent ratios. The key step, a heterocyclization reaction, proceeds by N,N-bond formation and delivers the 2H-indazole scaffold. Automated preparative HPLC was utilized to provide pure compounds on a 10+ mg scale.

  3. Parallel NPARC: Implementation and Performance

    NASA Technical Reports Server (NTRS)

    Townsend, S. E.

    1996-01-01

    Version 3 of the NPARC Navier-Stokes code includes support for large-grain (block level) parallelism using explicit message passing between a heterogeneous collection of computers. This capability has the potential for significant performance gains, depending upon the block data distribution. The parallel implementation uses a master/worker arrangement of processes. The master process assigns blocks to workers, controls worker actions, and provides remote file access for the workers. The processes communicate via explicit message passing using an interface library which provides portability to a number of message passing libraries, such as PVM (Parallel Virtual Machine). A Bourne shell script is used to simplify the task of selecting hosts, starting processes, retrieving remote files, and terminating a computation. This script also provides a simple form of fault tolerance. An analysis of the computational performance of NPARC is presented, using data sets from an F/A-18 inlet study and a Rocket Based Combined Cycle Engine analysis. Parallel speedup and overall computational efficiency were obtained for various NPARC run parameters on a cluster of IBM RS6000 workstations. The data show that although NPARC performance compares favorably with the estimated potential parallelism, typical data sets used with previous versions of NPARC will often need to be reblocked for optimum parallel performance. In one of the cases studied, reblocking increased peak parallel speedup from 3.2 to 11.8.

  4. Parallel processing and expert systems

    NASA Technical Reports Server (NTRS)

    Lau, Sonie; Yan, Jerry C.

    1991-01-01

    Whether it be monitoring the thermal subsystem of Space Station Freedom, or controlling the navigation of the autonomous rover on Mars, NASA missions in the 1990s cannot enjoy an increased level of autonomy without the efficient implementation of expert systems. Merely increasing the computational speed of uniprocessors may not be able to guarantee that real-time demands are met for larger systems. Speedup via parallel processing must be pursued alongside the optimization of sequential implementations. Prototypes of parallel expert systems have been built at universities and industrial laboratories in the U.S. and Japan. The state-of-the-art research in progress related to parallel execution of expert systems is surveyed. The survey discusses multiprocessors for expert systems, parallel languages for symbolic computations, and mapping expert systems to multiprocessors. Results to date indicate that the parallelism achieved for these systems is small. The main reasons are (1) the body of knowledge applicable in any given situation and the amount of computation executed by each rule firing are small, (2) dividing the problem solving process into relatively independent partitions is difficult, and (3) implementation decisions that enable expert systems to be incrementally refined hamper compile-time optimization. In order to obtain greater speedups, data parallelism and application parallelism must be exploited.

  5. Parallel integer sorting with medium and fine-scale parallelism

    NASA Technical Reports Server (NTRS)

    Dagum, Leonardo

    1993-01-01

    Two new parallel integer sorting algorithms, queue-sort and barrel-sort, are presented and analyzed in detail. These algorithms do not have optimal parallel complexity, yet they show very good performance in practice. Queue-sort designed for fine-scale parallel architectures which allow the queueing of multiple messages to the same destination. Barrel-sort is designed for medium-scale parallel architectures with a high message passing overhead. The performance results from the implementation of queue-sort on a Connection Machine CM-2 and barrel-sort on a 128 processor iPSC/860 are given. The two implementations are found to be comparable in performance but not as good as a fully vectorized bucket sort on the Cray YMP.

  6. EFFICIENT SCHEDULING OF PARALLEL JOBS ON MASSIVELY PARALLEL SYSTEMS

    SciTech Connect

    F. PETRINI; W. FENG

    1999-09-01

    We present buffered coscheduling, a new methodology to multitask parallel jobs in a message-passing environment and to develop parallel programs that can pave the way to the efficient implementation of a distributed operating system. Buffered coscheduling is based on three innovative techniques: communication buffering, strobing, and non-blocking communication. By leveraging these techniques, we can perform effective optimizations based on the global status of the parallel machine rather than on the limited knowledge available locally to each processor. The advantages of buffered coscheduling include higher resource utilization, reduced communication overhead, efficient implementation of low-control strategies and fault-tolerant protocols, accurate performance modeling, and a simplified yet still expressive parallel programming model. Preliminary experimental results show that buffered coscheduling is very effective in increasing the overall performance in the presence of load imbalance and communication-intensive workloads.

  7. Template based parallel checkpointing in a massively parallel computer system

    DOEpatents

    Archer, Charles Jens; Inglett, Todd Alan

    2009-01-13

    A method and apparatus for a template based parallel checkpoint save for a massively parallel super computer system using a parallel variation of the rsync protocol, and network broadcast. In preferred embodiments, the checkpoint data for each node is compared to a template checkpoint file that resides in the storage and that was previously produced. Embodiments herein greatly decrease the amount of data that must be transmitted and stored for faster checkpointing and increased efficiency of the computer system. Embodiments are directed to a parallel computer system with nodes arranged in a cluster with a high speed interconnect that can perform broadcast communication. The checkpoint contains a set of actual small data blocks with their corresponding checksums from all nodes in the system. The data blocks may be compressed using conventional non-lossy data compression algorithms to further reduce the overall checkpoint size.

  8. Parallel Architecture For Robotics Computation

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Bejczy, Antal K.

    1990-01-01

    Universal Real-Time Robotic Controller and Simulator (URRCS) is highly parallel computing architecture for control and simulation of robot motion. Result of extensive algorithmic study of different kinematic and dynamic computational problems arising in control and simulation of robot motion. Study led to development of class of efficient parallel algorithms for these problems. Represents algorithmically specialized architecture, in sense capable of exploiting common properties of this class of parallel algorithms. System with both MIMD and SIMD capabilities. Regarded as processor attached to bus of external host processor, as part of bus memory.

  9. Multigrid on massively parallel architectures

    SciTech Connect

    Falgout, R D; Jones, J E

    1999-09-17

    The scalable implementation of multigrid methods for machines with several thousands of processors is investigated. Parallel performance models are presented for three different structured-grid multigrid algorithms, and a description is given of how these models can be used to guide implementation. Potential pitfalls are illustrated when moving from moderate-sized parallelism to large-scale parallelism, and results are given from existing multigrid codes to support the discussion. Finally, the use of mixed programming models is investigated for multigrid codes on clusters of SMPs.

  10. IOPA: I/O-aware parallelism adaption for parallel programs

    PubMed Central

    Liu, Tao; Liu, Yi; Qian, Chen; Qian, Depei

    2017-01-01

    With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of threads exist; on the contrary, too few threads will cause insufficient resource utilization and hurt performance. Therefore, programmers must pay much attention to parallelism control to find the appropriate number of I/O threads for an application. This paper proposes a parallelism control mechanism named IOPA that can adjust the parallelism of applications to adapt to the I/O capability of a system and balance computing resources and I/O bandwidth. The programming interface of IOPA is also provided to programmers to simplify parallel programming. IOPA is evaluated using multiple applications with both solid state and hard disk drives. The results show that the parallel applications using IOPA can achieve higher efficiency than those with a fixed number of threads. PMID:28278236

  11. Appendix E: Parallel Pascal development system

    NASA Technical Reports Server (NTRS)

    1985-01-01

    The Parallel Pascal Development System enables Parallel Pascal programs to be developed and tested on a conventional computer. It consists of several system programs, including a Parallel Pascal to standard Pascal translator, and a library of Parallel Pascal subprograms. The library includes subprograms for using Parallel Pascal on a parallel system with a fixed degree of parallelism, such as the Massively Parallel Processor, to conveniently manipulate arrays which have dimensions than the hardware. Programs can be conveninetly tested with small sized arrays on the conventional computer before attempting to run on a parallel system.

  12. Parallel hierarchical method in networks

    NASA Astrophysics Data System (ADS)

    Malinochka, Olha; Tymchenko, Leonid

    2007-09-01

    This method of parallel-hierarchical Q-transformation offers new approach to the creation of computing medium - of parallel -hierarchical (PH) networks, being investigated in the form of model of neurolike scheme of data processing [1-5]. The approach has a number of advantages as compared with other methods of formation of neurolike media (for example, already known methods of formation of artificial neural networks). The main advantage of the approach is the usage of multilevel parallel interaction dynamics of information signals at different hierarchy levels of computer networks, that enables to use such known natural features of computations organization as: topographic nature of mapping, simultaneity (parallelism) of signals operation, inlaid cortex, structure, rough hierarchy of the cortex, spatially correlated in time mechanism of perception and training [5].

  13. 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.

  14. "Feeling" Series and Parallel Resistances.

    ERIC Educational Resources Information Center

    Morse, Robert A.

    1993-01-01

    Equipped with drinking straws and stirring straws, a teacher can help students understand how resistances in electric circuits combine in series and in parallel. Follow-up suggestions are provided. (ZWH)

  15. Demonstrating Forces between Parallel Wires.

    ERIC Educational Resources Information Center

    Baker, Blane

    2000-01-01

    Describes a physics demonstration that dramatically illustrates the mutual repulsion (attraction) between parallel conductors using insulated copper wire, wooden dowels, a high direct current power supply, electrical tape, and an overhead projector. (WRM)

  16. Parallel programming of industrial applications

    SciTech Connect

    Heroux, M; Koniges, A; Simon, H

    1998-07-21

    In the introductory material, we overview the typical MPP environment for real application computing and the special tools available such as parallel debuggers and performance analyzers. Next, we draw from a series of real applications codes and discuss the specific challenges and problems that are encountered in parallelizing these individual applications. The application areas drawn from include biomedical sciences, materials processing and design, plasma and fluid dynamics, and others. We show how it was possible to get a particular application to run efficiently and what steps were necessary. Finally we end with a summary of the lessons learned from these applications and predictions for the future of industrial parallel computing. This tutorial is based on material from a forthcoming book entitled: "Industrial Strength Parallel Computing" to be published by Morgan Kaufmann Publishers (ISBN l-55860-54).

  17. Distinguishing serial and parallel parsing.

    PubMed

    Gibson, E; Pearlmutter, N J

    2000-03-01

    This paper discusses ways of determining whether the human parser is serial maintaining at most, one structural interpretation at each parse state, or whether it is parallel, maintaining more than one structural interpretation in at least some circumstances. We make four points. The first two counterclaims made by Lewis (2000): (1) that the availability of alternative structures should not vary as a function of the disambiguating material in some ranked parallel models; and (2) that parallel models predict a slow down during the ambiguous region for more syntactically ambiguous structures. Our other points concern potential methods for seeking experimental evidence relevant to the serial/parallel question. We discuss effects of the plausibility of a secondary structure in the ambiguous region (Pearlmutter & Mendelsohn, 1999) and suggest examining the distribution of reaction times in the disambiguating region.

  18. Address tracing for parallel machines

    NASA Technical Reports Server (NTRS)

    Stunkel, Craig B.; Janssens, Bob; Fuchs, W. Kent

    1991-01-01

    Recently implemented parallel system address-tracing methods based on several metrics are surveyed. The issues specific to collection of traces for both shared and distributed memory parallel computers are highlighted. Five general categories of address-trace collection methods are examined: hardware-captured, interrupt-based, simulation-based, altered microcode-based, and instrumented program-based traces. The problems unique to shared memory and distributed memory multiprocessors are examined separately.

  19. Parallel Algorithms for Image Analysis.

    DTIC Science & Technology

    1982-06-01

    8217 _ _ _ _ _ _ _ 4. TITLE (aid Subtitle) S. TYPE OF REPORT & PERIOD COVERED PARALLEL ALGORITHMS FOR IMAGE ANALYSIS TECHNICAL 6. PERFORMING O4G. REPORT NUMBER TR-1180...Continue on reverse side it neceesary aid Identlfy by block number) Image processing; image analysis ; parallel processing; cellular computers. 20... IMAGE ANALYSIS TECHNICAL 6. PERFORMING ONG. REPORT NUMBER TR-1180 - 7. AUTHOR(&) S. CONTRACT OR GRANT NUMBER(s) Azriel Rosenfeld AFOSR-77-3271 9

  20. Debugging in a parallel environment

    SciTech Connect

    Wasserman, H.J.; Griffin, J.H.

    1985-01-01

    This paper describes the preliminary results of a project investigating approaches to dynamic debugging in parallel processing systems. Debugging programs in a multiprocessing environment is particularly difficult because of potential errors in synchronization of tasks, data dependencies, sharing of data among tasks, and irreproducibility of specific machine instruction sequences from one job to the next. The basic methodology involved in predicate-based debuggers is given as well as other desirable features of dynamic parallel debugging. 13 refs.

  1. First-Principles Calculation, Synthesis, and Catalytic Properties of Rh-Cu Alloy Nanoparticles.

    PubMed

    Komatsu, Tokutaro; Kobayashi, Hirokazu; Kusada, Kohei; Kubota, Yoshiki; Takata, Masaki; Yamamoto, Tomokazu; Matsumura, Syo; Sato, Katsutoshi; Nagaoka, Katsutoshi; Kitagawa, Hiroshi

    2017-01-01

    The first synthesis of pure Rh1-x Cux solid-solution nanoparticles is reported. In contrast to the bulk state, the solid-solution phase was stable up to 750 °C. Based on facile density-functional calculations, we made a prediction that the catalytic activity of Rh1-x Cux can be maintained even with 50 at % replacement of Rh with Cu. The prediction was confirmed for the catalytic activities on CO and NOx conversions.

  2. Magnetic nanoparticles: synthesis, functionalization, and applications in bioimaging and magnetic energy storage

    PubMed Central

    Frey, Natalie A.; Peng, Sheng; Cheng, Kai; Sun, Shouheng

    2009-01-01

    This tutorial review summarizes the recent advances in the chemical synthesis and potential applications of monodisperse magnetic nanoparticles. After a brief introduction to nanomagnetism, the review focuses on recent developments in solution phase syntheses of monodisperse MFe2O4, Co, Fe, CoFe, FePt and SmCo5 nanoparticles. The review further outlines the surface, structural, and magnetic properties of these nanoparticles for biomedicine and magnetic energy storage applications. PMID:19690734

  3. Efficiency of parallel direct optimization

    NASA Technical Reports Server (NTRS)

    Janies, D. A.; Wheeler, W. C.

    2001-01-01

    Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size. c2001 The Willi Hennig Society.

  4. Architectures for reasoning in parallel

    NASA Technical Reports Server (NTRS)

    Hall, Lawrence O.

    1989-01-01

    The research conducted has dealt with rule-based expert systems. The algorithms that may lead to effective parallelization of them were investigated. Both the forward and backward chained control paradigms were investigated in the course of this work. The best computer architecture for the developed and investigated algorithms has been researched. Two experimental vehicles were developed to facilitate this research. They are Backpac, a parallel backward chained rule-based reasoning system and Datapac, a parallel forward chained rule-based reasoning system. Both systems have been written in Multilisp, a version of Lisp which contains the parallel construct, future. Applying the future function to a function causes the function to become a task parallel to the spawning task. Additionally, Backpac and Datapac have been run on several disparate parallel processors. The machines are an Encore Multimax with 10 processors, the Concert Multiprocessor with 64 processors, and a 32 processor BBN GP1000. Both the Concert and the GP1000 are switch-based machines. The Multimax has all its processors hung off a common bus. All are shared memory machines, but have different schemes for sharing the memory and different locales for the shared memory. The main results of the investigations come from experiments on the 10 processor Encore and the Concert with partitions of 32 or less processors. Additionally, experiments have been run with a stripped down version of EMYCIN.

  5. Efficiency of parallel direct optimization.

    PubMed

    Janies, D A; Wheeler, W C

    2001-03-01

    Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size.

  6. Linear quadratic optimal controller for cable-driven parallel robots

    NASA Astrophysics Data System (ADS)

    Abdolshah, Saeed; Shojaei Barjuei, Erfan

    2015-12-01

    In recent years, various cable-driven parallel robots have been investigated for their advantages, such as low structural weight, high acceleration, and large work-space, over serial and conventional parallel systems. However, the use of cables lowers the stiffness of these robots, which in turn may decrease motion accuracy. A linear quadratic (LQ) optimal controller can provide all the states of a system for the feedback, such as position and velocity. Thus, the application of such an optimal controller in cable-driven parallel robots can result in more efficient and accurate motion compared to the performance of classical controllers such as the proportional- integral-derivative controller. This paper presents an approach to apply the LQ optimal controller on cable-driven parallel robots. To employ the optimal control theory, the static and dynamic modeling of a 3-DOF planar cable-driven parallel robot (Feriba-3) is developed. The synthesis of the LQ optimal control is described, and the significant experimental results are presented and discussed.

  7. Endpoint-based parallel data processing in a parallel active messaging interface of a parallel computer

    DOEpatents

    Archer, Charles J; Blocksome, Michael E; Ratterman, Joseph D; Smith, Brian E

    2014-02-11

    Endpoint-based parallel data processing in a parallel active messaging interface ('PAMI') of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes coupled for data communications through the PAMI, including establishing a data communications geometry, the geometry specifying, for tasks representing processes of execution of the parallel application, a set of endpoints that are used in collective operations of the PAMI including a plurality of endpoints for one of the tasks; receiving in endpoints of the geometry an instruction for a collective operation; and executing the instruction for a collective opeartion through the endpoints in dependence upon the geometry, including dividing data communications operations among the plurality of endpoints for one of the tasks.

  8. Endpoint-based parallel data processing in a parallel active messaging interface of a parallel computer

    DOEpatents

    Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.

    2014-08-12

    Endpoint-based parallel data processing in a parallel active messaging interface (`PAMI`) of a parallel computer, the PAMI composed of data communications endpoints, each endpoint including a specification of data communications parameters for a thread of execution on a compute node, including specifications of a client, a context, and a task, the compute nodes coupled for data communications through the PAMI, including establishing a data communications geometry, the geometry specifying, for tasks representing processes of execution of the parallel application, a set of endpoints that are used in collective operations of the PAMI including a plurality of endpoints for one of the tasks; receiving in endpoints of the geometry an instruction for a collective operation; and executing the instruction for a collective operation through the endpoints in dependence upon the geometry, including dividing data communications operations among the plurality of endpoints for one of the tasks.

  9. The economics of parallel trade.

    PubMed

    Danzon, P M

    1998-03-01

    The potential for parallel trade in the European Union (EU) has grown with the accession of low price countries and the harmonisation of registration requirements. Parallel trade implies a conflict between the principle of autonomy of member states to set their own pharmaceutical prices, the principle of free trade and the industrial policy goal of promoting innovative research and development (R&D). Parallel trade in pharmaceuticals does not yield the normal efficiency gains from trade because countries achieve low pharmaceutical prices by aggressive regulation, not through superior efficiency. In fact, parallel trade reduces economic welfare by undermining price differentials between markets. Pharmaceutical R&D is a global joint cost of serving all consumers worldwide; it accounts for roughly 30% of total costs. Optimal (welfare maximising) pricing to cover joint costs (Ramsey pricing) requires setting different prices in different markets, based on inverse demand elasticities. By contrast, parallel trade and regulation based on international price comparisons tend to force price convergence across markets. In response, manufacturers attempt to set a uniform 'euro' price. The primary losers from 'euro' pricing will be consumers in low income countries who will face higher prices or loss of access to new drugs. In the long run, even higher income countries are likely to be worse off with uniform prices, because fewer drugs will be developed. One policy option to preserve price differentials is to exempt on-patent products from parallel trade. An alternative is confidential contracting between individual manufacturers and governments to provide country-specific ex post discounts from the single 'euro' wholesale price, similar to rebates used by managed care in the US. This would preserve differentials in transactions prices even if parallel trade forces convergence of wholesale prices.

  10. Parallel Implicit Algorithms for CFD

    NASA Technical Reports Server (NTRS)

    Keyes, David E.

    1998-01-01

    The main goal of this project was efficient distributed parallel and workstation cluster implementations of Newton-Krylov-Schwarz (NKS) solvers for implicit Computational Fluid Dynamics (CFD.) "Newton" refers to a quadratically convergent nonlinear iteration using gradient information based on the true residual, "Krylov" to an inner linear iteration that accesses the Jacobian matrix only through highly parallelizable sparse matrix-vector products, and "Schwarz" to a domain decomposition form of preconditioning the inner Krylov iterations with primarily neighbor-only exchange of data between the processors. Prior experience has established that Newton-Krylov methods are competitive solvers in the CFD context and that Krylov-Schwarz methods port well to distributed memory computers. The combination of the techniques into Newton-Krylov-Schwarz was implemented on 2D and 3D unstructured Euler codes on the parallel testbeds that used to be at LaRC and on several other parallel computers operated by other agencies or made available by the vendors. Early implementations were made directly in Massively Parallel Integration (MPI) with parallel solvers we adapted from legacy NASA codes and enhanced for full NKS functionality. Later implementations were made in the framework of the PETSC library from Argonne National Laboratory, which now includes pseudo-transient continuation Newton-Krylov-Schwarz solver capability (as a result of demands we made upon PETSC during our early porting experiences). A secondary project pursued with funding from this contract was parallel implicit solvers in acoustics, specifically in the Helmholtz formulation. A 2D acoustic inverse problem has been solved in parallel within the PETSC framework.

  11. Selective Access to Heterocyclic Sulfonamides and Sulfonyl Fluorides via a Parallel Medicinal Chemistry Enabled Method.

    PubMed

    Tucker, Joseph W; Chenard, Lois; Young, Joseph M

    2015-11-09

    A sulfur-functionalized aminoacrolein derivative is used for the efficient and selective synthesis of heterocyclic sulfonyl chlorides, sulfonyl fluorides, and sulfonamides. The development of a 3-step parallel medicinal chemistry (PMC) protocol for the synthesis of pyrazole-4-sulfonamides effectively demonstrates the utility of this reagent. This reactivity was expanded to provide rapid access to other heterocyclic sulfonyl fluorides, including pyrimidines and pyridines, whose corresponding sulfonyl chlorides lack suitable chemical stability.

  12. A parallel Jacobson-Oksman optimization algorithm. [parallel processing (computers)

    NASA Technical Reports Server (NTRS)

    Straeter, T. A.; Markos, A. T.

    1975-01-01

    A gradient-dependent optimization technique which exploits the vector-streaming or parallel-computing capabilities of some modern computers is presented. The algorithm, derived by assuming that the function to be minimized is homogeneous, is a modification of the Jacobson-Oksman serial minimization method. In addition to describing the algorithm, conditions insuring the convergence of the iterates of the algorithm and the results of numerical experiments on a group of sample test functions are presented. The results of these experiments indicate that this algorithm will solve optimization problems in less computing time than conventional serial methods on machines having vector-streaming or parallel-computing capabilities.

  13. Parallelizing Timed Petri Net simulations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.

    1993-01-01

    The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

  14. Visualizing Parallel Computer System Performance

    NASA Technical Reports Server (NTRS)

    Malony, Allen D.; Reed, Daniel A.

    1988-01-01

    Parallel computer systems are among the most complex of man's creations, making satisfactory performance characterization difficult. Despite this complexity, there are strong, indeed, almost irresistible, incentives to quantify parallel system performance using a single metric. The fallacy lies in succumbing to such temptations. A complete performance characterization requires not only an analysis of the system's constituent levels, it also requires both static and dynamic characterizations. Static or average behavior analysis may mask transients that dramatically alter system performance. Although the human visual system is remarkedly adept at interpreting and identifying anomalies in false color data, the importance of dynamic, visual scientific data presentation has only recently been recognized Large, complex parallel system pose equally vexing performance interpretation problems. Data from hardware and software performance monitors must be presented in ways that emphasize important events while eluding irrelevant details. Design approaches and tools for performance visualization are the subject of this paper.

  15. Features in Continuous Parallel Coordinates.

    PubMed

    Lehmann, Dirk J; Theisel, Holger

    2011-12-01

    Continuous Parallel Coordinates (CPC) are a contemporary visualization technique in order to combine several scalar fields, given over a common domain. They facilitate a continuous view for parallel coordinates by considering a smooth scalar field instead of a finite number of straight lines. We show that there are feature curves in CPC which appear to be the dominant structures of a CPC. We present methods to extract and classify them and demonstrate their usefulness to enhance the visualization of CPCs. In particular, we show that these feature curves are related to discontinuities in Continuous Scatterplots (CSP). We show this by exploiting a curve-curve duality between parallel and Cartesian coordinates, which is a generalization of the well-known point-line duality. Furthermore, we illustrate the theoretical considerations. Concluding, we discuss relations and aspects of the CPC's/CSP's features concerning the data analysis.

  16. PARAVT: Parallel Voronoi tessellation code

    NASA Astrophysics Data System (ADS)

    González, R. E.

    2016-10-01

    In this study, we present a new open source code for massive parallel computation of Voronoi tessellations (VT hereafter) in large data sets. The code is focused for astrophysical purposes where VT densities and neighbors are widely used. There are several serial Voronoi tessellation codes, however no open source and parallel implementations are available to handle the large number of particles/galaxies in current N-body simulations and sky surveys. Parallelization is implemented under MPI and VT using Qhull library. Domain decomposition takes into account consistent boundary computation between tasks, and includes periodic conditions. In addition, the code computes neighbors list, Voronoi density, Voronoi cell volume, density gradient for each particle, and densities on a regular grid. Code implementation and user guide are publicly available at https://github.com/regonzar/paravt.

  17. Parallel integrated frame synchronizer chip

    NASA Technical Reports Server (NTRS)

    Ghuman, Parminder Singh (Inventor); Solomon, Jeffrey Michael (Inventor); Bennett, Toby Dennis (Inventor)

    2000-01-01

    A parallel integrated frame synchronizer which implements a sequential pipeline process wherein serial data in the form of telemetry data or weather satellite data enters the synchronizer by means of a front-end subsystem and passes to a parallel correlator subsystem or a weather satellite data processing subsystem. When in a CCSDS mode, data from the parallel correlator subsystem passes through a window subsystem, then to a data alignment subsystem and then to a bit transition density (BTD)/cyclical redundancy check (CRC) decoding subsystem. Data from the BTD/CRC decoding subsystem or data from the weather satellite data processing subsystem is then fed to an output subsystem where it is output from a data output port.

  18. Fast data parallel polygon rendering

    SciTech Connect

    Ortega, F.A.; Hansen, C.D.

    1993-09-01

    This paper describes a parallel method for polygonal rendering on a massively parallel SIMD machine. This method, based on a simple shading model, is targeted for applications which require very fast polygon rendering for extremely large sets of polygons such as is found in many scientific visualization applications. The algorithms described in this paper are incorporated into a library of 3D graphics routines written for the Connection Machine. The routines are implemented on both the CM-200 and the CM-5. This library enables a scientists to display 3D shaded polygons directly from a parallel machine without the need to transmit huge amounts of data to a post-processing rendering system.

  19. Massively Parallel MRI Detector Arrays

    PubMed Central

    Keil, Boris; Wald, Lawrence L

    2013-01-01

    Originally proposed as a method to increase sensitivity by extending the locally high-sensitivity of small surface coil elements to larger areas, the term parallel imaging now includes the use of array coils to perform image encoding. This methodology has impacted clinical imaging to the point where many examinations are performed with an array comprising multiple smaller surface coil elements as the detector of the MR signal. This article reviews the theoretical and experimental basis for the trend towards higher channel counts relying on insights gained from modeling and experimental studies as well as the theoretical analysis of the so-called “ultimate” SNR and g-factor. We also review the methods for optimally combining array data and changes in RF methodology needed to construct massively parallel MRI detector arrays and show some examples of state-of-the-art for highly accelerated imaging with the resulting highly parallel arrays. PMID:23453758

  20. Parallel Adaptive Mesh Refinement Library

    NASA Technical Reports Server (NTRS)

    Mac-Neice, Peter; Olson, Kevin

    2005-01-01

    Parallel Adaptive Mesh Refinement Library (PARAMESH) is a package of Fortran 90 subroutines designed to provide a computer programmer with an easy route to extension of (1) a previously written serial code that uses a logically Cartesian structured mesh into (2) a parallel code with adaptive mesh refinement (AMR). Alternatively, in its simplest use, and with minimal effort, PARAMESH can operate as a domain-decomposition tool for users who want to parallelize their serial codes but who do not wish to utilize adaptivity. The package builds a hierarchy of sub-grids to cover the computational domain of a given application program, with spatial resolution varying to satisfy the demands of the application. The sub-grid blocks form the nodes of a tree data structure (a quad-tree in two or an oct-tree in three dimensions). Each grid block has a logically Cartesian mesh. The package supports one-, two- and three-dimensional models.

  1. Hybrid parallel programming with MPI and Unified Parallel C.

    SciTech Connect

    Dinan, J.; Balaji, P.; Lusk, E.; Sadayappan, P.; Thakur, R.; Mathematics and Computer Science; The Ohio State Univ.

    2010-01-01

    The Message Passing Interface (MPI) is one of the most widely used programming models for parallel computing. However, the amount of memory available to an MPI process is limited by the amount of local memory within a compute node. Partitioned Global Address Space (PGAS) models such as Unified Parallel C (UPC) are growing in popularity because of their ability to provide a shared global address space that spans the memories of multiple compute nodes. However, taking advantage of UPC can require a large recoding effort for existing parallel applications. In this paper, we explore a new hybrid parallel programming model that combines MPI and UPC. This model allows MPI programmers incremental access to a greater amount of memory, enabling memory-constrained MPI codes to process larger data sets. In addition, the hybrid model offers UPC programmers an opportunity to create static UPC groups that are connected over MPI. As we demonstrate, the use of such groups can significantly improve the scalability of locality-constrained UPC codes. This paper presents a detailed description of the hybrid model and demonstrates its effectiveness in two applications: a random access benchmark and the Barnes-Hut cosmological simulation. Experimental results indicate that the hybrid model can greatly enhance performance; using hybrid UPC groups that span two cluster nodes, RA performance increases by a factor of 1.33 and using groups that span four cluster nodes, Barnes-Hut experiences a twofold speedup at the expense of a 2% increase in code size.

  2. Medipix2 parallel readout system

    NASA Astrophysics Data System (ADS)

    Fanti, V.; Marzeddu, R.; Randaccio, P.

    2003-08-01

    A fast parallel readout system based on a PCI board has been developed in the framework of the Medipix collaboration. The readout electronics consists of two boards: the motherboard directly interfacing the Medipix2 chip, and the PCI board with digital I/O ports 32 bits wide. The device driver and readout software have been developed at low level in Assembler to allow fast data transfer and image reconstruction. The parallel readout permits a transfer rate up to 64 Mbytes/s. http://medipix.web.cern ch/MEDIPIX/

  3. Gang scheduling a parallel machine

    SciTech Connect

    Gorda, B.C.; Brooks, E.D. III.

    1991-03-01

    Program development on parallel machines can be a nightmare of scheduling headaches. We have developed a portable time sharing mechanism to handle the problem of scheduling gangs of processors. User program and their gangs of processors are put to sleep and awakened by the gang scheduler to provide a time sharing environment. Time quantums are adjusted according to priority queues and a system of fair share accounting. The initial platform for this software is the 128 processor BBN TC2000 in use in the Massively Parallel Computing Initiative at the Lawrence Livermore National Laboratory. 2 refs., 1 fig.

  4. Gang scheduling a parallel machine

    SciTech Connect

    Gorda, B.C.; Brooks, E.D. III.

    1991-12-01

    Program development on parallel machines can be a nightmare of scheduling headaches. We have developed a portable time sharing mechanism to handle the problem of scheduling gangs of processes. User programs and their gangs of processes are put to sleep and awakened by the gang scheduler to provide a time sharing environment. Time quantum are adjusted according to priority queues and a system of fair share accounting. The initial platform for this software is the 128 processor BBN TC2000 in use in the Massively Parallel Computing Initiative at the Lawrence Livermore National Laboratory.

  5. The Complexity of Parallel Algorithms,

    DTIC Science & Technology

    1985-11-01

    Much of this work was done in collaboration with my advisor, Ernst Mayr . He was also supported in part by ONR contract N00014-85-C-0731. F ’. Table...Helinbold and Mayr in their algorithn to compute an optimal two processor schedule [HM2]. One of the promising developments in parallel algorithms is that...lei can be solved by it fast parallel algorithmmmi if the nmlmmmibers are smiall. llehmibold and Mayr JIlM I] have slhowm that. if Ole job timies are

  6. Further optimization of detritylation in solid-phase oligodeoxyribonucleotide synthesis.

    PubMed

    Tram, Kha; Sanghvi, Yogesh S; Yan, Hongbin

    2011-01-01

    Various conditions for optimum detritylation (i.e., the removal of 5'-O-trityl protecting groups) during solid-phase synthesis of oligodeoxyribonucleotides were investigated. Di- and tri-chloroacetic acids of variable concentrations were used to study the removal of the 4,4'-dimethoxytrityl (DMTr) group. It was found that the DMTr group could be completely removed under much milder acidic conditions than what are currently used for automated solid-phase synthesis. The 2,7-dimethylpixyl (DMPx) is proposed as an alternative and more readily removable group for the protection of the 5'-OH functions both in solid- and solution-phase synthesis. The improved detritylation conditions are expected to minimize the waste and offer a protocol for incorporation of acid sensitive building-blocks in oligonucleotides.

  7. Investigation of the solid- and solution-phase binding reactivities of continuous epitopes recognized by polyclonal guinea-pig anti-recombinant bovine growth hormone antisera.

    PubMed

    Beattie, J

    1992-09-01

    We have used the technique of multiple pin peptide synthesis to identify three major continuous epitopes in the recombinant bovine (rb) GH molecule. We have synthesized these peptides, residues 24-40, 139-152 and 179-189, as N-terminally acetylated, C-terminal amides and confirmed their reactivity in a standard solid-phase ELISA. Subsequently, for epitope 139-152, we have synthesized a peptide affinity column and used this to isolate antibodies with this epitope specificity from whole antiserum. In addition, we demonstrate that under native conditions in a liquid phase RIA, these antibodies will precipitate [125I]rbGH. Further, peptide 139-152 itself also cross-reacts in an rbGH RIA inhibiting binding by up to 20%. Our data suggest that during the immune response to rbGH in guinea-pigs a substantial part of the B-cell response is directed to the 139-152 region and that this part of the protein is a native epitope.

  8. Parallel algorithms for placement and routing in VLSI design. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Brouwer, Randall Jay

    1991-01-01

    The computational requirements for high quality synthesis, analysis, and verification of very large scale integration (VLSI) designs have rapidly increased with the fast growing complexity of these designs. Research in the past has focused on the development of heuristic algorithms, special purpose hardware accelerators, or parallel algorithms for the numerous design tasks to decrease the time required for solution. Two new parallel algorithms are proposed for two VLSI synthesis tasks, standard cell placement and global routing. The first algorithm, a parallel algorithm for global routing, uses hierarchical techniques to decompose the routing problem into independent routing subproblems that are solved in parallel. Results are then presented which compare the routing quality to the results of other published global routers and which evaluate the speedups attained. The second algorithm, a parallel algorithm for cell placement and global routing, hierarchically integrates a quadrisection placement algorithm, a bisection placement algorithm, and the previous global routing algorithm. Unique partitioning techniques are used to decompose the various stages of the algorithm into independent tasks which can be evaluated in parallel. Finally, results are presented which evaluate the various algorithm alternatives and compare the algorithm performance to other placement programs. Measurements are presented on the parallel speedups available.

  9. Parallelizing Deadlock Resolution in Symbolic Synthesis of Distributed Programs

    DTIC Science & Technology

    2008-01-01

    follows. In Sections 2 and 3, we present precise defini- tions for distributed programs, specifications, and fault- tolerance. We formally state the...Subsequently, experimental results and analysis are presented in Section 6. Related work is discussed in Section 7. Finally, we conclude in Section...infinite com- putation by stuttering at sl. On the other hand, if there exists a state sd such that there is no outgoing transition (or a self-loop

  10. File concepts for parallel I/O

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas W.

    1989-01-01

    The subject of input/output (I/O) was often neglected in the design of parallel computer systems, although for many problems I/O rates will limit the speedup attainable. The I/O problem is addressed by considering the role of files in parallel systems. The notion of parallel files is introduced. Parallel files provide for concurrent access by multiple processes, and utilize parallelism in the I/O system to improve performance. Parallel files can also be used conventionally by sequential programs. A set of standard parallel file organizations is proposed, organizations are suggested, using multiple storage devices. Problem areas are also identified and discussed.

  11. Matpar: Parallel Extensions for MATLAB

    NASA Technical Reports Server (NTRS)

    Springer, P. L.

    1998-01-01

    Matpar is a set of client/server software that allows a MATLAB user to take advantage of a parallel computer for very large problems. The user can replace calls to certain built-in MATLAB functions with calls to Matpar functions.

  12. Parallel, Distributed Scripting with Python

    SciTech Connect

    Miller, P J

    2002-05-24

    Parallel computers used to be, for the most part, one-of-a-kind systems which were extremely difficult to program portably. With SMP architectures, the advent of the POSIX thread API and OpenMP gave developers ways to portably exploit on-the-box shared memory parallelism. Since these architectures didn't scale cost-effectively, distributed memory clusters were developed. The associated MPI message passing libraries gave these systems a portable paradigm too. Having programmers effectively use this paradigm is a somewhat different question. Distributed data has to be explicitly transported via the messaging system in order for it to be useful. In high level languages, the MPI library gives access to data distribution routines in C, C++, and FORTRAN. But we need more than that. Many reasonable and common tasks are best done in (or as extensions to) scripting languages. Consider sysadm tools such as password crackers, file purgers, etc ... These are simple to write in a scripting language such as Python (an open source, portable, and freely available interpreter). But these tasks beg to be done in parallel. Consider the a password checker that checks an encrypted password against a 25,000 word dictionary. This can take around 10 seconds in Python (6 seconds in C). It is trivial to parallelize if you can distribute the information and co-ordinate the work.

  13. Fast, Massively Parallel Data Processors

    NASA Technical Reports Server (NTRS)

    Heaton, Robert A.; Blevins, Donald W.; Davis, ED

    1994-01-01

    Proposed fast, massively parallel data processor contains 8x16 array of processing elements with efficient interconnection scheme and options for flexible local control. Processing elements communicate with each other on "X" interconnection grid with external memory via high-capacity input/output bus. This approach to conditional operation nearly doubles speed of various arithmetic operations.

  14. Optical Interferometric Parallel Data Processor

    NASA Technical Reports Server (NTRS)

    Breckinridge, J. B.

    1987-01-01

    Image data processed faster than in present electronic systems. Optical parallel-processing system effectively calculates two-dimensional Fourier transforms in time required by light to travel from plane 1 to plane 8. Coherence interferometer at plane 4 splits light into parts that form double image at plane 6 if projection screen placed there.

  15. Tutorial: Parallel Simulation on Supercomputers

    SciTech Connect

    Perumalla, Kalyan S

    2012-01-01

    This tutorial introduces typical hardware and software characteristics of extant and emerging supercomputing platforms, and presents issues and solutions in executing large-scale parallel discrete event simulation scenarios on such high performance computing systems. Covered topics include synchronization, model organization, example applications, and observed performance from illustrative large-scale runs.

  16. The physics of parallel machines

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.

    1988-01-01

    The idea is considered that architectures for massively parallel computers must be designed to go beyond supporting a particular class of algorithms to supporting the underlying physical processes being modelled. Physical processes modelled by partial differential equations (PDEs) are discussed. Also discussed is the idea that an efficient architecture must go beyond nearest neighbor mesh interconnections and support global and hierarchical communications.

  17. Parallel distributed computing using Python

    NASA Astrophysics Data System (ADS)

    Dalcin, Lisandro D.; Paz, Rodrigo R.; Kler, Pablo A.; Cosimo, Alejandro

    2011-09-01

    This work presents two software components aimed to relieve the costs of accessing high-performance parallel computing resources within a Python programming environment: MPI for Python and PETSc for Python. MPI for Python is a general-purpose Python package that provides bindings for the Message Passing Interface (MPI) standard using any back-end MPI implementation. Its facilities allow parallel Python programs to easily exploit multiple processors using the message passing paradigm. PETSc for Python provides access to the Portable, Extensible Toolkit for Scientific Computation (PETSc) libraries. Its facilities allow sequential and parallel Python applications to exploit state of the art algorithms and data structures readily available in PETSc for the solution of large-scale problems in science and engineering. MPI for Python and PETSc for Python are fully integrated to PETSc-FEM, an MPI and PETSc based parallel, multiphysics, finite elements code developed at CIMEC laboratory. This software infrastructure supports research activities related to simulation of fluid flows with applications ranging from the design of microfluidic devices for biochemical analysis to modeling of large-scale stream/aquifer interactions.

  18. PALM: a Parallel Dynamic Coupler

    NASA Astrophysics Data System (ADS)

    Thevenin, A.; Morel, T.

    2008-12-01

    In order to efficiently represent complex systems, numerical modeling has to rely on many physical models at a time: an ocean model coupled with an atmospheric model is at the basis of climate modeling. The continuity of the solution is granted only if these models can constantly exchange information. PALM is a coupler allowing the concurrent execution and the intercommunication of programs not having been especially designed for that. With PALM, the dynamic coupling approach is introduced: a coupled component can be launched and can release computers' resources upon termination at any moment during the simulation. In order to exploit as much as possible computers' possibilities, the PALM coupler handles two levels of parallelism. The first level concerns the components themselves. While managing the resources, PALM allocates the number of processes which are necessary to any coupled component. These models can be parallel programs based on domain decomposition with MPI or applications multithreaded with OpenMP. The second level of parallelism is a task parallelism: one can define a coupling algorithm allowing two or more programs to be executed in parallel. PALM applications are implemented via a Graphical User Interface called PrePALM. In this GUI, the programmer initially defines the coupling algorithm then he describes the actual communications between the models. PALM offers a very high flexibility for testing different coupling techniques and for reaching the best load balance in a high performance computer. The transformation of computational independent code is almost straightforward. The other qualities of PALM are its easy set-up, its flexibility, its performances, the simple updates and evolutions of the coupled application and the many side services and functions that it offers.

  19. Flow invariant droplet formation for stable parallel microreactors

    PubMed Central

    Riche, Carson T.; Roberts, Emily J.; Gupta, Malancha; Brutchey, Richard L.; Malmstadt, Noah

    2016-01-01

    The translation of batch chemistries onto continuous flow platforms requires addressing the issues of consistent fluidic behaviour, channel fouling and high-throughput processing. Droplet microfluidic technologies reduce channel fouling and provide an improved level of control over heat and mass transfer to control reaction kinetics. However, in conventional geometries, the droplet size is sensitive to changes in flow rates. Here we report a three-dimensional droplet generating device that exhibits flow invariant behaviour and is robust to fluctuations in flow rate. In addition, the droplet generator is capable of producing droplet volumes spanning four orders of magnitude. We apply this device in a parallel network to synthesize platinum nanoparticles using an ionic liquid solvent, demonstrate reproducible synthesis after recycling the ionic liquid, and double the reaction yield compared with an analogous batch synthesis. PMID:26902825

  20. Flow invariant droplet formation for stable parallel microreactors

    NASA Astrophysics Data System (ADS)

    Riche, Carson T.; Roberts, Emily J.; Gupta, Malancha; Brutchey, Richard L.; Malmstadt, Noah

    2016-02-01

    The translation of batch chemistries onto continuous flow platforms requires addressing the issues of consistent fluidic behaviour, channel fouling and high-throughput processing. Droplet microfluidic technologies reduce channel fouling and provide an improved level of control over heat and mass transfer to control reaction kinetics. However, in conventional geometries, the droplet size is sensitive to changes in flow rates. Here we report a three-dimensional droplet generating device that exhibits flow invariant behaviour and is robust to fluctuations in flow rate. In addition, the droplet generator is capable of producing droplet volumes spanning four orders of magnitude. We apply this device in a parallel network to synthesize platinum nanoparticles using an ionic liquid solvent, demonstrate reproducible synthesis after recycling the ionic liquid, and double the reaction yield compared with an analogous batch synthesis.

  1. Structure-based parallel medicinal chemistry approach to improve metabolic stability of benzopyran COX-2 inhibitors.

    PubMed

    Xing, Li; Hamper, Bruce C; Fletcher, Theresa R; Wendling, Jay M; Carter, Jeffery; Gierse, James K; Liao, Subo

    2011-02-01

    Combination of the structure-based design and solid-phase parallel synthesis provided an integrated approach to rapidly develop the structure-activity relationship of benzopyran COX-2 inhibitors. Binding free energies predicted by free energy perturbation theory yielded good agreement with experimental results. New potent and selective lead compounds with improved metabolic properties were identified.

  2. Multilevel decomposition of complete vehicle configuration in a parallel computing environment

    NASA Technical Reports Server (NTRS)

    Bhatt, Vinay; Ragsdell, K. M.

    1989-01-01

    This research summarizes various approaches to multilevel decomposition to solve large structural problems. A linear decomposition scheme based on the Sobieski algorithm is selected as a vehicle for automated synthesis of a complete vehicle configuration in a parallel processing environment. The research is in a developmental state. Preliminary numerical results are presented for several example problems.

  3. Static stability of parallel operation of asynchronized generators in an electrical system

    NASA Astrophysics Data System (ADS)

    Plotnikova, T. V.; Sokur, P. V.; Tuzov, P. Yu.; Shakaryan, Yu. G.

    2014-12-01

    The static stability of single and parallel operations of an asynchronized generator (ASG) in a long-distance power transmission line is investigated. The synthesis of the ASG excitation control law at which set of the machine's stable operating conditions G s will comprise sufficiently conservative set of permissible operating conditions G p is considered.

  4. Synthesis of Cu2ZnSnS4 nanocrystal ink and its use for solar cells.

    PubMed

    Guo, Qijie; Hillhouse, Hugh W; Agrawal, Rakesh

    2009-08-26

    Cu(2)ZnSnS(4) (CZTS) and Cu(2)ZnSnSe(4) (CZTSe) based solar cells are promising candidates for low cost solar cells due to the natural abundance and low toxicity of the constituent elements. Here, we present the first reported synthesis of colloidal CZTS nanocrystals using a simple solution-phase method. Solar cells fabricated using selenized CZTS nanocrystal inks had a power conversion efficiency of 0.74% under AM1.5G illumination.

  5. Task parallelism and high-performance languages

    SciTech Connect

    Foster, I.

    1996-03-01

    The definition of High Performance Fortran (HPF) is a significant event in the maturation of parallel computing: it represents the first parallel language that has gained widespread support from vendors and users. The subject of this paper is to incorporate support for task parallelism. The term task parallelism refers to the explicit creation of multiple threads of control, or tasks, which synchronize and communicate under programmer control. Task and data parallelism are complementary rather than competing programming models. While task parallelism is more general and can be used to implement algorithms that are not amenable to data-parallel solutions, many problems can benefit from a mixed approach, with for example a task-parallel coordination layer integrating multiple data-parallel computations. Other problems admit to both data- and task-parallel solutions, with the better solution depending on machine characteristics, compiler performance, or personal taste. For these reasons, we believe that a general-purpose high-performance language should integrate both task- and data-parallel constructs. The challenge is to do so in a way that provides the expressivity needed for applications, while preserving the flexibility and portability of a high-level language. In this paper, we examine and illustrate the considerations that motivate the use of task parallelism. We also describe one particular approach to task parallelism in Fortran, namely the Fortran M extensions. Finally, we contrast Fortran M with other proposed approaches and discuss the implications of this work for task parallelism and high-performance languages.

  6. A generalized parallel replica dynamics

    NASA Astrophysics Data System (ADS)

    Binder, Andrew; Lelièvre, Tony; Simpson, Gideon

    2015-03-01

    Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying stochastic process to a quasi-stationary distribution. Two requirements for applying parallel replica dynamics are knowledge of the time scale on which the process converges to the quasi-stationary distribution and a mechanism for generating samples from this distribution. By combining a Fleming-Viot particle system with convergence diagnostics to simultaneously identify when the process converges while also generating samples, we can address both points. This variation on the algorithm is illustrated with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.

  7. Merlin - Massively parallel heterogeneous computing

    NASA Technical Reports Server (NTRS)

    Wittie, Larry; Maples, Creve

    1989-01-01

    Hardware and software for Merlin, a new kind of massively parallel computing system, are described. Eight computers are linked as a 300-MIPS prototype to develop system software for a larger Merlin network with 16 to 64 nodes, totaling 600 to 3000 MIPS. These working prototypes help refine a mapped reflective memory technique that offers a new, very general way of linking many types of computer to form supercomputers. Processors share data selectively and rapidly on a word-by-word basis. Fast firmware virtual circuits are reconfigured to match topological needs of individual application programs. Merlin's low-latency memory-sharing interfaces solve many problems in the design of high-performance computing systems. The Merlin prototypes are intended to run parallel programs for scientific applications and to determine hardware and software needs for a future Teraflops Merlin network.

  8. Parallel supercomputing with commodity components

    SciTech Connect

    Warren, M.S.; Goda, M.P.; Becker, D.J.

    1997-09-01

    We have implemented a parallel computer architecture based entirely upon commodity personal computer components. Using 16 Intel Pentium Pro microprocessors and switched fast ethernet as a communication fabric, we have obtained sustained performance on scientific applications in excess of one Gigaflop. During one production astrophysics treecode simulation, we performed 1.2 x 10{sup 15} floating point operations (1.2 Petaflops) over a three week period, with one phase of that simulation running continuously for two weeks without interruption. We report on a variety of disk, memory and network benchmarks. We also present results from the NAS parallel benchmark suite, which indicate that this architecture is competitive with current commercial architectures. In addition, we describe some software written to support efficient message passing, as well as a Linux device driver interface to the Pentium hardware performance monitoring registers.

  9. ASP: a parallel computing technology

    NASA Astrophysics Data System (ADS)

    Lea, R. M.

    1990-09-01

    ASP modules constitute the basis of a parallel computing technology platform for the rapid development of a broad range of numeric and symbolic information processing systems. Based on off-the-shelf general-purpose hardware and software modules ASP technology is intended to increase productivity in the development (and competitiveness in the marketing) of cost-effective low-MIMD/high-SIMD Massively Parallel Processor (MPPs). The paper discusses ASP module philosophy and demonstrates how ASP modules can satisfy the market algorithmic architectural and engineering requirements of such MPPs. In particular two specific ASP modules based on VLSI and WSI technologies are studied as case examples of ASP technology the latter reporting 1 TOPS/fl3 1 GOPS/W and 1 MOPS/$ as ball-park figures-of-merit of cost-effectiveness.

  10. Parallel processing spacecraft communication system

    NASA Technical Reports Server (NTRS)

    Bolotin, Gary S. (Inventor); Donaldson, James A. (Inventor); Luong, Huy H. (Inventor); Wood, Steven H. (Inventor)

    1998-01-01

    An uplink controlling assembly speeds data processing using a special parallel codeblock technique. A correct start sequence initiates processing of a frame. Two possible start sequences can be used; and the one which is used determines whether data polarity is inverted or non-inverted. Processing continues until uncorrectable errors are found. The frame ends by intentionally sending a block with an uncorrectable error. Each of the codeblocks in the frame has a channel ID. Each channel ID can be separately processed in parallel. This obviates the problem of waiting for error correction processing. If that channel number is zero, however, it indicates that the frame of data represents a critical command only. That data is handled in a special way, independent of the software. Otherwise, the processed data further handled using special double buffering techniques to avoid problems from overrun. When overrun does occur, the system takes action to lose only the oldest data.

  11. A generalized parallel replica dynamics

    SciTech Connect

    Binder, Andrew; Lelièvre, Tony; Simpson, Gideon

    2015-03-01

    Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying stochastic process to a quasi-stationary distribution. Two requirements for applying parallel replica dynamics are knowledge of the time scale on which the process converges to the quasi-stationary distribution and a mechanism for generating samples from this distribution. By combining a Fleming–Viot particle system with convergence diagnostics to simultaneously identify when the process converges while also generating samples, we can address both points. This variation on the algorithm is illustrated with various numerical examples, including those with entropic barriers and the 2D Lennard-Jones cluster of seven atoms.

  12. Parallel supercomputing with commodity components

    NASA Technical Reports Server (NTRS)

    Warren, M. S.; Goda, M. P.; Becker, D. J.

    1997-01-01

    We have implemented a parallel computer architecture based entirely upon commodity personal computer components. Using 16 Intel Pentium Pro microprocessors and switched fast ethernet as a communication fabric, we have obtained sustained performance on scientific applications in excess of one Gigaflop. During one production astrophysics treecode simulation, we performed 1.2 x 10(sup 15) floating point operations (1.2 Petaflops) over a three week period, with one phase of that simulation running continuously for two weeks without interruption. We report on a variety of disk, memory and network benchmarks. We also present results from the NAS parallel benchmark suite, which indicate that this architecture is competitive with current commercial architectures. In addition, we describe some software written to support efficient message passing, as well as a Linux device driver interface to the Pentium hardware performance monitoring registers.

  13. Parallel multiplex laser feedback interferometry

    SciTech Connect

    Zhang, Song; Tan, Yidong; Zhang, Shulian

    2013-12-15

    We present a parallel multiplex laser feedback interferometer based on spatial multiplexing which avoids the signal crosstalk in the former feedback interferometer. The interferometer outputs two close parallel laser beams, whose frequencies are shifted by two acousto-optic modulators by 2Ω simultaneously. A static reference mirror is inserted into one of the optical paths as the reference optical path. The other beam impinges on the target as the measurement optical path. Phase variations of the two feedback laser beams are simultaneously measured through heterodyne demodulation with two different detectors. Their subtraction accurately reflects the target displacement. Under typical room conditions, experimental results show a resolution of 1.6 nm and accuracy of 7.8 nm within the range of 100 μm.

  14. Parallelism in Manipulator Dynamics. Revision.

    DTIC Science & Technology

    1983-12-01

    excessive, and a VLSI implementation architecutre is suggested. We indicate possible appli- cations to incorporating dynamical considerations into...Inverse Dynamics problem. It investigates the high degree of parallelism inherent in the computations , and presents two "mathematically exact" formulations...and a 3 b Cases ............. ... 109 5 .9-- i 0. OVERVIEW The Inverse Dynamics problem consists (loosely) of computing the motor torques necessary to

  15. Parallel Symmetric Eigenvalue Problem Solvers

    DTIC Science & Technology

    2015-05-01

    graduate school. Debugging somebody else’s MPI code is an immensely frustrating experience, but he would regularly stay late at the oce to assist me...cessfully. In addition, I will describe the parallel kernels required by my code . 5 The next sections will describe my Fortran-based implementations of...Sandia’s publicly available Trace- Min code . Each of the methods has its own unique advantages and disadvantages, summarized in table 3.1. In short, I

  16. Parallel Algorithms for Computer Vision.

    DTIC Science & Technology

    1987-01-01

    73 755 P fiu.LEL ALORITHMS FOR CO PUTER VISIO (U) /MASSACHUSETTS INST OF TECH CRMORIDGE T P00010 ET AL.JAN 8? ETL-0456 DACA7-05-C-8IIO m 7E F/0 1...regularization principles, such as edge detection, stereo , motion, surface interpolation and shape from shading. The basic members of class I are convolution...them in collabo- ration with Thinking Machines Corporation): * Parallel convolution * Zero-crossing detection * Stereo -matching * Surface reconstruction

  17. Lightweight Specifications for Parallel Correctness

    DTIC Science & Technology

    2012-12-05

    this burden, to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204... George Necula Professor David Wessel Fall 2012 1 Abstract Lightweight Specifications for Parallel Correctness by Jacob Samuels Burnim Doctor of Philosophy...enthusiasm and endless flow of ideas, and for his keen research sense. I would also like to thank George Necula for chairing my qualifying exam committee and

  18. National Combustion Code: Parallel Performance

    NASA Technical Reports Server (NTRS)

    Babrauckas, Theresa

    2001-01-01

    This report discusses the National Combustion Code (NCC). The NCC is an integrated system of codes for the design and analysis of combustion systems. The advanced features of the NCC meet designers' requirements for model accuracy and turn-around time. The fundamental features at the inception of the NCC were parallel processing and unstructured mesh. The design and performance of the NCC are discussed.

  19. Parallel Algorithms for Computer Vision.

    DTIC Science & Technology

    1989-01-01

    demonstrated the Vision Machine system processing images and recognizing objects through the inte- gration of several visual cues. The first version of the...achievements. n 2.1 The Vision Machine The overall organization of tie Vision Machine systeliis ased. o parallel processing of tie images by independent...smoothed and made dense by exploiting known constraints within each process (for example., that disparity is smooth). This is the stage of approximation

  20. Parallel strategies for SAR processing

    NASA Astrophysics Data System (ADS)

    Segoviano, Jesus A.

    2004-12-01

    This article proposes a series of strategies for improving the computer process of the Synthetic Aperture Radar (SAR) signal treatment, following the three usual lines of action to speed up the execution of any computer program. On the one hand, it is studied the optimization of both, the data structures and the application architecture used on it. On the other hand it is considered a hardware improvement. For the former, they are studied both, the usually employed SAR process data structures, proposing the use of parallel ones and the way the parallelization of the algorithms employed on the process is implemented. Besides, the parallel application architecture classifies processes between fine/coarse grain. These are assigned to individual processors or separated in a division among processors, all of them in their corresponding architectures. For the latter, it is studied the hardware employed on the computer parallel process used in the SAR handling. The improvement here refers to several kinds of platforms in which the SAR process is implemented, shared memory multicomputers, and distributed memory multiprocessors. A comparison between them gives us some guidelines to follow in order to get a maximum throughput with a minimum latency and a maximum effectiveness with a minimum cost, all together with a limited complexness. It is concluded and described, that the approach consisting of the processing of the algorithms in a GNU/Linux environment, together with a Beowulf cluster platform offers, under certain conditions, the best compromise between performance and cost, and promises the major development in the future for the Synthetic Aperture Radar computer power thirsty applications in the next years.

  1. Parallel Power Grid Simulation Toolkit

    SciTech Connect

    Smith, Steve; Kelley, Brian; Banks, Lawrence; Top, Philip; Woodward, Carol

    2015-09-14

    ParGrid is a 'wrapper' that integrates a coupled Power Grid Simulation toolkit consisting of a library to manage the synchronization and communication of independent simulations. The included library code in ParGid, named FSKIT, is intended to support the coupling multiple continuous and discrete even parallel simulations. The code is designed using modern object oriented C++ methods utilizing C++11 and current Boost libraries to ensure compatibility with multiple operating systems and environments.

  2. Solution- and solid-phase oligosaccharide synthesis using glucosyl iodides: a comparative study.

    PubMed

    Lam, Son N; Gervay-Hague, Jacquelyn

    2002-11-19

    Glycosyl iodide donors have been used in both solid- and solution-phase syntheses yielding alpha-(1 --> 6)-linked glucosyl oligomers in highly efficient protocols. While the solid-phase strategy offers advantages in terms of ease of purification, it requires a total of 7.5 equiv of donor and approximately 12 h to complete the incorporation of one monosaccharide unit. In contrast, solution-phase methods require only 2.5 equiv of donor and 2-3 h reaction time per glycosylation. Moreover, since the reactions are virtually quantitative (> 90%) column chromatography of the material is facile. The overall advantages of solution-phase oligosaccharide synthesis were further illustrated in the convergent synthesis of a hexamer (methoxycarbonylmethyl 6-O-acetyl-2,3,4-tri-O-benzyl-alpha-D-glucopyranosyl-(1 --> 6)-tetrakis-(2,3,4-tri-O-benzyl-alpha-D-glucopyranosyl-(1 --> 6))-2,3,4-tri-O-benzyl-1-thio-alpha-D-glucopyranoside) that was constructed from dimer donor iodides in a two-plus-two and a two-plus-four fashion.

  3. [Total Synthesis of Biologically Active Natural Products toward Elucidation of the Mode of Action].

    PubMed

    Yoshida, Masahito

    2015-01-01

    Total synthesis of biologically active cyclodepsipeptide destruxin E using solid- and solution-phase synthesis is described. The solid-phase synthesis of destruxin E was initially investigated for the efficient synthesis of destruxin analogues. Peptide elongation from polymer-supported β-alanine was efficiently performed using DIC/HOBt or PyBroP/DIEA, and subsequent cleavage from the polymer-support under weakly acidic conditions furnished a cyclization precursor in moderate yield. Macrolactonization of the cyclization precursor was smoothly performed using 2-methyl-6-nitrobenzoic anhydride (MNBA)/4-(dimethylamino)pyridine N-oxide (DMAPO) to afford macrolactone in moderate yield. Finally, formation of the epoxide in the side chain via three steps provided destruxin E, and the stereochemistry of the epoxide was determined to be S. Its diastereomer, epi-destruxin E, was also synthesized in the same manner used to synthesize the natural product. The stereochemistry of the epoxide was critical for the V-ATPase inhibition; natural product destruxin E exhibited 10-fold more potent V-ATPase inhibition than epi-destruxin E. Next, the scalable synthesis of destruxin E for in vivo study was also performed via solution-phase synthesis. The scalable synthesis of a key component, (S)-HA-Pro-OH, was achieved using osmium-catalyzed diastereoselective dihydroxylation with (DHQD)2PHAL as a chiral ligand; peptide synthesis using Cbz-protected amino acid derivatives furnished the cyclization precursor on a gram-scale. Macrolactonization smoothly provided the macrolactone without forming a dimerized product, even at 6 mM, and the synthesis of destruxin E was achieved via three steps on a gram scale in high purity (>98%).

  4. Parallel processing of genomics data

    NASA Astrophysics Data System (ADS)

    Agapito, Giuseppe; Guzzi, Pietro Hiram; Cannataro, Mario

    2016-10-01

    The availability of high-throughput experimental platforms for the analysis of biological samples, such as mass spectrometry, microarrays and Next Generation Sequencing, have made possible to analyze a whole genome in a single experiment. Such platforms produce an enormous volume of data per single experiment, thus the analysis of this enormous flow of data poses several challenges in term of data storage, preprocessing, and analysis. To face those issues, efficient, possibly parallel, bioinformatics software needs to be used to preprocess and analyze data, for instance to highlight genetic variation associated with complex diseases. In this paper we present a parallel algorithm for the parallel preprocessing and statistical analysis of genomics data, able to face high dimension of data and resulting in good response time. The proposed system is able to find statistically significant biological markers able to discriminate classes of patients that respond to drugs in different ways. Experiments performed on real and synthetic genomic datasets show good speed-up and scalability.

  5. Parallelism in integrated fluidic circuits

    NASA Astrophysics Data System (ADS)

    Bousse, Luc J.; Kopf-Sill, Anne R.; Parce, J. W.

    1998-04-01

    Many research groups around the world are working on integrated microfluidics. The goal of these projects is to automate and integrate the handling of liquid samples and reagents for measurement and assay procedures in chemistry and biology. Ultimately, it is hoped that this will lead to a revolution in chemical and biological procedures similar to that caused in electronics by the invention of the integrated circuit. The optimal size scale of channels for liquid flow is determined by basic constraints to be somewhere between 10 and 100 micrometers . In larger channels, mixing by diffusion takes too long; in smaller channels, the number of molecules present is so low it makes detection difficult. At Caliper, we are making fluidic systems in glass chips with channels in this size range, based on electroosmotic flow, and fluorescence detection. One application of this technology is rapid assays for drug screening, such as enzyme assays and binding assays. A further challenge in this area is to perform multiple functions on a chip in parallel, without a large increase in the number of inputs and outputs. A first step in this direction is a fluidic serial-to-parallel converter. Fluidic circuits will be shown with the ability to distribute an incoming serial sample stream to multiple parallel channels.

  6. Highly parallel sparse Cholesky factorization

    NASA Technical Reports Server (NTRS)

    Gilbert, John R.; Schreiber, Robert

    1990-01-01

    Several fine grained parallel algorithms were developed and compared to compute the Cholesky factorization of a sparse matrix. The experimental implementations are on the Connection Machine, a distributed memory SIMD machine whose programming model conceptually supplies one processor per data element. In contrast to special purpose algorithms in which the matrix structure conforms to the connection structure of the machine, the focus is on matrices with arbitrary sparsity structure. The most promising algorithm is one whose inner loop performs several dense factorizations simultaneously on a 2-D grid of processors. Virtually any massively parallel dense factorization algorithm can be used as the key subroutine. The sparse code attains execution rates comparable to those of the dense subroutine. Although at present architectural limitations prevent the dense factorization from realizing its potential efficiency, it is concluded that a regular data parallel architecture can be used efficiently to solve arbitrarily structured sparse problems. A performance model is also presented and it is used to analyze the algorithms.

  7. Parallel Environment for Quantum Computing

    NASA Astrophysics Data System (ADS)

    Tabakin, Frank; Diaz, Bruno Julia

    2009-03-01

    To facilitate numerical study of noise and decoherence in QC algorithms,and of the efficacy of error correction schemes, we have developed a Fortran 90 quantum computer simulator with parallel processing capabilities. It permits rapid evaluation of quantum algorithms for a large number of qubits and for various ``noise'' scenarios. State vectors are distributed over many processors, to employ a large number of qubits. Parallel processing is implemented by the Message-Passing Interface protocol. A description of how to spread the wave function components over many processors, along with how to efficiently describe the action of general one- and two-qubit operators on these state vectors will be delineated.Grover's search and Shor's factoring algorithms with noise will be discussed as examples. A major feature of this work is that concurrent versions of the algorithms can be evaluated with each version subject to diverse noise effects, corresponding to solving a stochastic Schrodinger equation. The density matrix for the ensemble of such noise cases is constructed using parallel distribution methods to evaluate its associated entropy. Applications of this powerful tool is made to delineate the stability and correction of QC processes using Hamiltonian based dynamics.

  8. Parallel Markov chain Monte Carlo simulations.

    PubMed

    Ren, Ruichao; Orkoulas, G

    2007-06-07

    With strict detailed balance, parallel Monte Carlo simulation through domain decomposition cannot be validated with conventional Markov chain theory, which describes an intrinsically serial stochastic process. In this work, the parallel version of Markov chain theory and its role in accelerating Monte Carlo simulations via cluster computing is explored. It is shown that sequential updating is the key to improving efficiency in parallel simulations through domain decomposition. A parallel scheme is proposed to reduce interprocessor communication or synchronization, which slows down parallel simulation with increasing number of processors. Parallel simulation results for the two-dimensional lattice gas model show substantial reduction of simulation time for systems of moderate and large size.

  9. Parallel Markov chain Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Ren, Ruichao; Orkoulas, G.

    2007-06-01

    With strict detailed balance, parallel Monte Carlo simulation through domain decomposition cannot be validated with conventional Markov chain theory, which describes an intrinsically serial stochastic process. In this work, the parallel version of Markov chain theory and its role in accelerating Monte Carlo simulations via cluster computing is explored. It is shown that sequential updating is the key to improving efficiency in parallel simulations through domain decomposition. A parallel scheme is proposed to reduce interprocessor communication or synchronization, which slows down parallel simulation with increasing number of processors. Parallel simulation results for the two-dimensional lattice gas model show substantial reduction of simulation time for systems of moderate and large size.

  10. Multi-objective optimization of a parallel ankle rehabilitation robot using modified differential evolution algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Congzhe; Fang, Yuefa; Guo, Sheng

    2015-07-01

    Dimensional synthesis is one of the most difficult issues in the field of parallel robots with actuation redundancy. To deal with the optimal design of a redundantly actuated parallel robot used for ankle rehabilitation, a methodology of dimensional synthesis based on multi-objective optimization is presented. First, the dimensional synthesis of the redundant parallel robot is formulated as a nonlinear constrained multi-objective optimization problem. Then four objective functions, separately reflecting occupied space, input/output transmission and torque performances, and multi-criteria constraints, such as dimension, interference and kinematics, are defined. In consideration of the passive exercise of plantar/dorsiflexion requiring large output moment, a torque index is proposed. To cope with the actuation redundancy of the parallel robot, a new output transmission index is defined as well. The multi-objective optimization problem is solved by using a modified Differential Evolution(DE) algorithm, which is characterized by new selection and mutation strategies. Meanwhile, a special penalty method is presented to tackle the multi-criteria constraints. Finally, numerical experiments for different optimization algorithms are implemented. The computation results show that the proposed indices of output transmission and torque, and constraint handling are effective for the redundant parallel robot; the modified DE algorithm is superior to the other tested algorithms, in terms of the ability of global search and the number of non-dominated solutions. The proposed methodology of multi-objective optimization can be also applied to the dimensional synthesis of other redundantly actuated parallel robots only with rotational movements.

  11. Binding of nitrate to a CuII-cyclen complex bearing a ferrocenyl pendant: synthesis, solid-state X-ray structure, and solution-phase electrochemical and spectrophotometric studies.

    PubMed

    Gasser, Gilles; Belousoff, Matthew J; Bond, Alan M; Spiccia, Leone

    2007-05-14

    The reaction of Cu(NO3)2.3H2O with the ligand 1-(ferrocenemethyl)-1,4,7,10-tetraazacyclododecane (L) in acetonitrile leads to the formation of a blue complex, [Cu(L)(NO3)][NO3] (C1). The X-ray structure determination shows an unexpected binding of a nitrate anion in that the CuII center is surrounded by four N atoms of the 1,4,7,10-tetraazacyclododecane (cyclen) macrocycle and two O atoms from a chelating nitrate anion, both Cu-O distances being below the sums of the van de Waals radii. Hydrogen-bonding interactions in the crystal lattice and a weak interaction between a second nitrate O and the CuII center in C1 give rise to a highly distorted CuII geometry relative to that found in the known structure of [Cu(cyclen)(NO3)][NO3] (C5). Electrochemical studies in acetonitrile containing 0.1 M [Bu4N][NO3] as the supporting electrolyte showed that oxidation of C1 in this medium exhibits a single reversible one-electron step with a formal potential E degrees f of +85 mV vs Fc0/+ (Fc = ferrocene). This process is associated with oxidation of the ferrocenyl pendant group. Additionally, a reversible one-electron reduction reaction with an E degrees f value of -932 mV vs Fc0/+, attributed to the CuII/I redox couple, is detected. Gradual change of the supporting electrolyte from 0.1 M [Bu4N][NO3] to the poorly coordinating [Bu4N][PF6] electrolyte, at constant ionic strength, led to a positive potential shift in E degrees f values by +107 and +39 mV for the CuII/I(C1) and Fc0/+(C1) redox couples, respectively. Analysis of these electrochemical data and UV-vis spectra is consistent with the probable presence of the complexes C1, [Cu(L)(CH3CN)2]2+ (C2), [Cu(L)(CH3CN)(NO3)]+ (C3), and [Cu(L)(NO3)2] (C4) as the major species in nitrate-containing acetonitrile solutions. In weakly solvating nitromethane, the extent of nitrate complexation remains significant even at low nitrate concentrations, due to the lack of solvent competition.

  12. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    SciTech Connect

    Unknown

    1999-04-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  13. Alternative fuels and chemicals from synthesis gas

    SciTech Connect

    Unknown

    1998-08-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  14. Alternative Fuels and Chemicals from Synthesis Gas

    SciTech Connect

    Peter Tijrn

    2003-01-02

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  15. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    SciTech Connect

    Unknown

    1999-01-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  16. ALTERNATIVE FUELS AND CHEMICALS FROM SYNTHESIS GAS

    SciTech Connect

    Unknown

    1998-01-01

    The overall objectives of this program are to investigate potential technologies for the conversion of synthesis gas to oxygenated and hydrocarbon fuels and industrial chemicals, and to demonstrate the most promising technologies at DOE's LaPorte, Texas, Slurry Phase Alternative Fuels Development Unit (AFDU). The program will involve a continuation of the work performed under the Alternative Fuels from Coal-Derived Synthesis Gas Program and will draw upon information and technologies generated in parallel current and future DOE-funded contracts.

  17. CdS and Cd-Free Buffer Layers on Solution Phase Grown Cu2ZnSn(SxSe1- x)4 :Band Alignments and Electronic Structure Determined with Femtosecond Ultraviolet Photoemission Spectroscopy

    SciTech Connect

    Haight, Richard; Barkhouse, Aaron; Wang, Wei; Yu, Luo; Shao, Xiaoyan; Mitzi, David; Hiroi, Homare; Sugimoto, Hiroki

    2013-12-02

    The heterojunctions formed between solution phase grown Cu2ZnSn(SxSe1- x)4(CZTS,Se) and a number of important buffer materials including CdS, ZnS, ZnO, and In2S3, were studied using femtosecond ultraviolet photoemission spectroscopy (fs-UPS) and photovoltage spectroscopy. With this approach we extract the magnitude and direction of the CZTS,Se band bending, locate the Fermi level within the band gaps of absorber and buffer and measure the absorber/buffer band offsets under flatband conditions. We will also discuss two-color pump/probe experiments in which the band bending in the buffer layer can be independently determined. Finally, studies of the bare CZTS,Se surface will be discussed including our observation of mid-gap Fermi level pinning and its relation to Voc limitations and bulk defects.

  18. Parallelizing alternating direction implicit solver on GPUs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We present a parallel Alternating Direction Implicit (ADI) solver on GPUs. Our implementation significantly improves existing implementations in two aspects. First, we address the scalability issue of existing Parallel Cyclic Reduction (PCR) implementations by eliminating their hardware resource con...

  19. Implementing clips on a parallel computer

    NASA Technical Reports Server (NTRS)

    Riley, Gary

    1987-01-01

    The C language integrated production system (CLIPS) is a forward chaining rule based language to provide training and delivery for expert systems. Conceptually, rule based languages have great potential for benefiting from the inherent parallelism of the algorithms that they employ. During each cycle of execution, a knowledge base of information is compared against a set of rules to determine if any rules are applicable. Parallelism also can be employed for use with multiple cooperating expert systems. To investigate the potential benefits of using a parallel computer to speed up the comparison of facts to rules in expert systems, a parallel version of CLIPS was developed for the FLEX/32, a large grain parallel computer. The FLEX implementation takes a macroscopic approach in achieving parallelism by splitting whole sets of rules among several processors rather than by splitting the components of an individual rule among processors. The parallel CLIPS prototype demonstrates the potential advantages of integrating expert system tools with parallel computers.

  20. Synthesis and characterization of hybrid nanostructures

    PubMed Central

    Mokari, Taleb

    2011-01-01

    There has been significant interest in the development of multicomponent nanocrystals formed by the assembly of two or more different materials with control over size, shape, composition, and spatial orientation. In particular, the selective growth of metals on the tips of semiconductor nanorods and wires can act to couple the electrical and optical properties of semiconductors with the unique properties of various metals. Here, we outline our progress on the solution-phase synthesis of metal-semiconductor heterojunctions formed by the growth of Au, Pt, or other binary catalytic metal systems on metal (Cd, Pb, Cu)-chalcogenide nanostructures. We show the ability to grow the metal on various shapes (spherical, rods, hexagonal prisms, and wires). Furthermore, manipulating the composition of the metal nanoparticles is also shown, where PtNi and PtCo alloys are our main focus. The magnetic and electrical properties of the developed hybrid nanostructures are shown. PMID:22110873

  1. Parallel molecular dynamics: Communication requirements for massively parallel machines

    NASA Astrophysics Data System (ADS)

    Taylor, Valerie E.; Stevens, Rick L.; Arnold, Kathryn E.

    1995-05-01

    Molecular mechanics and dynamics are becoming widely used to perform simulations of molecular systems from large-scale computations of materials to the design and modeling of drug compounds. In this paper we address two major issues: a good decomposition method that can take advantage of future massively parallel processing systems for modest-sized problems in the range of 50,000 atoms and the communication requirements needed to achieve 30 to 40% efficiency on MPPs. We analyzed a scalable benchmark molecular dynamics program executing on the Intel Touchstone Deleta parallelized with an interaction decomposition method. Using a validated analytical performance model of the code, we determined that for an MPP with a four-dimensional mesh topology and 400 MHz processors the communication startup time must be at most 30 clock cycles and the network bandwidth must be at least 2.3 GB/s. This configuration results in 30 to 40% efficiency of the MPP for a problem with 50,000 atoms executing on 50,000 processors.

  2. Force user's manual: A portable, parallel FORTRAN

    NASA Technical Reports Server (NTRS)

    Jordan, Harry F.; Benten, Muhammad S.; Arenstorf, Norbert S.; Ramanan, Aruna V.

    1990-01-01

    The use of Force, a parallel, portable FORTRAN on shared memory parallel computers is described. Force simplifies writing code for parallel computers and, once the parallel code is written, it is easily ported to computers on which Force is installed. Although Force is nearly the same for all computers, specific details are included for the Cray-2, Cray-YMP, Convex 220, Flex/32, Encore, Sequent, Alliant computers on which it is installed.

  3. Automatic Multilevel Parallelization Using OpenMP

    NASA Technical Reports Server (NTRS)

    Jin, Hao-Qiang; Jost, Gabriele; Yan, Jerry; Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Biegel, Bryan (Technical Monitor)

    2002-01-01

    In this paper we describe the extension of the CAPO (CAPtools (Computer Aided Parallelization Toolkit) OpenMP) parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report some results for several benchmark codes and one full application that have been parallelized using our system.

  4. The electron signature of parallel electric fields

    NASA Astrophysics Data System (ADS)

    Burch, J. L.; Gurgiolo, C.; Menietti, J. D.

    1990-12-01

    Dynamics Explorer I High-Altitude Plasma Instrument electron data are presented. The electron distribution functions have characteristics expected of a region of parallel electric fields. The data are consistent with previous test-particle simulations for observations within parallel electric field regions which indicate that typical hole, bump, and loss-cone electron distributions, which contain evidence for parallel potential differences both above and below the point of observation, are not expected to occur in regions containing actual parallel electric fields.

  5. Debugging Parallel Programs with Instant Replay.

    DTIC Science & Technology

    1986-09-01

    produce the same results. In this paper we present a general solution for reproducing the execution behavior of parallel programs, termed Instant Replay...Instant Replay on the BBN Butterfly Parallel Processor, and discuss how it can be incorporated into the debugging cycle for parallel programs. This...program often do not produce the same results. In this paper we present a general solution for reproducing the execution behavior of parallel

  6. Parallel machine architecture and compiler design facilities

    NASA Technical Reports Server (NTRS)

    Kuck, David J.; Yew, Pen-Chung; Padua, David; Sameh, Ahmed; Veidenbaum, Alex

    1990-01-01

    The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role.

  7. Global Arrays Parallel Programming Toolkit

    SciTech Connect

    Nieplocha, Jaroslaw; Krishnan, Manoj Kumar; Palmer, Bruce J.; Tipparaju, Vinod; Harrison, Robert J.; Chavarría-Miranda, Daniel

    2011-01-01

    The two predominant classes of programming models for parallel computing are distributed memory and shared memory. Both shared memory and distributed memory models have advantages and shortcomings. Shared memory model is much easier to use but it ignores data locality/placement. Given the hierarchical nature of the memory subsystems in modern computers this characteristic can have a negative impact on performance and scalability. Careful code restructuring to increase data reuse and replacing fine grain load/stores with block access to shared data can address the problem and yield performance for shared memory that is competitive with message-passing. However, this performance comes at the cost of compromising the ease of use that the shared memory model advertises. Distributed memory models, such as message-passing or one-sided communication, offer performance and scalability but they are difficult to program. The Global Arrays toolkit attempts to offer the best features of both models. It implements a shared-memory programming model in which data locality is managed by the programmer. This management is achieved by calls to functions that transfer data between a global address space (a distributed array) and local storage. In this respect, the GA model has similarities to the distributed shared-memory models that provide an explicit acquire/release protocol. However, the GA model acknowledges that remote data is slower to access than local data and allows data locality to be specified by the programmer and hence managed. GA is related to the global address space languages such as UPC, Titanium, and, to a lesser extent, Co-Array Fortran. In addition, by providing a set of data-parallel operations, GA is also related to data-parallel languages such as HPF, ZPL, and Data Parallel C. However, the Global Array programming model is implemented as a library that works with most languages used for technical computing and does not rely on compiler technology for achieving

  8. High Performance Parallel Computational Nanotechnology

    NASA Technical Reports Server (NTRS)

    Saini, Subhash; Craw, James M. (Technical Monitor)

    1995-01-01

    At a recent press conference, NASA Administrator Dan Goldin encouraged NASA Ames Research Center to take a lead role in promoting research and development of advanced, high-performance computer technology, including nanotechnology. Manufacturers of leading-edge microprocessors currently perform large-scale simulations in the design and verification of semiconductor devices and microprocessors. Recently, the need for this intensive simulation and modeling analysis has greatly increased, due in part to the ever-increasing complexity of these devices, as well as the lessons of experiences such as the Pentium fiasco. Simulation, modeling, testing, and validation will be even more important for designing molecular computers because of the complex specification of millions of atoms, thousands of assembly steps, as well as the simulation and modeling needed to ensure reliable, robust and efficient fabrication of the molecular devices. The software for this capacity does not exist today, but it can be extrapolated from the software currently used in molecular modeling for other applications: semi-empirical methods, ab initio methods, self-consistent field methods, Hartree-Fock methods, molecular mechanics; and simulation methods for diamondoid structures. In as much as it seems clear that the application of such methods in nanotechnology will require powerful, highly powerful systems, this talk will discuss techniques and issues for performing these types of computations on parallel systems. We will describe system design issues (memory, I/O, mass storage, operating system requirements, special user interface issues, interconnects, bandwidths, and programming languages) involved in parallel methods for scalable classical, semiclassical, quantum, molecular mechanics, and continuum models; molecular nanotechnology computer-aided designs (NanoCAD) techniques; visualization using virtual reality techniques of structural models and assembly sequences; software required to

  9. Precisely-controlled fabrication of single ZnO nanoemitter arrays and their possible application in low energy parallel electron beam exposure.

    PubMed

    He, H; She, J C; Huang, Y F; Deng, S Z; Xu, N S

    2012-03-21

    Precisely-controlled fabrication of single ZnO nanoemitter arrays and their possible application in low energy parallel electron beam exposure are reported. A well defined polymethyl methacrylate (PMMA) nanohole template was employed for local solution-phase growth of single ZnO nanoemitter arrays. Chlorine plasma etching for surface smoothing and pulsed-laser illumination in nitrogen for nitrogen doping were performed, which can significantly enhance the electron emission and improve the emitter-to-emitter uniformity in performance. Mechanisms responsible for the field emission enhancing effect are proposed. Low voltage (368 V) e-beam exposure was performed by using a ZnO nanoemitter array and a periodical hole pattern (0.72-1.26 μm in diameter) was produced on a thin (25 nm) PMMA. The work demonstrates the feasibility of utilizing single ZnO nano-field emitter arrays for low voltage parallel electron beam lithography.

  10. Parallel Computing Using Web Servers and "Servlets".

    ERIC Educational Resources Information Center

    Lo, Alfred; Bloor, Chris; Choi, Y. K.

    2000-01-01

    Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

  11. Identifying, Quantifying, Extracting and Enhancing Implicit Parallelism

    ERIC Educational Resources Information Center

    Agarwal, Mayank

    2009-01-01

    The shift of the microprocessor industry towards multicore architectures has placed a huge burden on the programmers by requiring explicit parallelization for performance. Implicit Parallelization is an alternative that could ease the burden on programmers by parallelizing applications "under the covers" while maintaining sequential semantics…

  12. 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…

  13. Coordination in serial-parallel image processing

    NASA Astrophysics Data System (ADS)

    Wójcik, Waldemar; Dubovoi, Vladymyr M.; Duda, Marina E.; Romaniuk, Ryszard S.; Yesmakhanova, Laura; Kozbakova, Ainur

    2015-12-01

    Serial-parallel systems used to convert the image. The control of their work results with the need to solve coordination problem. The paper summarizes the model of coordination of resource allocation in relation to the task of synchronizing parallel processes; the genetic algorithm of coordination developed, its adequacy verified in relation to the process of parallel image processing.

  14. Scalable Parallel Algebraic Multigrid Solvers

    SciTech Connect

    Bank, R; Lu, S; Tong, C; Vassilevski, P

    2005-03-23

    The authors propose a parallel algebraic multilevel algorithm (AMG), which has the novel feature that the subproblem residing in each processor is defined over the entire partition domain, although the vast majority of unknowns for each subproblem are associated with the partition owned by the corresponding processor. This feature ensures that a global coarse description of the problem is contained within each of the subproblems. The advantages of this approach are that interprocessor communication is minimized in the solution process while an optimal order of convergence rate is preserved; and the speed of local subproblem solvers can be maximized using the best existing sequential algebraic solvers.

  15. Parallel Assembly of LIGA Components

    SciTech Connect

    Christenson, T.R.; Feddema, J.T.

    1999-03-04

    In this paper, a prototype robotic workcell for the parallel assembly of LIGA components is described. A Cartesian robot is used to press 386 and 485 micron diameter pins into a LIGA substrate and then place a 3-inch diameter wafer with LIGA gears onto the pins. Upward and downward looking microscopes are used to locate holes in the LIGA substrate, pins to be pressed in the holes, and gears to be placed on the pins. This vision system can locate parts within 3 microns, while the Cartesian manipulator can place the parts within 0.4 microns.

  16. True Shear Parallel Plate Viscometer

    NASA Technical Reports Server (NTRS)

    Ethridge, Edwin; Kaukler, William

    2010-01-01

    This viscometer (which can also be used as a rheometer) is designed for use with liquids over a large temperature range. The device consists of horizontally disposed, similarly sized, parallel plates with a precisely known gap. The lower plate is driven laterally with a motor to apply shear to the liquid in the gap. The upper plate is freely suspended from a double-arm pendulum with a sufficiently long radius to reduce height variations during the swing to negligible levels. A sensitive load cell measures the shear force applied by the liquid to the upper plate. Viscosity is measured by taking the ratio of shear stress to shear rate.

  17. Scheduling Tasks In Parallel Processing

    NASA Technical Reports Server (NTRS)

    Price, Camille C.; Salama, Moktar A.

    1989-01-01

    Algorithms sought to minimize time and cost of computation. Report describes research on scheduling of computations tasks in system of multiple identical data processors operating in parallel. Computational intractability requires use of suboptimal heuristic algorithms. First algorithm called "list heuristic", variation of classical list scheduling. Second algorithm called "cluster heuristic" applied to tightly coupled tasks and consists of four phases. Third algorithm called "exchange heuristic", iterative-improvement algorithm beginning with initial feasible assignment of tasks to processors and periods of time. Fourth algorithm is iterative one for optimal assignment of tasks and based on concept called "simulated annealing" because of mathematical resemblance to aspects of physical annealing processes.

  18. Heart Fibrillation and Parallel Supercomputers

    NASA Technical Reports Server (NTRS)

    Kogan, B. Y.; Karplus, W. J.; Chudin, E. E.

    1997-01-01

    The Luo and Rudy 3 cardiac cell mathematical model is implemented on the parallel supercomputer CRAY - T3D. The splitting algorithm combined with variable time step and an explicit method of integration provide reasonable solution times and almost perfect scaling for rectilinear wave propagation. The computer simulation makes it possible to observe new phenomena: the break-up of spiral waves caused by intracellular calcium and dynamics and the non-uniformity of the calcium distribution in space during the onset of the spiral wave.

  19. Ammonia synthesis

    SciTech Connect

    Mandelik, B.G.; Cassata, J.R.; Katy, P.J.S.; Van Dijk, C.P.

    1986-02-04

    In a process for producing ammonia in a synthesis loop in which fresh synthesis gas containing hydrogen, nitrogen and, lesser amounts of argon and methane is combined with a hydrogen enriched recycle gas to provide combined synthesis gas, the combined synthesis is introduced to and reacted over ammonia synthesis catalyst under synthesis conditions to provide converted gas containing ammonia, hydrogen, and nitrogen. The ammonia is recovered from the converted gas to provide recycle gas, and a purge stream is removed from the synthesis loop. A hydrogen-rich gas is recovered from the purge stream, and the hydrogen-rich gas is combined with the recycle gas to provide the hydrogen enriched gas. The improvement described in this patent consists of (a) providing the fresh synthesis gas at a hydrogen to nitrogen molar ratio between 1.7 and 2.5 and providing the hydrogen enriched recycle gas at a hydrogen to nitrogen molar ratio between 0.5 and 1.7 to provide the combined synthesis gas at a hydrogen to nitrogen molar ratio between 0.8 and 1.8. The volumetric flow rate ratio of the hydrogen enriched recycle gas to the fresh synthesis gas is between 2.2 and 3.7; and (b) introducing the combined synthesis gas from step (a) to an ammonia synthesis catalyst at a temperature between 315/sup 0/C. and 400/sup 0/C. and a pressure between 50 kg/cm/sup 2/ and 150 kg/cm/sup 2/.

  20. Xyce parallel electronic simulator design.

    SciTech Connect

    Thornquist, Heidi K.; Rankin, Eric Lamont; Mei, Ting; Schiek, Richard Louis; Keiter, Eric Richard; Russo, Thomas V.

    2010-09-01

    This document is the Xyce Circuit Simulator developer guide. Xyce has been designed from the 'ground up' to be a SPICE-compatible, distributed memory parallel circuit simulator. While it is in many respects a research code, Xyce is intended to be a production simulator. As such, having software quality engineering (SQE) procedures in place to insure a high level of code quality and robustness are essential. Version control, issue tracking customer support, C++ style guildlines and the Xyce release process are all described. The Xyce Parallel Electronic Simulator has been under development at Sandia since 1999. Historically, Xyce has mostly been funded by ASC, the original focus of Xyce development has primarily been related to circuits for nuclear weapons. However, this has not been the only focus and it is expected that the project will diversify. Like many ASC projects, Xyce is a group development effort, which involves a number of researchers, engineers, scientists, mathmaticians and computer scientists. In addition to diversity of background, it is to be expected on long term projects for there to be a certain amount of staff turnover, as people move on to different projects. As a result, it is very important that the project maintain high software quality standards. The point of this document is to formally document a number of the software quality practices followed by the Xyce team in one place. Also, it is hoped that this document will be a good source of information for new developers.

  1. Parallel job-scheduling algorithms

    SciTech Connect

    Rodger, S.H.

    1989-01-01

    In this thesis, we consider solving job scheduling problems on the CREW PRAM model. We show how to adapt Cole's pipeline merge technique to yield several efficient parallel algorithms for a number of job scheduling problems and one optimal parallel algorithm for the following job scheduling problem: Given a set of n jobs defined by release times, deadlines and processing times, find a schedule that minimizes the maximum lateness of the jobs and allows preemption when the jobs are scheduled to run on one machine. In addition, we present the first NC algorithm for the following job scheduling problem: Given a set of n jobs defined by release times, deadlines and unit processing times, determine if there is a schedule of jobs on one machine, and calculate the schedule if it exists. We identify the notion of a canonical schedule, which is the type of schedule our algorithm computes if there is a schedule. Our algorithm runs in O((log n){sup 2}) time and uses O(n{sup 2}k{sup 2}) processors, where k is the minimum number of distinct offsets of release times or deadlines.

  2. Partitioning in parallel processing of production systems

    SciTech Connect

    Oflazer, K.

    1987-01-01

    This thesis presents research on certain issues related to parallel processing of production systems. It first presents a parallel production system interpreter that has been implemented on a four-processor multiprocessor. This parallel interpreter is based on Forgy's OPS5 interpreter and exploits production-level parallelism in production systems. Runs on the multiprocessor system indicate that it is possible to obtain speed-up of around 1.7 in the match computation for certain production systems when productions are split into three sets that are processed in parallel. The next issue addressed is that of partitioning a set of rules to processors in a parallel interpreter with production-level parallelism, and the extent of additional improvement in performance. The partitioning problem is formulated and an algorithm for approximate solutions is presented. The thesis next presents a parallel processing scheme for OPS5 production systems that allows some redundancy in the match computation. This redundancy enables the processing of a production to be divided into units of medium granularity each of which can be processed in parallel. Subsequently, a parallel processor architecture for implementing the parallel processing algorithm is presented.

  3. Bioinspired synthesis of magnetic nanoparticles

    SciTech Connect

    David, Anand

    2009-01-01

    goal of this project is to understand the mechanism of magnetite particle synthesis in the presence of the biomineralization proteins, mms6 and C25. Previous work has hypothesized that the mms6 protein helps to template magnetite and cobalt ferrite particle synthesis and that the C25 protein templates cobalt ferrite formation. However, the effect of parameters such as the protein concentration on the particle formation is still unknown. It is expected that the protein concentration significantly affects the nucleation and growth of magnetite. Since the protein provides iron-binding sites, it is expected that magnetite crystals would nucleate at those sites. In addition, in the previous work, the reaction medium after completion of the reaction was in the solution phase, and magnetic particles had a tendency to fall to the bottom of the medium and aggregate. The research presented in this thesis involves solid Pluronic gel phase reactions, which can be studied readily using small-angle x-ray scattering, which is not possible for the solution phase experiments. In addition, the concentration effect of both of the proteins on magnetite crystal formation was studied.

  4. ProperCAD: A portable object-oriented parallel environment for VLSI CAD

    NASA Technical Reports Server (NTRS)

    Ramkumar, Balkrishna; Banerjee, Prithviraj

    1993-01-01

    Most parallel algorithms for VLSI CAD proposed to date have one important drawback: they work efficiently only on machines that they were designed for. As a result, algorithms designed to date are dependent on the architecture for which they are developed and do not port easily to other parallel architectures. A new project under way to address this problem is described. A Portable object-oriented parallel environment for CAD algorithms (ProperCAD) is being developed. The objectives of this research are (1) to develop new parallel algorithms that run in a portable object-oriented environment (CAD algorithms using a general purpose platform for portable parallel programming called CARM is being developed and a C++ environment that is truly object-oriented and specialized for CAD applications is also being developed); and (2) to design the parallel algorithms around a good sequential algorithm with a well-defined parallel-sequential interface (permitting the parallel algorithm to benefit from future developments in sequential algorithms). One CAD application that has been implemented as part of the ProperCAD project, flat VLSI circuit extraction, is described. The algorithm, its implementation, and its performance on a range of parallel machines are discussed in detail. It currently runs on an Encore Multimax, a Sequent Symmetry, Intel iPSC/2 and i860 hypercubes, a NCUBE 2 hypercube, and a network of Sun Sparc workstations. Performance data for other applications that were developed are provided: namely test pattern generation for sequential circuits, parallel logic synthesis, and standard cell placement.

  5. Parallel processing for scientific computations

    NASA Technical Reports Server (NTRS)

    Alkhatib, Hasan S.

    1991-01-01

    The main contribution of the effort in the last two years is the introduction of the MOPPS system. After doing extensive literature search, we introduced the system which is described next. MOPPS employs a new solution to the problem of managing programs which solve scientific and engineering applications on a distributed processing environment. Autonomous computers cooperate efficiently in solving large scientific problems with this solution. MOPPS has the advantage of not assuming the presence of any particular network topology or configuration, computer architecture, or operating system. It imposes little overhead on network and processor resources while efficiently managing programs concurrently. The core of MOPPS is an intelligent program manager that builds a knowledge base of the execution performance of the parallel programs it is managing under various conditions. The manager applies this knowledge to improve the performance of future runs. The program manager learns from experience.

  6. Hybrid Optimization Parallel Search PACKage

    SciTech Connect

    2009-11-10

    HOPSPACK is open source software for solving optimization problems without derivatives. Application problems may have a fully nonlinear objective function, bound constraints, and linear and nonlinear constraints. Problem variables may be continuous, integer-valued, or a mixture of both. The software provides a framework that supports any derivative-free type of solver algorithm. Through the framework, solvers request parallel function evaluation, which may use MPI (multiple machines) or multithreading (multiple processors/cores on one machine). The framework provides a Cache and Pending Cache of saved evaluations that reduces execution time and facilitates restarts. Solvers can dynamically create other algorithms to solve subproblems, a useful technique for handling multiple start points and integer-valued variables. HOPSPACK ships with the Generating Set Search (GSS) algorithm, developed at Sandia as part of the APPSPACK open source software project.

  7. Parallel Performance Characterization of Columbia

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak

    2004-01-01

    Using a collection of benchmark problems of increasing levels of realism and computational effort, we will characterize the strengths and limitations of the 10,240 processor Columbia system to deliver supercomputing value to application scientists. Scientists need to be able to determine if and how they can utilize Columbia to carry extreme workloads, either in terms of ultra-large applications that cannot be run otherwise (capability), or in terms of very large ensembles of medium-scale applications to populate response matrices (capacity). We select existing application benchmarks that scale from a small number of processors to the entire machine, and that highlight different issues in running supercomputing-calss applicaions, such as the various types of memory access, file I/O, inter- and intra-node communications and parallelization paradigms. http://www.nas.nasa.gov/Software/NPB/

  8. Information hiding in parallel programs

    SciTech Connect

    Foster, I.

    1992-01-30

    A fundamental principle in program design is to isolate difficult or changeable design decisions. Application of this principle to parallel programs requires identification of decisions that are difficult or subject to change, and the development of techniques for hiding these decisions. We experiment with three complex applications, and identify mapping, communication, and scheduling as areas in which decisions are particularly problematic. We develop computational abstractions that hide such decisions, and show that these abstractions can be used to develop elegant solutions to programming problems. In particular, they allow us to encode common structures, such as transforms, reductions, and meshes, as software cells and templates that can reused in different applications. An important characteristic of these structures is that they do not incorporate mapping, communication, or scheduling decisions: these aspects of the design are specified separately, when composing existing structures to form applications. This separation of concerns allows the same cells and templates to be reused in different contexts.

  9. Embodied and Distributed Parallel DJing.

    PubMed

    Cappelen, Birgitta; Andersson, Anders-Petter

    2016-01-01

    Everyone has a right to take part in cultural events and activities, such as music performances and music making. Enforcing that right, within Universal Design, is often limited to a focus on physical access to public areas, hearing aids etc., or groups of persons with special needs performing in traditional ways. The latter might be people with disabilities, being musicians playing traditional instruments, or actors playing theatre. In this paper we focus on the innovative potential of including people with special needs, when creating new cultural activities. In our project RHYME our goal was to create health promoting activities for children with severe disabilities, by developing new musical and multimedia technologies. Because of the users' extreme demands and rich contribution, we ended up creating both a new genre of musical instruments and a new art form. We call this new art form Embodied and Distributed Parallel DJing, and the new genre of instruments for Empowering Multi-Sensorial Things.

  10. Parallel spinors on flat manifolds

    NASA Astrophysics Data System (ADS)

    Sadowski, Michał

    2006-05-01

    Let p(M) be the dimension of the vector space of parallel spinors on a closed spin manifold M. We prove that every finite group G is the holonomy group of a closed flat spin manifold M(G) such that p(M(G))>0. If the holonomy group Hol(M) of M is cyclic, then we give an explicit formula for p(M) another than that given in [R.J. Miatello, R.A. Podesta, The spectrum of twisted Dirac operators on compact flat manifolds, Trans. Am. Math. Soc., in press]. We answer the question when p(M)>0 if Hol(M) is a cyclic group of prime order or dim⁡M≤4.

  11. Device for balancing parallel strings

    DOEpatents

    Mashikian, Matthew S.

    1985-01-01

    A battery plant is described which features magnetic circuit means in association with each of the battery strings in the battery plant for balancing the electrical current flow through the battery strings by equalizing the voltage across each of the battery strings. Each of the magnetic circuit means generally comprises means for sensing the electrical current flow through one of the battery strings, and a saturable reactor having a main winding connected electrically in series with the battery string, a bias winding connected to a source of alternating current and a control winding connected to a variable source of direct current controlled by the sensing means. Each of the battery strings is formed by a plurality of batteries connected electrically in series, and these battery strings are connected electrically in parallel across common bus conductors.

  12. Parallel network simulations with NEURON.

    PubMed

    Migliore, M; Cannia, C; Lytton, W W; Markram, Henry; Hines, M L

    2006-10-01

    The NEURON simulation environment has been extended to support parallel network simulations. Each processor integrates the equations for its subnet over an interval equal to the minimum (interprocessor) presynaptic spike generation to postsynaptic spike delivery connection delay. The performance of three published network models with very different spike patterns exhibits superlinear speedup on Beowulf clusters and demonstrates that spike communication overhead is often less than the benefit of an increased fraction of the entire problem fitting into high speed cache. On the EPFL IBM Blue Gene, almost linear speedup was obtained up to 100 processors. Increasing one model from 500 to 40,000 realistic cells exhibited almost linear speedup on 2,000 processors, with an integration time of 9.8 seconds and communication time of 1.3 seconds. The potential for speed-ups of several orders of magnitude makes practical the running of large network simulations that could otherwise not be explored.

  13. Parallel computing in enterprise modeling.

    SciTech Connect

    Goldsby, Michael E.; Armstrong, Robert C.; Shneider, Max S.; Vanderveen, Keith; Ray, Jaideep; Heath, Zach; Allan, Benjamin A.

    2008-08-01

    This report presents the results of our efforts to apply high-performance computing to entity-based simulations with a multi-use plugin for parallel computing. We use the term 'Entity-based simulation' to describe a class of simulation which includes both discrete event simulation and agent based simulation. What simulations of this class share, and what differs from more traditional models, is that the result sought is emergent from a large number of contributing entities. Logistic, economic and social simulations are members of this class where things or people are organized or self-organize to produce a solution. Entity-based problems never have an a priori ergodic principle that will greatly simplify calculations. Because the results of entity-based simulations can only be realized at scale, scalable computing is de rigueur for large problems. Having said that, the absence of a spatial organizing principal makes the decomposition of the problem onto processors problematic. In addition, practitioners in this domain commonly use the Java programming language which presents its own problems in a high-performance setting. The plugin we have developed, called the Parallel Particle Data Model, overcomes both of these obstacles and is now being used by two Sandia frameworks: the Decision Analysis Center, and the Seldon social simulation facility. While the ability to engage U.S.-sized problems is now available to the Decision Analysis Center, this plugin is central to the success of Seldon. Because Seldon relies on computationally intensive cognitive sub-models, this work is necessary to achieve the scale necessary for realistic results. With the recent upheavals in the financial markets, and the inscrutability of terrorist activity, this simulation domain will likely need a capability with ever greater fidelity. High-performance computing will play an important part in enabling that greater fidelity.

  14. Integrated Task and Data Parallel Programming

    NASA Technical Reports Server (NTRS)

    Grimshaw, A. S.

    1998-01-01

    This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated

  15. Computer-Aided Parallelizer and Optimizer

    NASA Technical Reports Server (NTRS)

    Jin, Haoqiang

    2011-01-01

    The Computer-Aided Parallelizer and Optimizer (CAPO) automates the insertion of compiler directives (see figure) to facilitate parallel processing on Shared Memory Parallel (SMP) machines. While CAPO currently is integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise), CAPO was independently developed at Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedural data dependence analysis, and generates OpenMP directives. Due to the widely supported OpenMP standard, the generated OpenMP codes have the potential to run on a wide range of SMP machines. CAPO relies on accurate interprocedural data dependence information currently provided by CAPTools. Compiler directives are generated through identification of parallel loops in the outermost level, construction of parallel regions around parallel loops and optimization of parallel regions, and insertion of directives with automatic identification of private, reduction, induction, and shared variables. Attempts also have been made to identify potential pipeline parallelism (implemented with point-to-point synchronization). Although directives are generated automatically, user interaction with the tool is still important for producing good parallel codes. A comprehensive graphical user interface is included for users to interact with the parallelization process.

  16. Parallel processing considerations for image recognition tasks

    NASA Astrophysics Data System (ADS)

    Simske, Steven J.

    2011-01-01

    Many image recognition tasks are well-suited to parallel processing. The most obvious example is that many imaging tasks require the analysis of multiple images. From this standpoint, then, parallel processing need be no more complicated than assigning individual images to individual processors. However, there are three less trivial categories of parallel processing that will be considered in this paper: parallel processing (1) by task; (2) by image region; and (3) by meta-algorithm. Parallel processing by task allows the assignment of multiple workflows-as diverse as optical character recognition [OCR], document classification and barcode reading-to parallel pipelines. This can substantially decrease time to completion for the document tasks. For this approach, each parallel pipeline is generally performing a different task. Parallel processing by image region allows a larger imaging task to be sub-divided into a set of parallel pipelines, each performing the same task but on a different data set. This type of image analysis is readily addressed by a map-reduce approach. Examples include document skew detection and multiple face detection and tracking. Finally, parallel processing by meta-algorithm allows different algorithms to be deployed on the same image simultaneously. This approach may result in improved accuracy.

  17. Superresolution of interference fringes in parallel four-step phase-shifting digital holography.

    PubMed

    Tahara, Tatsuki; Lee, Yonghee; Ito, Yasunori; Xia, Peng; Shimozato, Yuki; Takahashi, Yuki; Awatsuji, Yasuhiro; Nishio, Kenzo; Ura, Shogo; Kubota, Toshihiro; Matoba, Osamu

    2014-03-15

    A superresolution method for interference fringes obtained by parallel four-step phase-shifting digital holography is proposed. A complex amplitude distribution of an object wave is derived from a recorded hologram by parallel phase-shifting interferometry using two pixels without any interpolation procedures. Multiple distributions are derived by changing one of the two pixels when conducting phase-shifting interferometry. The angular spectrum distribution of the object wave is obtained by both the Fourier transforms and synthesis of the spectrum distribution from the Fourier-transformed images in the spatial frequency domain. Available space bandwidth is extended to half of that of an image sensor.

  18. Magnesium Solution Phase Catholyte Seawater Electrochemical System

    DTIC Science & Technology

    1999-03-02

    battery is placed in salt water . The � patent also describes 19 a method of producing electricity by positioning the anode and 20 cathode in a...by a line 26 16 with a source of an electrolyte such as sea water . Also 17 connected by a line 28 under the control of a valve 30 to the 18 suction...6.69 Whr/g 8 Mg - NaOCl 3.60 V 1.42 Ahr/g 5.11 Whr/g 9 Mg - AgCl 2.92 V 0.35 Ahr/g 1.02 Whr/g 10 Mg - CuCl 2.84 V 0.48 Ahr/g 1.36 Whr

  19. Towards Distributed Memory Parallel Program Analysis

    SciTech Connect

    Quinlan, D; Barany, G; Panas, T

    2008-06-17

    This paper presents a parallel attribute evaluation for distributed memory parallel computer architectures where previously only shared memory parallel support for this technique has been developed. Attribute evaluation is a part of how attribute grammars are used for program analysis within modern compilers. Within this work, we have extended ROSE, a open compiler infrastructure, with a distributed memory parallel attribute evaluation mechanism to support user defined global program analysis required for some forms of security analysis which can not be addressed by a file by file view of large scale applications. As a result, user defined security analyses may now run in parallel without the user having to specify the way data is communicated between processors. The automation of communication enables an extensible open-source parallel program analysis infrastructure.

  20. Runtime volume visualization for parallel CFD

    NASA Technical Reports Server (NTRS)

    Ma, Kwan-Liu

    1995-01-01

    This paper discusses some aspects of design of a data distributed, massively parallel volume rendering library for runtime visualization of parallel computational fluid dynamics simulations in a message-passing environment. Unlike the traditional scheme in which visualization is a postprocessing step, the rendering is done in place on each node processor. Computational scientists who run large-scale simulations on a massively parallel computer can thus perform interactive monitoring of their simulations. The current library provides an interface to handle volume data on rectilinear grids. The same design principles can be generalized to handle other types of grids. For demonstration, we run a parallel Navier-Stokes solver making use of this rendering library on the Intel Paragon XP/S. The interactive visual response achieved is found to be very useful. Performance studies show that the parallel rendering process is scalable with the size of the simulation as well as with the parallel computer.

  1. Parallel reactor systems for bioprocess development.

    PubMed

    Weuster-Botz, Dirk

    2005-01-01

    Controlled parallel bioreactor systems allow fed-batch operation at early stages of process development. The characteristics of shaken bioreactors operated in parallel (shake flask, microtiter plate), sparged bioreactors (small-scale bubble column) and stirred bioreactors (stirred-tank, stirred column) are briefly summarized. Parallel fed-batch operation is achieved with an intermittent feeding and pH-control system for up to 16 bioreactors operated in parallel on a scale of 100 ml. Examples of the scale-up and scale-down of pH-controlled microbial fed-batch processes demonstrate that controlled parallel reactor systems can result in more effective bioprocess development. Future developments are also outlined, including units of 48 parallel stirred-tank reactors with individual pH- and pO2-controls and automation as well as liquid handling system, operated on a scale of ml.

  2. Linearly exact parallel closures for slab geometry

    NASA Astrophysics Data System (ADS)

    Ji, Jeong-Young; Held, Eric D.; Jhang, Hogun

    2013-08-01

    Parallel closures are obtained by solving a linearized kinetic equation with a model collision operator using the Fourier transform method. The closures expressed in wave number space are exact for time-dependent linear problems to within the limits of the model collision operator. In the adiabatic, collisionless limit, an inverse Fourier transform is performed to obtain integral (nonlocal) parallel closures in real space; parallel heat flow and viscosity closures for density, temperature, and flow velocity equations replace Braginskii's parallel closure relations, and parallel flow velocity and heat flow closures for density and temperature equations replace Spitzer's parallel transport relations. It is verified that the closures reproduce the exact linear response function of Hammett and Perkins [Phys. Rev. Lett. 64, 3019 (1990)] for Landau damping given a temperature gradient. In contrast to their approximate closures where the vanishing viscosity coefficient numerically gives an exact response, our closures relate the heat flow and nonvanishing viscosity to temperature and flow velocity (gradients).

  3. Design considerations for parallel graphics libraries

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas W.

    1994-01-01

    Applications which run on parallel supercomputers are often characterized by massive datasets. Converting these vast collections of numbers to visual form has proven to be a powerful aid to comprehension. For a variety of reasons, it may be desirable to provide this visual feedback at runtime. One way to accomplish this is to exploit the available parallelism to perform graphics operations in place. In order to do this, we need appropriate parallel rendering algorithms and library interfaces. This paper provides a tutorial introduction to some of the issues which arise in designing parallel graphics libraries and their underlying rendering algorithms. The focus is on polygon rendering for distributed memory message-passing systems. We illustrate our discussion with examples from PGL, a parallel graphics library which has been developed on the Intel family of parallel systems.

  4. Automatic Multilevel Parallelization Using OpenMP

    NASA Technical Reports Server (NTRS)

    Jin, Hao-Qiang; Jost, Gabriele; Yan, Jerry; Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Biegel, Bryan (Technical Monitor)

    2002-01-01

    In this paper we describe the extension of the CAPO parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report first results for several benchmark codes and one full application that have been parallelized using our system.

  5. Inverse Kinematics for a Parallel Myoelectric Elbow

    DTIC Science & Technology

    2001-10-25

    Inverse Kinematics for a Parallel Myoelectric Elbow A. Z. Escudero, Ja. Álvarez, L. Leija. Center of Research and Advanced Studies of the IPN...replacement above elbow are serial mechanisms driven by a DC motor and they include only one active articulation for the elbow [1]. Parallel mechanisms...are rather scarce [2]. The inverse kinematics model of a 3-degree of freedom parallel prosthetic elbow mechanism is reported. The mathematical

  6. Parallel computations and control of adaptive structures

    NASA Technical Reports Server (NTRS)

    Park, K. C.; Alvin, Kenneth F.; Belvin, W. Keith; Chong, K. P. (Editor); Liu, S. C. (Editor); Li, J. C. (Editor)

    1991-01-01

    The equations of motion for structures with adaptive elements for vibration control are presented for parallel computations to be used as a software package for real-time control of flexible space structures. A brief introduction of the state-of-the-art parallel computational capability is also presented. Time marching strategies are developed for an effective use of massive parallel mapping, partitioning, and the necessary arithmetic operations. An example is offered for the simulation of control-structure interaction on a parallel computer and the impact of the approach presented for applications in other disciplines than aerospace industry is assessed.

  7. Parallel auto-correlative statistics with VTK.

    SciTech Connect

    Pebay, Philippe Pierre; Bennett, Janine Camille

    2013-08-01

    This report summarizes existing statistical engines in VTK and presents both the serial and parallel auto-correlative statistics engines. It is a sequel to [PT08, BPRT09b, PT09, BPT09, PT10] which studied the parallel descriptive, correlative, multi-correlative, principal component analysis, contingency, k-means, and order statistics engines. The ease of use of the new parallel auto-correlative statistics engine is illustrated by the means of C++ code snippets and algorithm verification is provided. This report justifies the design of the statistics engines with parallel scalability in mind, and provides scalability and speed-up analysis results for the autocorrelative statistics engine.

  8. Parallel programming in Split-C

    SciTech Connect

    Culler, D.E.; Dusseau, A.; Goldstein, S.C.; Krishnamurthy, A.; Lumetta, S.; Eicken, T. von; Yelick, K.

    1993-12-31

    The authors introduce the Split-C language, a parallel extension of C intended for high performance programming on distributed memory multiprocessors, and demonstrate the use of the language in optimizing parallel programs. Split-C provides a global address space with a clear concept of locality and unusual assignment operators. These are used as tools to reduce the frequency and cost of remote access. The language allows a mixture of shared memory, message passing, and data parallel programming styles while providing efficient access to the underlying machine. They demonstrate the basic language concepts using regular and irregular parallel programs and give performance results for various stages of program optimization.

  9. Shared-memory parallel programming in C++

    SciTech Connect

    Beck, B. )

    1990-07-01

    This paper discusses how researchers have produced a set of portable parallel-programming constructs for C, implemented in M4 macros. These parallel-programming macros are available under the name Parmacs. The Parmacs macros let one write parallel C programs for shared-memory, distributed-memory, and mixed-memory (shared and distributed) systems. They have been implemented on several machines. Because Parmacs offers useful parallel-programming features, the author has considered how these problems might be overcome or avoided. The author thought that using C++, rather than C, would address these problems adequately, and describes the C++ features exploited. The work described addresses shared-memory constructs.

  10. Parallel Algorithms for the Exascale Era

    SciTech Connect

    Robey, Robert W.

    2016-10-19

    New parallel algorithms are needed to reach the Exascale level of parallelism with millions of cores. We look at some of the research developed by students in projects at LANL. The research blends ideas from the early days of computing while weaving in the fresh approach brought by students new to the field of high performance computing. We look at reproducibility of global sums and why it is important to parallel computing. Next we look at how the concept of hashing has led to the development of more scalable algorithms suitable for next-generation parallel computers. Nearly all of this work has been done by undergraduates and published in leading scientific journals.

  11. A parallel algorithm for global routing

    NASA Technical Reports Server (NTRS)

    Brouwer, Randall J.; Banerjee, Prithviraj

    1990-01-01

    A Parallel Hierarchical algorithm for Global Routing (PHIGURE) is presented. The router is based on the work of Burstein and Pelavin, but has many extensions for general global routing and parallel execution. Main features of the algorithm include structured hierarchical decomposition into separate independent tasks which are suitable for parallel execution and adaptive simplex solution for adding feedthroughs and adjusting channel heights for row-based layout. Alternative decomposition methods and the various levels of parallelism available in the algorithm are examined closely. The algorithm is described and results are presented for a shared-memory multiprocessor implementation.

  12. Conformal pure radiation with parallel rays

    NASA Astrophysics Data System (ADS)

    Leistner, Thomas; Nurowski, Paweł

    2012-03-01

    We define pure radiation metrics with parallel rays to be n-dimensional pseudo-Riemannian metrics that admit a parallel null line bundle K and whose Ricci tensor vanishes on vectors that are orthogonal to K. We give necessary conditions in terms of the Weyl, Cotton and Bach tensors for a pseudo-Riemannian metric to be conformal to a pure radiation metric with parallel rays. Then, we derive conditions in terms of the tractor calculus that are equivalent to the existence of a pure radiation metric with parallel rays in a conformal class. We also give analogous results for n-dimensional pseudo-Riemannian pp-waves.

  13. Parallel Genetic Algorithm for Alpha Spectra Fitting

    NASA Astrophysics Data System (ADS)

    García-Orellana, Carlos J.; Rubio-Montero, Pilar; González-Velasco, Horacio

    2005-01-01

    We present a performance study of alpha-particle spectra fitting using parallel Genetic Algorithm (GA). The method uses a two-step approach. In the first step we run parallel GA to find an initial solution for the second step, in which we use Levenberg-Marquardt (LM) method for a precise final fit. GA is a high resources-demanding method, so we use a Beowulf cluster for parallel simulation. The relationship between simulation time (and parallel efficiency) and processors number is studied using several alpha spectra, with the aim of obtaining a method to estimate the optimal processors number that must be used in a simulation.

  14. Parallel processing for scientific computations

    NASA Technical Reports Server (NTRS)

    Alkhatib, Hasan S.

    1995-01-01

    The scope of this project dealt with the investigation of the requirements to support distributed computing of scientific computations over a cluster of cooperative workstations. Various experiments on computations for the solution of simultaneous linear equations were performed in the early phase of the project to gain experience in the general nature and requirements of scientific applications. A specification of a distributed integrated computing environment, DICE, based on a distributed shared memory communication paradigm has been developed and evaluated. The distributed shared memory model facilitates porting existing parallel algorithms that have been designed for shared memory multiprocessor systems to the new environment. The potential of this new environment is to provide supercomputing capability through the utilization of the aggregate power of workstations cooperating in a cluster interconnected via a local area network. Workstations, generally, do not have the computing power to tackle complex scientific applications, making them primarily useful for visualization, data reduction, and filtering as far as complex scientific applications are concerned. There is a tremendous amount of computing power that is left unused in a network of workstations. Very often a workstation is simply sitting idle on a desk. A set of tools can be developed to take advantage of this potential computing power to create a platform suitable for large scientific computations. The integration of several workstations into a logical cluster of distributed, cooperative, computing stations presents an alternative to shared memory multiprocessor systems. In this project we designed and evaluated such a system.

  15. Parallel Computing for Brain Simulation.

    PubMed

    Pastur-Romay, L A; Porto-Pazos, A B; Cedrón, F; Pazos, A

    2016-11-04

    The human brain is the most complex system in the known universe, but it is the most unknown system. It allows the human beings to possess extraordinary capacities. However, we don´t understand yet how and why most of these capacities are produced. For decades, it have been tried that the computers reproduces these capacities. On one hand, to help understanding the nervous system. On the other hand, to process the data in a more efficient way than before. It is intended to make the computers process the information like the brain does it. The important technological developments and the big multidisciplinary projects have allowed create the first simulation with a number of neurons similar to the human brain neurons number. This paper presents an update review about the main research projects that are trying of simulate and/or emulate the human brain. They employ different types of computational models using parallel computing: digital models, analog models and hybrid models. This review includes the actual applications of these works and also the future trends. We have reviewed some works that look for a step forward in Neuroscience and other ones that look for a breakthrough in Computer Science (neuromorphic hardware, machine learning techniques). We summarize the most outstanding characteristics of them and present the latest advances and future plans. In addition, this review remarks the importance of considering not only neurons: the computational models of the brain should include glial cells, given the proven importance of the astrocytes in the information processing.

  16. Parallel methods for the flight simulation model

    SciTech Connect

    Xiong, Wei Zhong; Swietlik, C.

    1994-06-01

    The Advanced Computer Applications Center (ACAC) has been involved in evaluating advanced parallel architecture computers and the applicability of these machines to computer simulation models. The advanced systems investigated include parallel machines with shared. memory and distributed architectures consisting of an eight processor Alliant FX/8, a twenty four processor sor Sequent Symmetry, Cray XMP, IBM RISC 6000 model 550, and the Intel Touchstone eight processor Gamma and 512 processor Delta machines. Since parallelizing a truly efficient application program for the parallel machine is a difficult task, the implementation for these machines in a realistic setting has been largely overlooked. The ACAC has developed considerable expertise in optimizing and parallelizing application models on a collection of advanced multiprocessor systems. One of aspect of such an application model is the Flight Simulation Model, which used a set of differential equations to describe the flight characteristics of a launched missile by means of a trajectory. The Flight Simulation Model was written in the FORTRAN language with approximately 29,000 lines of source code. Depending on the number of trajectories, the computation can require several hours to full day of CPU time on DEC/VAX 8650 system. There is an impetus to reduce the execution time and utilize the advanced parallel architecture computing environment available. ACAC researchers developed a parallel method that allows the Flight Simulation Model to be able to run in parallel on the multiprocessor system. For the benchmark data tested, the parallel Flight Simulation Model implemented on the Alliant FX/8 has achieved nearly linear speedup. In this paper, we describe a parallel method for the Flight Simulation Model. We believe the method presented in this paper provides a general concept for the design of parallel applications. This concept, in most cases, can be adapted to many other sequential application programs.

  17. Recent Improvements to HST Parallel Scheduling

    NASA Astrophysics Data System (ADS)

    Henry, Ronald; Butschky, Mike

    The Hubble Space Telescope (HST) has several scientific instruments (SIs) that may be used at any given time. Most primary visits submitted by HST observers only use one SI, leaving the other SIs free to be requested by ``pure parallel'' observing programs. In order to accomplish this, separate scheduling units (SUs) for each parallel SI must be created and then scheduled by the Science Planning and Scheduling System (SPSS), taking into account numerous orbital and scientific constraints. The Parallel Observation Matching System (POMS) has the task of matching parallel visits to primary observations and ``crafting'' appropriate parallel SUs at each opportunity, taking scientific criteria and orbital constraints into account. The process for planning and scheduling parallel observations is thus quite different from the process for primary science. In the past, custom crafting rules for each parallel program were necessary, requiring full-time support from a software developer. In addition, because POMS ran as a standalone system, its ability to model how long parallel SUs would take was limited, especially with the flexible buffer-management schemes used for the second-generation SIs. A new version of POMS was developed in 1997. This version uses a formal proposal syntax (the same used for primary observations) for parallels, so that different proposals can be handled uniformly and without the need for customized ``crafting rules.'' In addition, POMS is integrated with the Transformation (TRANS) planning system in order to give it full knowledge of overheads within an SU, eliminating the need for ad hoc modeling. The power and versatility of this approach has paid off in improved utilization of parallel opportunities, greatly reduced maintenance costs, and an ability to gracefully handle new parallel proposals and new SIs with minimal software effort. This paper discusses the requirements, design, and operational results of the new POMS.

  18. 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…

  19. 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.

  20. Prototyping Parallel and Distributed Programs in Proteus

    DTIC Science & Technology

    1990-10-01

    Cole90, Gibb89]. " Highly-parallel processors - Applications for highly-parallel machines such as the CM- 2 or the iPSC are programmed using data...Programming, (Prentice-Hall, Englewood Cliffs, NJ) 1990. [Gibb89] Gibbons , P.B., "A more practical PRAM model", in: Proceedings of the First ACM

  1. Simulation Exploration through Immersive Parallel Planes: Preprint

    SciTech Connect

    Brunhart-Lupo, Nicholas; Bush, Brian W.; Gruchalla, Kenny; Smith, Steve

    2016-03-01

    We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, each individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.

  2. Parallel computation with the spectral element method

    SciTech Connect

    Ma, Hong

    1995-12-01

    Spectral element models for the shallow water equations and the Navier-Stokes equations have been successfully implemented on a data parallel supercomputer, the Connection Machine model CM-5. The nonstaggered grid formulations for both models are described, which are shown to be especially efficient in data parallel computing environment.

  3. Predicting Protein Structure Using Parallel Genetic Algorithms.

    DTIC Science & Technology

    1994-12-01

    By " Predicting rotein Structure D istribticfiar.. ................ Using Parallel Genetic Algorithms ,Avaiu " ’ •"... Dist THESIS I IGeorge H...iiLite-d Approved for public release; distribution unlimited AFIT/ GCS /ENG/94D-03 Predicting Protein Structure Using Parallel Genetic Algorithms ...1-1 1.2 Genetic Algorithms ......... ............................ 1-3 1.3 The Protein Folding Problem

  4. Parallel Activation in Bilingual Phonological Processing

    ERIC Educational Resources Information Center

    Lee, Su-Yeon

    2011-01-01

    In bilingual language processing, the parallel activation hypothesis suggests that bilinguals activate their two languages simultaneously during language processing. Support for the parallel activation mainly comes from studies of lexical (word-form) processing, with relatively less attention to phonological (sound) processing. According to…

  5. Serial Order: A Parallel Distributed Processing Approach.

    ERIC Educational Resources Information Center

    Jordan, Michael I.

    Human behavior shows a variety of serially ordered action sequences. This paper presents a theory of serial order which describes how sequences of actions might be learned and performed. In this theory, parallel interactions across time (coarticulation) and parallel interactions across space (dual-task interference) are viewed as two aspects of a…

  6. MULTIOBJECTIVE PARALLEL GENETIC ALGORITHM FOR WASTE MINIMIZATION

    EPA Science Inventory

    In this research we have developed an efficient multiobjective parallel genetic algorithm (MOPGA) for waste minimization problems. This MOPGA integrates PGAPack (Levine, 1996) and NSGA-II (Deb, 2000) with novel modifications. PGAPack is a master-slave parallel implementation of a...

  7. Parallel Narrative Structure in Paul Harding's "Tinkers"

    ERIC Educational Resources Information Center

    Çirakli, Mustafa Zeki

    2014-01-01

    The present paper explores the implications of parallel narrative structure in Paul Harding's "Tinkers" (2009). Besides primarily recounting the two sets of parallel narratives, "Tinkers" also comprises of seemingly unrelated fragments such as excerpts from clock repair manuals and diaries. The main stories, however, told…

  8. Parallel Computing Strategies for Irregular Algorithms

    NASA Technical Reports Server (NTRS)

    Biswas, Rupak; Oliker, Leonid; Shan, Hongzhang; Biegel, Bryan (Technical Monitor)

    2002-01-01

    Parallel computing promises several orders of magnitude increase in our ability to solve realistic computationally-intensive problems, but relies on their efficient mapping and execution on large-scale multiprocessor architectures. Unfortunately, many important applications are irregular and dynamic in nature, making their effective parallel implementation a daunting task. Moreover, with the proliferation of parallel architectures and programming paradigms, the typical scientist is faced with a plethora of questions that must be answered in order to obtain an acceptable parallel implementation of the solution algorithm. In this paper, we consider three representative irregular applications: unstructured remeshing, sparse matrix computations, and N-body problems, and parallelize them using various popular programming paradigms on a wide spectrum of computer platforms ranging from state-of-the-art supercomputers to PC clusters. We present the underlying problems, the solution algorithms, and the parallel implementation strategies. Smart load-balancing, partitioning, and ordering techniques are used to enhance parallel performance. Overall results demonstrate the complexity of efficiently parallelizing irregular algorithms.

  9. Parallel unstructured grid generation for computational aerosciences

    NASA Technical Reports Server (NTRS)

    Shephard, Mark S.

    1993-01-01

    The objective of this research project is to develop efficient parallel automatic grid generation procedures for use in computational aerosciences. This effort is focused on a parallel version of the Finite Octree grid generator. Progress made during the first six months is reported.

  10. Extended cooperative control synthesis

    NASA Technical Reports Server (NTRS)

    Davidson, John B.; Schmidt, David K.

    1994-01-01

    This paper reports on research for extending the Cooperative Control Synthesis methodology to include a more accurate modeling of the pilot's controller dynamics. Cooperative Control Synthesis (CCS) is a methodology that addresses the problem of how to design control laws for piloted, high-order, multivariate systems and/or non-conventional dynamic configurations in the absence of flying qualities specifications. This is accomplished by emphasizing the parallel structure inherent in any pilot-controlled, augmented vehicle. The original CCS methodology is extended to include the Modified Optimal Control Model (MOCM), which is based upon the optimal control model of the human operator developed by Kleinman, Baron, and Levison in 1970. This model provides a modeling of the pilot's compensation dynamics that is more accurate than the simplified pilot dynamic representation currently in the CCS methodology. Inclusion of the MOCM into the CCS also enables the modeling of pilot-observation perception thresholds and pilot-observation attention allocation affects. This Extended Cooperative Control Synthesis (ECCS) allows for the direct calculation of pilot and system open- and closed-loop transfer functions in pole/zero form and is readily implemented in current software capable of analysis and design for dynamic systems. Example results based upon synthesizing an augmentation control law for an acceleration command system in a compensatory tracking task using the ECCS are compared with a similar synthesis performed by using the original CCS methodology. The ECCS is shown to provide augmentation control laws that yield more favorable, predicted closed-loop flying qualities and tracking performance than those synthesized using the original CCS methodology.

  11. Differences Between Distributed and Parallel Systems

    SciTech Connect

    Brightwell, R.; Maccabe, A.B.; Rissen, R.

    1998-10-01

    Distributed systems have been studied for twenty years and are now coming into wider use as fast networks and powerful workstations become more readily available. In many respects a massively parallel computer resembles a network of workstations and it is tempting to port a distributed operating system to such a machine. However, there are significant differences between these two environments and a parallel operating system is needed to get the best performance out of a massively parallel system. This report characterizes the differences between distributed systems, networks of workstations, and massively parallel systems and analyzes the impact of these differences on operating system design. In the second part of the report, we introduce Puma, an operating system specifically developed for massively parallel systems. We describe Puma portals, the basic building blocks for message passing paradigms implemented on top of Puma, and show how the differences observed in the first part of the report have influenced the design and implementation of Puma.

  12. Parallel-In-Time For Moving Meshes

    SciTech Connect

    Falgout, R. D.; Manteuffel, T. A.; Southworth, B.; Schroder, J. 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 applied 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.

  13. Configuration space representation in parallel coordinates

    NASA Technical Reports Server (NTRS)

    Fiorini, Paolo; Inselberg, Alfred

    1989-01-01

    By means of a system of parallel coordinates, a nonprojective mapping from R exp N to R squared is obtained for any positive integer N. In this way multivariate data and relations can be represented in the Euclidean plane (embedded in the projective plane). Basically, R squared with Cartesian coordinates is augmented by N parallel axes, one for each variable. The N joint variables of a robotic device can be represented graphically by using parallel coordinates. It is pointed out that some properties of the relation are better perceived visually from the parallel coordinate representation, and that new algorithms and data structures can be obtained from this representation. The main features of parallel coordinates are described, and an example is presented of their use for configuration space representation of a mechanical arm (where Cartesian coordinates cannot be used).

  14. Implementation and performance of parallel Prolog interpreter

    SciTech Connect

    Wei, S.; Kale, L.V.; Balkrishna, R. . Dept. of Computer Science)

    1988-01-01

    In this paper, the authors discuss the implementation of a parallel Prolog interpreter on different parallel machines. The implementation is based on the REDUCE--OR process model which exploits both AND and OR parallelism in logic programs. It is machine independent as it runs on top of the chare-kernel--a machine-independent parallel programming system. The authors also give the performance of the interpreter running a diverse set of benchmark pargrams on parallel machines including shared memory systems: an Alliant FX/8, Sequent and a MultiMax, and a non-shared memory systems: Intel iPSC/32 hypercube, in addition to its performance on a multiprocessor simulation system.

  15. Parallel Algebraic Multigrid Methods - High Performance Preconditioners

    SciTech Connect

    Yang, U M

    2004-11-11

    The development of high performance, massively parallel computers and the increasing demands of computationally challenging applications have necessitated the development of scalable solvers and preconditioners. One of the most effective ways to achieve scalability is the use of multigrid or multilevel techniques. Algebraic multigrid (AMG) is a very efficient algorithm for solving large problems on unstructured grids. While much of it can be parallelized in a straightforward way, some components of the classical algorithm, particularly the coarsening process and some of the most efficient smoothers, are highly sequential, and require new parallel approaches. This chapter presents the basic principles of AMG and gives an overview of various parallel implementations of AMG, including descriptions of parallel coarsening schemes and smoothers, some numerical results as well as references to existing software packages.

  16. A parallel variable metric optimization algorithm

    NASA Technical Reports Server (NTRS)

    Straeter, T. A.

    1973-01-01

    An algorithm, designed to exploit the parallel computing or vector streaming (pipeline) capabilities of computers is presented. When p is the degree of parallelism, then one cycle of the parallel variable metric algorithm is defined as follows: first, the function and its gradient are computed in parallel at p different values of the independent variable; then the metric is modified by p rank-one corrections; and finally, a single univariant minimization is carried out in the Newton-like direction. Several properties of this algorithm are established. The convergence of the iterates to the solution is proved for a quadratic functional on a real separable Hilbert space. For a finite-dimensional space the convergence is in one cycle when p equals the dimension of the space. Results of numerical experiments indicate that the new algorithm will exploit parallel or pipeline computing capabilities to effect faster convergence than serial techniques.

  17. National Combustion Code: Parallel Implementation and Performance

    NASA Technical Reports Server (NTRS)

    Quealy, A.; Ryder, R.; Norris, A.; Liu, N.-S.

    2000-01-01

    The National Combustion Code (NCC) is being developed by an industry-government team for the design and analysis of combustion systems. CORSAIR-CCD is the current baseline reacting flow solver for NCC. This is a parallel, unstructured grid code which uses a distributed memory, message passing model for its parallel implementation. The focus of the present effort has been to improve the performance of the NCC flow solver to meet combustor designer requirements for model accuracy and analysis turnaround time. Improving the performance of this code contributes significantly to the overall reduction in time and cost of the combustor design cycle. This paper describes the parallel implementation of the NCC flow solver and summarizes its current parallel performance on an SGI Origin 2000. Earlier parallel performance results on an IBM SP-2 are also included. The performance improvements which have enabled a turnaround of less than 15 hours for a 1.3 million element fully reacting combustion simulation are described.

  18. Parallelization of a Compositional Reservoir Simulator

    NASA Astrophysics Data System (ADS)

    Reme, Hilde; Åge Øye, Geir; Espedal, Magne S.; Fladmark, Gunnar E.

    A finite volume dicretization has been used to solve compositional flow in porous media. Secondary migration in fractured rocks has been the main motivation for the work. Multipoint flux approximation has been implemented and adaptive local grid refinement, based on domain decomposition, is used at fractures and faults. The parallelization method, which is described in this paper, strongly promotes code reuse and gives a very high level of parallelization despite low implementation costs. The programming framework is also portable to other platforms or other applications. We have presented computer experiments to examine the parallel efficiency of the implemented parallel simulator with respect to scalability and speedup. Keywords: porous media, multipoint flux approximation, domain decomposition, parallelization

  19. Genetic Parallel Programming: design and implementation.

    PubMed

    Cheang, Sin Man; Leung, Kwong Sak; Lee, Kin Hong

    2006-01-01

    This paper presents a novel Genetic Parallel Programming (GPP) paradigm for evolving parallel programs running on a Multi-Arithmetic-Logic-Unit (Multi-ALU) Processor (MAP). The MAP is a Multiple Instruction-streams, Multiple Data-streams (MIMD), general-purpose register machine that can be implemented on modern Very Large-Scale Integrated Circuits (VLSIs) in order to evaluate genetic programs at high speed. For human programmers, writing parallel programs is more difficult than writing sequential programs. However, experimental results show that GPP evolves parallel programs with less computational effort than that of their sequential counterparts. It creates a new approach to evolving a feasible problem solution in parallel program form and then serializes it into a sequential program if required. The effectiveness and efficiency of GPP are investigated using a suite of 14 well-studied benchmark problems. Experimental results show that GPP speeds up evolution substantially.

  20. Parallel hypergraph partitioning for scientific computing.

    SciTech Connect

    Heaphy, Robert; Devine, Karen Dragon; Catalyurek, Umit; Bisseling, Robert; Hendrickson, Bruce Alan; Boman, Erik Gunnar

    2005-07-01

    Graph partitioning is often used for load balancing in parallel computing, but it is known that hypergraph partitioning has several advantages. First, hypergraphs more accurately model communication volume, and second, they are more expressive and can better represent nonsymmetric problems. Hypergraph partitioning is particularly suited to parallel sparse matrix-vector multiplication, a common kernel in scientific computing. We present a parallel software package for hypergraph (and sparse matrix) partitioning developed at Sandia National Labs. The algorithm is a variation on multilevel partitioning. Our parallel implementation is novel in that it uses a two-dimensional data distribution among processors. We present empirical results that show our parallel implementation achieves good speedup on several large problems (up to 33 million nonzeros) with up to 64 processors on a Linux cluster.

  1. Broadcasting a message in a parallel computer

    DOEpatents

    Berg, Jeremy E.; Faraj, Ahmad A.

    2011-08-02

    Methods, systems, and products are disclosed for broadcasting a message in a parallel computer. The parallel computer includes a plurality of compute nodes connected together using a data communications network. The data communications network optimized for point to point data communications and is characterized by at least two dimensions. The compute nodes are organized into at least one operational group of compute nodes for collective parallel operations of the parallel computer. One compute node of the operational group assigned to be a logical root. Broadcasting a message in a parallel computer includes: establishing a Hamiltonian path along all of the compute nodes in at least one plane of the data communications network and in the operational group; and broadcasting, by the logical root to the remaining compute nodes, the logical root's message along the established Hamiltonian path.

  2. Sequential bioequivalence approaches for parallel designs.

    PubMed

    Fuglsang, Anders

    2014-05-01

    Regulators in EU, USA and Canada allow the use of two-stage approaches for evaluation of bioequivalence. The purpose of this paper is to evaluate such designs for parallel groups using trial simulations. The methods developed by Diane Potvin and co-workers were adapted to parallel designs. Trials were simulated and evaluated on basis of either equal or unequal variances between treatment groups. Methods B and C of Potvin et al., when adapted for parallel designs, protected well against type I error rate inflation under all of the simulated scenarios. Performance characteristics of the new parallel design methods showed little dependence on the assumption of equality of the test and reference variances. This is the first paper to describe the performance of two-stage approaches for parallel designs used to evaluate bioequivalence. The results may prove useful to sponsors developing formulations where crossover designs for bioequivalence evaluation are undesirable.

  3. Synthesis and cytotoxic activity of 4-N-carboxybutyl-5-fluorocytosyl-Arg-Gln-Trp-Arg-Arg-Trp-Trp-Gln-Arg-NH₂.

    PubMed

    Somlai, Csaba; Correche, Estela; Olivella, Monica; Tolosa, Laia; Lechon, Maria José Gomez; Dombi, György; Tóth, Gábor K; Penke, Botond; Enriz, Ricardo D

    2012-07-01

    The chemical synthesis of 4-N-carboxybutyl-5-fluorocytosine (II) in solution phase starting from 5-fluorocytosine and the solid phase synthesis of Arg-Gln-Trp-Arg-Arg-Trp-Trp-Gln-Arg-NH(2) attached to the 4-N-carboxybutyl-5-fluorocytosine residue at the N-terminus of the peptide (III) via peptide bond formation is reported. The target compound exhibited a significant cytotoxic activity against a culture of HepG2 cells. In addition our results demonstrated that this new compound affect cell viability, produce mitochondrial dysfunction as well as interfere with intracellular calcium homeostasis control; leading to cell malfunction and death.

  4. Sequential and parallel dual labeling of nanoparticles using click chemistry.

    PubMed

    Zong, Hong; Goonewardena, Sascha N; Chang, Huai-Ning; Otis, James B; Baker, James R

    2014-11-01

    Bioorthogonal 'click' reactions have recently emerged as promising tools for chemistry and biological applications. By using a combination of two different 'click' reactions, 'double-click' strategies have been developed to attach multiple labels onto biomacromolecules. These strategies require multi-step modifications of the biomacromolecules that can lead to heterogeneity in the final conjugates. Herein, we report the synthesis and characterization of a set of three trifunctional linkers. The linkers having alkyne and cyclooctyne moieties that are capable of participating in sequential copper(I)-catalyzed and copper-free cycloaddition reactions with azides. We have also prepared a linker comprised of an alkyne and a 1,2,4,5-terazine moiety that allows for simultaneous cycloaddition reactions with azides and trans-cyclooctenes, respectively. These linkers can be attached to synthetic or biological macromolecules to create a platform capable of sequential or parallel 'double-click' labeling in biological systems. We show this potential using a generation 5 (G5) polyamidoamine (PAMAM) dendrimer in combination with the clickable linkers. The dendrimers were successfully modified with these linkers and we demonstrate both sequential and parallel 'double-click' labeling with fluorescent reporters. We anticipate that these linkers will have a variety of application including molecular imaging and monitoring of macromolecule interactions in biological systems.

  5. Freezing of parallel hard cubes with rounded edges.

    PubMed

    Marechal, Matthieu; Zimmermann, Urs; Löwen, Hartmut

    2012-04-14

    The freezing transition in a classical three-dimensional system of rounded hard cubes with fixed, equal orientations is studied by computer simulation and fundamental-measure density functional theory. By switching the rounding parameter s from zero to one, one can smoothly interpolate between cubes with sharp edges and hard spheres. The equilibrium phase diagram of rounded parallel hard cubes is computed as a function of their volume fraction and the rounding parameter s. The second order freezing transition known for oriented cubes at s = 0 is found to be persistent up to s = 0.65. The fluid freezes into a simple-cubic crystal which exhibits a large vacancy concentration. Upon a further increase of s, the continuous freezing is replaced by a first-order transition into either a sheared simple cubic lattice or a deformed face-centered cubic lattice with two possible unit cells: body-centered orthorhombic or base-centered monoclinic. In principle, a system of parallel cubes could be realized in experiments on colloids using advanced synthesis techniques and a combination of external fields.

  6. Parallel microwave chemistry in silicon carbide microtiter platforms: a review.

    PubMed

    Kappe, C Oliver; Damm, Markus

    2012-02-01

    In this review, applications of silicon carbide-based microtiter platforms designed for use in combination with dedicated multimode microwave reactors are described. These platforms are employed not only for the efficient parallel synthesis of compound libraries, but also in the context of high-throughput reaction screening/optimization and a number of other (bio)analytical and biomedical applications. Since the semiconducting plate material (silicon carbide) is strongly microwave absorbing and possesses high thermal conductivity, no temperature gradients across the microtiter plate exist. Therefore, many of the disadvantages experienced in attempting to perform microtiter plate chemistry under conventional microwave conditions can be eliminated. In general, the silicon carbide-based microtiter platforms allow sealed vessel processing (either directly in the well or in glass vials placed into the wells) of volumes ranging from 0.02-3.0 mL at a maximum temperature/pressure limit of 200°C/20 bar. Depending on the specific plate and rotor configuration, a maximum of 80-192 transformations can be carried out in parallel in a single microwave irradiation experiment under strict temperature control. A platform type utilizing HPLC/GC vials as reaction vessels allows analysis directly from the reaction vessel eliminating the need for a transfer step from the reaction to the analysis vial. The latter system is particularly useful for analytical applications as well as reaction optimization/screening.

  7. Multirate-based fast parallel algorithms for 2-D DHT-based real-valued discrete Gabor transform.

    PubMed

    Tao, Liang; Kwan, Hon Keung

    2012-07-01

    Novel algorithms for the multirate and fast parallel implementation of the 2-D discrete Hartley transform (DHT)-based real-valued discrete Gabor transform (RDGT) and its inverse transform are presented in this paper. A 2-D multirate-based analysis convolver bank is designed for the 2-D RDGT, and a 2-D multirate-based synthesis convolver bank is designed for the 2-D inverse RDGT. The parallel channels in each of the two convolver banks have a unified structure and can apply the 2-D fast DHT algorithm to speed up their computations. The computational complexity of each parallel channel is low and is independent of the Gabor oversampling rate. All the 2-D RDGT coefficients of an image are computed in parallel during the analysis process and can be reconstructed in parallel during the synthesis process. The computational complexity and time of the proposed parallel algorithms are analyzed and compared with those of the existing fastest algorithms for 2-D discrete Gabor transforms. The results indicate that the proposed algorithms are the fastest, which make them attractive for real-time image processing.

  8. Code Parallelization with CAPO: A User Manual

    NASA Technical Reports Server (NTRS)

    Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry; Biegel, Bryan (Technical Monitor)

    2001-01-01

    A software tool has been developed to assist the parallelization of scientific codes. This tool, CAPO, extends an existing parallelization toolkit, CAPTools developed at the University of Greenwich, to generate OpenMP parallel codes for shared memory architectures. This is an interactive toolkit to transform a serial Fortran application code to an equivalent parallel version of the software - in a small fraction of the time normally required for a manual parallelization. We first discuss the way in which loop types are categorized and how efficient OpenMP directives can be defined and inserted into the existing code using the in-depth interprocedural analysis. The use of the toolkit on a number of application codes ranging from benchmark to real-world application codes is presented. This will demonstrate the great potential of using the toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of processors. The second part of the document gives references to the parameters and the graphic user interface implemented in the toolkit. Finally a set of tutorials is included for hands-on experiences with this toolkit.

  9. Automatic Generation of Directive-Based Parallel Programs for Shared Memory Parallel Systems

    NASA Technical Reports Server (NTRS)

    Jin, Hao-Qiang; Yan, Jerry; Frumkin, Michael

    2000-01-01

    The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. As great progress was made in hardware and software technologies, performance of parallel programs with compiler directives has demonstrated large improvement. The introduction of OpenMP directives, the industrial standard for shared-memory programming, has minimized the issue of portability. Due to its ease of programming and its good performance, the technique has become very popular. In this study, we have extended CAPTools, a computer-aided parallelization toolkit, to automatically generate directive-based, OpenMP, parallel programs. We outline techniques used in the implementation of the tool and present test results on the NAS parallel benchmarks and ARC3D, a CFD application. This work demonstrates the great potential of using computer-aided tools to quickly port parallel programs and also achieve good performance.

  10. Xyce parallel electronic simulator : users' guide.

    SciTech Connect

    Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Warrender, Christina E.; Keiter, Eric Richard; Pawlowski, Roger Patrick

    2011-05-01

    This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) 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; (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only); and (4) 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 parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory 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. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a unique

  11. Scaffold oriented synthesis. Part 4: design, synthesis and biological evaluation of novel 5-substituted indazoles as potent and selective kinase inhibitors employing heterocycle forming and multicomponent reactions.

    PubMed

    Akritopoulou-Zanze, Irini; Wakefield, Brian D; Gasiecki, Alan; Kalvin, Douglas; Johnson, Eric F; Kovar, Peter; Djuric, Stevan W

    2011-03-01

    We report the synthesis and biological evaluation of 5-substituted indazoles as kinase inhibitors. The compounds were synthesized in a parallel synthesis fashion from readily available starting materials employing heterocycle forming and multicomponent reactions and were evaluated against a panel of kinase assays. Potent inhibitors were identified for Gsk3β, Rock2, and Egfr.

  12. Infrared colloidal lead chalcogenide nanocrystals: synthesis, properties, and photovoltaic applications.

    PubMed

    Fu, Huiying; Tsang, Sai-Wing

    2012-04-07

    Simple solution phase, catalyst-free synthetic approaches that offer monodispersed, well passivated, and non-aggregated colloidal semiconductor nanocrystals have presented many research opportunities not only for fundamental science but also for technological applications. The ability to tune the electrical and optical properties of semiconductor nanocrystals by manipulating the size and shape of the crystals during the colloidal synthesis provides potential benefits to a variety of applications including photovoltaic devices, light-emitting diodes, field effect transistors, biological imaging/labeling, and more. Recent advances in the synthesis and characterization of colloidal lead chalcogenide nanocrystals and the achievements in colloidal PbS or PbSe nanocrystals solar cells have demonstrated the promising application of infrared-emitting colloidal lead chalcogenide nanocrystals in photovoltaic devices. Here, we review recent progress in the synthesis and optical properties of colloidal lead chalcogenide nanocrystals. We focus in particular upon the size- and shape-controlled synthesis of PbS, PbSe, and PbTe nanocrystals by using different precursors and various stabilizing surfactants for the growth of the colloidal nanocrystals. We also summarize recent advancements in the field of colloidal nanocrystals solar cells based on colloidal PbS and PbSe nanocrystals.

  13. Parallelization of the Implicit RPLUS Algorithm

    NASA Technical Reports Server (NTRS)

    Orkwis, Paul D.

    1997-01-01

    The multiblock reacting Navier-Stokes flow solver RPLUS2D was modified for parallel implementation. Results for non-reacting flow calculations of this code indicate parallelization efficiencies greater than 84% are possible for a typical test problem. Results tend to improve as the size of the problem increases. The convergence rate of the scheme is degraded slightly when additional artificial block boundaries are included for the purpose of parallelization. However, this degradation virtually disappears if the solution is converged near to machine zero. Recommendations are made for further code improvements to increase efficiency, correct bugs in the original version, and study decomposition effectiveness.

  14. Parallelization of the Implicit RPLUS Algorithm

    NASA Technical Reports Server (NTRS)

    Orkwis, Paul D.

    1994-01-01

    The multiblock reacting Navier-Stokes flow-solver RPLUS2D was modified for parallel implementation. Results for non-reacting flow calculations of this code indicate parallelization efficiencies greater than 84% are possible for a typical test problem. Results tend to improve as the size of the problem increases. The convergence rate of the scheme is degraded slightly when additional artificial block boundaries are included for the purpose of parallelization. However, this degradation virtually disappears if the solution is converged near to machine zero. Recommendations are made for further code improvements to increase efficiency, correct bugs in the original version, and study decomposition effectiveness.

  15. Knowledge representation into Ada parallel processing

    NASA Technical Reports Server (NTRS)

    Masotto, Tom; Babikyan, Carol; Harper, Richard

    1990-01-01

    The Knowledge Representation into Ada Parallel Processing project is a joint NASA and Air Force funded project to demonstrate the execution of intelligent systems in Ada on the Charles Stark Draper Laboratory fault-tolerant parallel processor (FTPP). Two applications were demonstrated - a portion of the adaptive tactical navigator and a real time controller. Both systems are implemented as Activation Framework Objects on the Activation Framework intelligent scheduling mechanism developed by Worcester Polytechnic Institute. The implementations, results of performance analyses showing speedup due to parallelism and initial efficiency improvements are detailed and further areas for performance improvements are suggested.

  16. Time-parallel multiscale/multiphysics framework

    SciTech Connect

    Frantziskonis, G.; Muralidharan, Krishna; Deymier, Pierre; Simunovic, Srdjan; Nukala, Phani K; Pannala, Sreekanth

    2009-01-01

    We introduce the time-parallel compound wavelet matrix method (tpCWM) for modeling the temporal evolution of multiscale and multiphysics systems. The method couples time parallel (TP) and CWM methods operating at different spatial and temporal scales. We demonstrate the efficiency of our approach on two examples: a chemical reaction kinetic system and a non-linear predator prey system. Our results indicate that the tpCWM technique is capable of accelerating time-to-solution by 2 3-orders of magnitude and is amenable to efficient parallel implementation.

  17. Language constructs for modular parallel programs

    SciTech Connect

    Foster, I.

    1996-03-01

    We describe programming language constructs that facilitate the application of modular design techniques in parallel programming. These constructs allow us to isolate resource management and processor scheduling decisions from the specification of individual modules, which can themselves encapsulate design decisions concerned with concurrence, communication, process mapping, and data distribution. This approach permits development of libraries of reusable parallel program components and the reuse of these components in different contexts. In particular, alternative mapping strategies can be explored without modifying other aspects of program logic. We describe how these constructs are incorporated in two practical parallel programming languages, PCN and Fortran M. Compilers have been developed for both languages, allowing experimentation in substantial applications.

  18. Distributed parallel messaging for multiprocessor systems

    SciTech Connect

    Chen, Dong; Heidelberger, Philip; Salapura, Valentina; Senger, Robert M; Steinmacher-Burrow, Burhard; Sugawara, Yutaka

    2013-06-04

    A method and apparatus for distributed parallel messaging in a parallel computing system. The apparatus includes, at each node of a multiprocessor network, multiple injection messaging engine units and reception messaging engine units, each implementing a DMA engine and each supporting both multiple packet injection into and multiple reception from a network, in parallel. The reception side of the messaging unit (MU) includes a switch interface enabling writing of data of a packet received from the network to the memory system. The transmission side of the messaging unit, includes switch interface for reading from the memory system when injecting packets into the network.

  19. Parallel path aspects of transmission modeling

    SciTech Connect

    Kavicky, J.A.; Shahidehpour, S.M.

    1996-11-01

    This paper examines the present methods and modeling techniques available to address the effects of parallel flows resulting from various firm and short-term energy transactions. A survey of significant methodologies is conducted to determine the present status of parallel flow transaction modeling. The strengths and weaknesses of these approaches are identified to suggest areas of further modeling improvements. The motivating force behind this research is to improve transfer capability assessment accuracy by suggesting a real-time modeling environment that adequately represents the influences of parallel flows while recognizing operational constraints and objectives.

  20. Fast combinatorial optimization with parallel digital computers.

    PubMed

    Kakeya, H; Okabe, Y

    2000-01-01

    This paper presents an algorithm which realizes fast search for the solutions of combinatorial optimization problems with parallel digital computers.With the standard weight matrices designed for combinatorial optimization, many iterations are required before convergence to a quasioptimal solution even when many digital processors can be used in parallel. By removing the components of the eingenvectors with eminent negative eigenvalues of the weight matrix, the proposed algorithm avoids oscillation and realizes energy reduction under synchronous discrete dynamics, which enables parallel digital computers to obtain quasi-optimal solutions with much less time than the conventional algorithm.

  1. Synchronization Of Parallel Discrete Event Simulations

    NASA Technical Reports Server (NTRS)

    Steinman, Jeffrey S.

    1992-01-01

    Adaptive, parallel, discrete-event-simulation-synchronization algorithm, Breathing Time Buckets, developed in Synchronous Parallel Environment for Emulation and Discrete Event Simulation (SPEEDES) operating system. Algorithm allows parallel simulations to process events optimistically in fluctuating time cycles that naturally adapt while simulation in progress. Combines best of optimistic and conservative synchronization strategies while avoiding major disadvantages. Algorithm processes events optimistically in time cycles adapting while simulation in progress. Well suited for modeling communication networks, for large-scale war games, for simulated flights of aircraft, for simulations of computer equipment, for mathematical modeling, for interactive engineering simulations, and for depictions of flows of information.

  2. Heterogeneous parallel programming capability. Final report

    SciTech Connect

    Flower, J.W.; Kolawa, A.

    1990-11-30

    In creating a heterogeneous parallel processing capability we are really trying to approach three basic problems with current systems: (1) Supercomputer and parallel computer hardware architectures vary widely but need to support one or two fairly standard programming languages and programming models. A particularly important issue concerns the short life cycle of individual hardware designs; (2) Many algorithms require capabilities beyond the reach of single superconducters but could be approached by several machines working together; and (3) Performing a given task requires integration of a system that may contain many components in addition to the super or parallel computer itself. Peripherals from many different manufacturers must be incorporated.

  3. Social Problems and Deviance: Some Parallel Issues

    ERIC Educational Resources Information Center

    Kitsuse, John I.; Spector, Malcolm

    1975-01-01

    Explores parallel developments in labeling theory and in the value conflict approach to social problems. Similarities in their critiques of functionalism and etiological theory as well as their emphasis on the definitional process are noted. (Author)

  4. Visualization and Tracking of Parallel CFD Simulations

    NASA Technical Reports Server (NTRS)

    Vaziri, Arsi; Kremenetsky, Mark

    1995-01-01

    We describe a system for interactive visualization and tracking of a 3-D unsteady computational fluid dynamics (CFD) simulation on a parallel computer. CM/AVS, a distributed, parallel implementation of a visualization environment (AVS) runs on the CM-5 parallel supercomputer. A CFD solver is run as a CM/AVS module on the CM-5. Data communication between the solver, other parallel visualization modules, and a graphics workstation, which is running AVS, are handled by CM/AVS. Partitioning of the visualization task, between CM-5 and the workstation, can be done interactively in the visual programming environment provided by AVS. Flow solver parameters can also be altered by programmable interactive widgets. This system partially removes the requirement of storing large solution files at frequent time steps, a characteristic of the traditional 'simulate (yields) store (yields) visualize' post-processing approach.

  5. Data parallel sorting for particle simulation

    NASA Technical Reports Server (NTRS)

    Dagum, Leonardo

    1992-01-01

    Sorting on a parallel architecture is a communications intensive event which can incur a high penalty in applications where it is required. In the case of particle simulation, only integer sorting is necessary, and sequential implementations easily attain the minimum performance bound of O (N) for N particles. Parallel implementations, however, have to cope with the parallel sorting problem which, in addition to incurring a heavy communications cost, can make the minimun performance bound difficult to attain. This paper demonstrates how the sorting problem in a particle simulation can be reduced to a merging problem, and describes an efficient data parallel algorithm to solve this merging problem in a particle simulation. The new algorithm is shown to be optimal under conditions usual for particle simulation, and its fieldwise implementation on the Connection Machine is analyzed in detail. The new algorithm is about four times faster than a fieldwise implementation of radix sort on the Connection Machine.

  6. Runtime support for parallelizing data mining algorithms

    NASA Astrophysics Data System (ADS)

    Jin, Ruoming; Agrawal, Gagan

    2002-03-01

    With recent technological advances, shared memory parallel machines have become more scalable, and offer large main memories and high bus bandwidths. They are emerging as good platforms for data warehousing and data mining. In this paper, we focus on shared memory parallelization of data mining algorithms. We have developed a series of techniques for parallelization of data mining algorithms, including full replication, full locking, fixed locking, optimized full locking, and cache-sensitive locking. Unlike previous work on shared memory parallelization of specific data mining algorithms, all of our techniques apply to a large number of common data mining algorithms. In addition, we propose a reduction-object based interface for specifying a data mining algorithm. We show how our runtime system can apply any of the technique we have developed starting from a common specification of the algorithm.

  7. Parallel processing of a rotating shaft simulation

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.

    1989-01-01

    A FORTRAN program describing the vibration modes of a rotor-bearing system is analyzed for parellelism in this simulation using a Pascal-like structured language. Potential vector operations are also identified. A critical path through the simulation is identified and used in conjunction with somewhat fictitious processor characteristics to determine the time to calculate the problem on a parallel processing system having those characteristics. A parallel processing overhead time is included as a parameter for proper evaluation of the gain over serial calculation. The serial calculation time is determined for the same fictitious system. An improvement of up to 640 percent is possible depending on the value of the overhead time. Based on the analysis, certain conclusions are drawn pertaining to the development needs of parallel processing technology, and to the specification of parallel processing systems to meet computational needs.

  8. NAS Parallel Benchmarks, Multi-Zone Versions

    NASA Technical Reports Server (NTRS)

    vanderWijngaart, Rob F.; Haopiang, Jin

    2003-01-01

    We describe an extension of the NAS Parallel Benchmarks (NPB) suite that involves solving the application benchmarks LU, BT and SP on collections of loosely coupled discretization meshes. The solutions on the meshes are updated independently, but after each time step they exchange boundary value information. This strategy, which is common among structured-mesh production flow solver codes in use at NASA Ames and elsewhere, provides relatively easily exploitable coarse-grain parallelism between meshes. Since the individual application benchmarks also allow fine-grain parallelism themselves, this NPB extension, named NPB Multi-Zone (NPB-MZ), is a good candidate for testing hybrid and multi-level parallelization tools and strategies.

  9. Asynchronous parallel pattern search for nonlinear optimization

    SciTech Connect

    P. D. Hough; T. G. Kolda; V. J. Torczon

    2000-01-01

    Parallel pattern search (PPS) can be quite useful for engineering optimization problems characterized by a small number of variables (say 10--50) and by expensive objective function evaluations such as complex simulations that take from minutes to hours to run. However, PPS, which was originally designed for execution on homogeneous and tightly-coupled parallel machine, is not well suited to the more heterogeneous, loosely-coupled, and even fault-prone parallel systems available today. Specifically, PPS is hindered by synchronization penalties and cannot recover in the event of a failure. The authors introduce a new asynchronous and fault tolerant parallel pattern search (AAPS) method and demonstrate its effectiveness on both simple test problems as well as some engineering optimization problems

  10. Parallel programming with PCN. Revision 1

    SciTech Connect

    Foster, I.; Tuecke, S.

    1991-12-01

    PCN is a system for developing and executing parallel programs. It comprises a high-level programming language, tools for developing and debugging programs in this language, and interfaces to Fortran and C that allow the reuse of existing code in multilingual parallel programs. Programs developed using PCN are portable across many different workstations, networks, and parallel computers. This document provides all the information required to develop parallel programs with the PCN programming system. In includes both tutorial and reference material. It also presents the basic concepts that underly PCN, particularly where these are likely to be unfamiliar to the reader, and provides pointers to other documentation on the PCN language, programming techniques, and tools. PCN is in the public domain. The latest version of both the software and this manual can be obtained by anonymous FTP from Argonne National Laboratory in the directory pub/pcn at info.mcs.anl.gov (c.f. Appendix A).

  11. A Nomograph for Resistors in Parallel

    NASA Astrophysics Data System (ADS)

    Greenslade, Thomas B.

    2002-11-01

    The author has a large collection of 19th century textbooks, and found a quotation in one of them concerning a construction for finding the equivalent resistance of two resistors in parallel. This note discusses the equations.

  12. Parallel Implementation of the Discontinuous Galerkin Method

    NASA Technical Reports Server (NTRS)

    Baggag, Abdalkader; Atkins, Harold; Keyes, David

    1999-01-01

    This paper describes a parallel implementation of the discontinuous Galerkin method. Discontinuous Galerkin is a spatially compact method that retains its accuracy and robustness on non-smooth unstructured grids and is well suited for time dependent simulations. Several parallelization approaches are studied and evaluated. The most natural and symmetric of the approaches has been implemented in all object-oriented code used to simulate aeroacoustic scattering. The parallel implementation is MPI-based and has been tested on various parallel platforms such as the SGI Origin, IBM SP2, and clusters of SGI and Sun workstations. The scalability results presented for the SGI Origin show slightly superlinear speedup on a fixed-size problem due to cache effects.

  13. Feature Clustering for Accelerating Parallel Coordinate Descent

    SciTech Connect

    Scherrer, Chad; Tewari, Ambuj; Halappanavar, Mahantesh; Haglin, David J.

    2012-12-06

    We demonstrate an approach for accelerating calculation of the regularization path for L1 sparse logistic regression problems. We show the benefit of feature clustering as a preconditioning step for parallel block-greedy coordinate descent algorithms.

  14. Parallel algorithms for dynamically partitioning unstructured grids

    SciTech Connect

    Diniz, P.; Plimpton, S.; Hendrickson, B.; Leland, R.

    1994-10-01

    Grid partitioning is the method of choice for decomposing a wide variety of computational problems into naturally parallel pieces. In problems where computational load on the grid or the grid itself changes as the simulation progresses, the ability to repartition dynamically and in parallel is attractive for achieving higher performance. We describe three algorithms suitable for parallel dynamic load-balancing which attempt to partition unstructured grids so that computational load is balanced and communication is minimized. The execution time of algorithms and the quality of the partitions they generate are compared to results from serial partitioners for two large grids. The integration of the algorithms into a parallel particle simulation is also briefly discussed.

  15. The PISCES 2 parallel programming environment

    NASA Technical Reports Server (NTRS)

    Pratt, Terrence W.

    1987-01-01

    PISCES 2 is a programming environment for scientific and engineering computations on MIMD parallel computers. It is currently implemented on a flexible FLEX/32 at NASA Langley, a 20 processor machine with both shared and local memories. The environment provides an extended Fortran for applications programming, a configuration environment for setting up a run on the parallel machine, and a run-time environment for monitoring and controlling program execution. This paper describes the overall design of the system and its implementation on the FLEX/32. Emphasis is placed on several novel aspects of the design: the use of a carefully defined virtual machine, programmer control of the mapping of virtual machine to actual hardware, forces for medium-granularity parallelism, and windows for parallel distribution of data. Some preliminary measurements of storage use are included.

  16. Massively Parallel Computing: A Sandia Perspective

    SciTech Connect

    Dosanjh, Sudip S.; Greenberg, David S.; Hendrickson, Bruce; Heroux, Michael A.; Plimpton, Steve J.; Tomkins, James L.; Womble, David E.

    1999-05-06

    The computing power available to scientists and engineers has increased dramatically in the past decade, due in part to progress in making massively parallel computing practical and available. The expectation for these machines has been great. The reality is that progress has been slower than expected. Nevertheless, massively parallel computing is beginning to realize its potential for enabling significant break-throughs in science and engineering. This paper provides a perspective on the state of the field, colored by the authors' experiences using large scale parallel machines at Sandia National Laboratories. We address trends in hardware, system software and algorithms, and we also offer our view of the forces shaping the parallel computing industry.

  17. Improved chopper circuit uses parallel transistors

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Parallel transistor chopper circuit operates with one transistor in the forward mode and the other in the inverse mode. By using this method, it acts as a single, symmetrical, bidirectional transistor, and reduces and stabilizes the offset voltage.

  18. Molecular dynamics on hypercube parallel computers

    NASA Astrophysics Data System (ADS)

    Smith, W.

    1991-03-01

    The implementation of molecular dynamics on parallel computers is described, with particular reference to hypercube computers. Three particular algorithms are described: replicated data (RD); systolic loop (SLS-G), and parallelised link-cells (PLC), all of which have good load balancing. The performance characteristics of each algorithm and the factors affecting their scaling properties are discussed. The article is pedagogic in intent, to introduce a novice to the main aspects of parallel computing in molecular dynamics.

  19. Graphics-Based Parallel Programming Tools

    DTIC Science & Technology

    1991-09-01

    more general context by implementing perspective views within the Voyeur system [121. Voyeur is a more conventional tool for displaying application...Varadaraju. Interfacing Belvedere with Voyeur . Master’s Thesis, COINS Department, University of Massachusetts (June 1991). 13 David Socha and Mary L...Bailey and David Notkin, " Voyeur : Graphi- cal Views of Parallel Programs", SIGPLAN Workshop on Parallel and Distributed Debugging, pp. 206-215 (1988). 14

  20. Graphics-Based Parallel Programming Tools

    DTIC Science & Technology

    1992-01-01

    the Voyeur system [121. Voyeur is a more conventional tool for displaying application-specific visualizations of parallel programs [131 and it provides...Department. University of Massachusetts (June 1991). 13 David Socha and Mary L. Bailey and David Notkin. "’ Voyeur : Graphi- cal Views of Parallel Programs...Massachusetts (September 1991). Nandakumar Varadaraju. Interfacing Belvedere with Voyeur . Master’s The- sis. COINS Department. University of Massachusetts

  1. Voyeur: Graphical Views of Parallel Programs

    DTIC Science & Technology

    1988-04-01

    visualization, parallel debugging, moni torino 20. ABSTRACT (Continue ci reveree, eide if necessary and Identify by block number) ~9 Voyeur is a prototype...PAGE Dh- eaa,:~ Voyeur : Graphical Views of Parallel Programs David Socha, Mary Bailey and David Notkin Department of Computer Science, FR-35 University...of Washington Seattle, Washington 98195 TR 88-04-03 April 1988 Voyeur is a prototype system that facilitates the construction of application-specific

  2. Partitioning And Packing Equations For Parallel Processing

    NASA Technical Reports Server (NTRS)

    Arpasi, Dale J.; Milner, Edward J.

    1989-01-01

    Algorithm developed to identify parallelism in set of coupled ordinary differential equations that describe physical system and to divide set into parallel computational paths, along with parts of solution proceeds independently of others during at least part of time. Path-identifying algorithm creates number of paths consisting of equations that must be computed serially and table that gives dependent and independent arguments and "can start," "can end," and "must end" times of each equation. "Must end" time used subsequently by packing algorithm.

  3. Enhancing Scalability of Parallel Structured AMR Calculations

    SciTech Connect

    Wissink, A M; Hysom, D; Hornung, R D

    2003-02-10

    This paper discusses parallel scaling performance of large scale parallel structured adaptive mesh refinement (SAMR) calculations in SAMRAI. Previous work revealed that poor scaling qualities in the adaptive gridding operations in SAMR calculations cause them to become dominant for cases run on up to 512 processors. This work describes algorithms we have developed to enhance the efficiency of the adaptive gridding operations. Performance of the algorithms is evaluated for two adaptive benchmarks run on up 512 processors of an IBM SP system.

  4. Joint Experimentation on Scalable Parallel Processors (JESPP)

    DTIC Science & Technology

    2006-04-01

    SCALABLE PARALLEL PROCESSORS (JESPP) 6. AUTHOR(S) Dan M. Davis, Robert F. Lucas, Ke-Thia Yao, Gene Wagenbreth 5. FUNDING NUMBERS C...List of Papers • Robert J. Graebener, Gregory Rafuse, Robert Miller & Ke-Thia Yao, “The Road to Successful Joint Experimentation Starts at the...2003. • Robert F. Lucas & Dan M. Davis, “Joint Experimentation on Scalable Parallel Processors“, Interservice/Industry Training, Simulation, and

  5. LDV Measurement of Confined Parallel Jet Mixing

    SciTech Connect

    R.F. Kunz; S.W. D'Amico; P.F. Vassallo; M.A. Zaccaria

    2001-01-31

    Laser Doppler Velocimetry (LDV) measurements were taken in a confinement, bounded by two parallel walls, into which issues a row of parallel jets. Two-component measurements were taken of two mean velocity components and three Reynolds stress components. As observed in isolated three dimensional wall bounded jets, the transverse diffusion of the jets is quite large. The data indicate that this rapid mixing process is due to strong secondary flows, transport of large inlet intensities and Reynolds stress anisotropy effects.

  6. A survey of parallel programming tools

    NASA Technical Reports Server (NTRS)

    Cheng, Doreen Y.

    1991-01-01

    This survey examines 39 parallel programming tools. Focus is placed on those tool capabilites needed for parallel scientific programming rather than for general computer science. The tools are classified with current and future needs of Numerical Aerodynamic Simulator (NAS) in mind: existing and anticipated NAS supercomputers and workstations; operating systems; programming languages; and applications. They are divided into four categories: suggested acquisitions, tools already brought in; tools worth tracking; and tools eliminated from further consideration at this time.

  7. HOPSPACK: Hybrid Optimization Parallel Search Package.

    SciTech Connect

    Gray, Genetha Anne.; Kolda, Tamara G.; Griffin, Joshua; Taddy, Matt; Martinez-Canales, Monica L.

    2008-12-01

    In this paper, we describe the technical details of HOPSPACK (Hybrid Optimization Parallel SearchPackage), a new software platform which facilitates combining multiple optimization routines into asingle, tightly-coupled, hybrid algorithm that supports parallel function evaluations. The frameworkis designed such that existing optimization source code can be easily incorporated with minimalcode modification. By maintaining the integrity of each individual solver, the strengths and codesophistication of the original optimization package are retained and exploited.4

  8. Parallel algorithms for contour extraction and coding

    NASA Astrophysics Data System (ADS)

    Dinstein, Its'hak; Landau, Gad M.

    1990-07-01

    A parallel approach to contour extraction and coding on an Exclusive Read Exclusive Write (EREW) Parallel Random Access Machine (PRAM) is presented and analyzed. The algorithm is intended for binary images. The labeled contours can be represented by lists of coordinates, and/or chain codes, and/or any other user designed codes. Using O(n2/log n) processors, the algorithm runs in O(logn) time, where n by n is the size of the processed binary image.

  9. Parallel and Distributed Computing Combinatorial Algorithms

    DTIC Science & Technology

    1993-10-01

    FUPNDKC %2,•, PARALLEL AND DISTRIBUTED COMPUTING COMBINATORIAL ALGORITHMS 6. AUTHOR(S) 2304/DS F49620-92-J-0125 DR. LEIGHTON 7 PERFORMING ORGANIZATION NAME...on several problems involving parallel and distributed computing and combinatorial optimization. This research is reported in the numerous papers that...network decom- position. In Proceedings of the Eleventh Annual ACM Symposium on Principles of Distributed Computing , August 1992. [15] B. Awerbuch, B

  10. Computational electromagnetics and parallel dense matrix computations

    SciTech Connect

    Forsman, K.; Kettunen, L.; Gropp, W.; Levine, D.

    1995-06-01

    We present computational results using CORAL, a parallel, three-dimensional, nonlinear magnetostatic code based on a volume integral equation formulation. A key feature of CORAL is the ability to solve, in parallel, the large, dense systems of linear equations that are inherent in the use of integral equation methods. Using the Chameleon and PSLES libraries ensures portability and access to the latest linear algebra solution technology.

  11. Fast Parallel Computation Of Multibody Dynamics

    NASA Technical Reports Server (NTRS)

    Fijany, Amir; Kwan, Gregory L.; Bagherzadeh, Nader

    1996-01-01

    Constraint-force algorithm fast, efficient, parallel-computation algorithm for solving forward dynamics problem of multibody system like robot arm or vehicle. Solves problem in minimum time proportional to log(N) by use of optimal number of processors proportional to N, where N is number of dynamical degrees of freedom: in this sense, constraint-force algorithm both time-optimal and processor-optimal parallel-processing algorithm.

  12. Parallel computer methods for eigenvalue extraction

    NASA Technical Reports Server (NTRS)

    Akl, Fred

    1988-01-01

    A new numerical algorithm for the solution of large-order eigenproblems typically encountered in linear elastic finite element systems is presented. The architecture of parallel processing is used in the algorithm to achieve increased speed and efficiency of calculations. The algorithm is based on the frontal technique for the solution of linear simultaneous equations and the modified subspace eigenanalysis method for the solution of the eigenproblem. The advantages of this new algorithm in parallel computer architecture are discussed.

  13. Parallel algorithms for unconstrained optimizations by multisplitting

    SciTech Connect

    He, Qing

    1994-12-31

    In this paper a new parallel iterative algorithm for unconstrained optimization using the idea of multisplitting is proposed. This algorithm uses the existing sequential algorithms without any parallelization. Some convergence and numerical results for this algorithm are presented. The experiments are performed on an Intel iPSC/860 Hyper Cube with 64 nodes. It is interesting that the sequential implementation on one node shows that if the problem is split properly, the algorithm converges much faster than one without splitting.

  14. Computational electromagnetics and parallel dense matrix computations

    SciTech Connect

    Forsman, K.; Kettunen, L.; Gropp, W.

    1995-12-01

    We present computational results using CORAL, a parallel, three-dimensional, nonlinear magnetostatic code based on a volume integral equation formulation. A key feature of CORAL is the ability to solve, in parallel, the large, dense systems of linear equations that are inherent in the use of integral equation methods. Using the Chameleon and PSLES libraries ensures portability and access to the latest linear algebra solution technology.

  15. Algorithmic synthesis using Python compiler

    NASA Astrophysics Data System (ADS)

    Cieszewski, Radoslaw; Romaniuk, Ryszard; Pozniak, Krzysztof; Linczuk, Maciej

    2015-09-01

    This paper presents a python to VHDL compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and translate it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the programmed circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. This can be achieved by using many computational resources at the same time. Creating parallel programs implemented in FPGAs in pure HDL is difficult and time consuming. Using higher level of abstraction and High-Level Synthesis compiler implementation time can be reduced. The compiler has been implemented using the Python language. This article describes design, implementation and results of created tools.

  16. A parallel PCG solver for MODFLOW.

    PubMed

    Dong, Yanhui; Li, Guomin

    2009-01-01

    In order to simulate large-scale ground water flow problems more efficiently with MODFLOW, the OpenMP programming paradigm was used to parallelize the preconditioned conjugate-gradient (PCG) solver with in this study. Incremental parallelization, the significant advantage supported by OpenMP on a shared-memory computer, made the solver transit to a parallel program smoothly one block of code at a time. The parallel PCG solver, suitable for both MODFLOW-2000 and MODFLOW-2005, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. Based on the timing results, execution times using the parallel PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree.

  17. The Xyce Parallel Electronic Simulator - An Overview

    SciTech Connect

    HUTCHINSON,SCOTT A.; KEITER,ERIC R.; HOEKSTRA,ROBERT J.; WATTS,HERMAN A.; WATERS,ARLON J.; SCHELLS,REGINA L.; WIX,STEVEN D.

    2000-12-08

    The Xyce{trademark} Parallel Electronic Simulator has been written to support the simulation needs of the Sandia National Laboratories electrical designers. As such, the development has focused on providing the capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). In addition, they are providing improved performance for numerical kernels using state-of-the-art algorithms, support for modeling circuit phenomena at a variety of abstraction levels and using object-oriented and modern coding-practices that ensure the code will be maintainable and extensible far into the future. The code is a parallel code in the most general sense of the phrase--a message passing parallel implementation--which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Furthermore, careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved even as the number of processors grows.

  18. Parallel adaptive wavelet collocation method for PDEs

    SciTech Connect

    Nejadmalayeri, Alireza; Vezolainen, Alexei; Brown-Dymkoski, Eric; Vasilyev, Oleg V.

    2015-10-01

    A parallel adaptive wavelet collocation method for solving a large class of Partial Differential Equations is presented. The parallelization is achieved by developing an asynchronous parallel wavelet transform, which allows one to perform parallel wavelet transform and derivative calculations with only one data synchronization at the highest level of resolution. The data are stored using tree-like structure with tree roots starting at a priori defined level of resolution. Both static and dynamic domain partitioning approaches are developed. For the dynamic domain partitioning, trees are considered to be the minimum quanta of data to be migrated between the processes. This allows fully automated and efficient handling of non-simply connected partitioning of a computational domain. Dynamic load balancing is achieved via domain repartitioning during the grid adaptation step and reassigning trees to the appropriate processes to ensure approximately the same number of grid points on each process. The parallel efficiency of the approach is discussed based on parallel adaptive wavelet-based Coherent Vortex Simulations of homogeneous turbulence with linear forcing at effective non-adaptive resolutions up to 2048{sup 3} using as many as 2048 CPU cores.

  19. Parallel adaptive wavelet collocation method for PDEs

    NASA Astrophysics Data System (ADS)

    Nejadmalayeri, Alireza; Vezolainen, Alexei; Brown-Dymkoski, Eric; Vasilyev, Oleg V.

    2015-10-01

    A parallel adaptive wavelet collocation method for solving a large class of Partial Differential Equations is presented. The parallelization is achieved by developing an asynchronous parallel wavelet transform, which allows one to perform parallel wavelet transform and derivative calculations with only one data synchronization at the highest level of resolution. The data are stored using tree-like structure with tree roots starting at a priori defined level of resolution. Both static and dynamic domain partitioning approaches are developed. For the dynamic domain partitioning, trees are considered to be the minimum quanta of data to be migrated between the processes. This allows fully automated and efficient handling of non-simply connected partitioning of a computational domain. Dynamic load balancing is achieved via domain repartitioning during the grid adaptation step and reassigning trees to the appropriate processes to ensure approximately the same number of grid points on each process. The parallel efficiency of the approach is discussed based on parallel adaptive wavelet-based Coherent Vortex Simulations of homogeneous turbulence with linear forcing at effective non-adaptive resolutions up to 20483 using as many as 2048 CPU cores.

  20. Python based high-level synthesis compiler

    NASA Astrophysics Data System (ADS)

    Cieszewski, Radosław; Pozniak, Krzysztof; Romaniuk, Ryszard

    2014-11-01

    This paper presents a python based High-Level synthesis (HLS) compiler. The compiler interprets an algorithmic description of a desired behavior written in Python and map it to VHDL. FPGA combines many benefits of both software and ASIC implementations. Like software, the mapped circuit is flexible, and can be reconfigured over the lifetime of the system. FPGAs therefore have the potential to achieve far greater performance than software as a result of bypassing the fetch-decode-execute operations of traditional processors, and possibly exploiting a greater level of parallelism. Creating parallel programs implemented in FPGAs is not trivial. This article describes design, implementation and first results of created Python based compiler.

  1. Start/Pat; A parallel-programming toolkit

    SciTech Connect

    Appelbe, B.; Smith, K. ); McDowell, C. )

    1989-07-01

    How can you make Fortran code parallel without isolating the programmer from learning to understand and exploit parallelism effectively. With an interactive toolkit that automates parallelization as it educates. This paper discusses the Start/Pat toolkit.

  2. 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.

  3. Is N-acetylglutamate a short-term regulator of urea synthesis?

    PubMed Central

    Lund, P; Wiggins, D

    1984-01-01

    A method is described for determining N-acetylglutamate as glutamate. N-Acetylglutamate content of hepatocytes from 48 h-starved rats is high. It shows no parallelism with rates of urea synthesis from glutamine. We question its accepted function as a short-term regulator of urea synthesis. PMID:6721845

  4. Parallel phase model : a programming model for high-end parallel machines with manycores.

    SciTech Connect

    Wu, Junfeng; Wen, Zhaofang; Heroux, Michael Allen; Brightwell, Ronald Brian

    2009-04-01

    This paper presents a parallel programming model, Parallel Phase Model (PPM), for next-generation high-end parallel machines based on a distributed memory architecture consisting of a networked cluster of nodes with a large number of cores on each node. PPM has a unified high-level programming abstraction that facilitates the design and implementation of parallel algorithms to exploit both the parallelism of the many cores and the parallelism at the cluster level. The programming abstraction will be suitable for expressing both fine-grained and coarse-grained parallelism. It includes a few high-level parallel programming language constructs that can be added as an extension to an existing (sequential or parallel) programming language such as C; and the implementation of PPM also includes a light-weight runtime library that runs on top of an existing network communication software layer (e.g. MPI). Design philosophy of PPM and details of the programming abstraction are also presented. Several unstructured applications that inherently require high-volume random fine-grained data accesses have been implemented in PPM with very promising results.

  5. Design and Synthesis of Analogues of Marine Natural Product Galaxamide, an N-methylated Cyclic Pentapeptide, as Potential Anti-Tumor Agent in Vitro

    PubMed Central

    Lunagariya, Jignesh; Zhong, Shenghui; Chen, Jianwei; Bai, Defa; Bhadja, Poonam; Long, Weili; Liao, Xiaojian; Tang, Xiaoli; Xu, Shihai

    2016-01-01

    Herein, we report design and synthesis of novel 26 galaxamide analogues with N-methylated cyclo-pentapeptide, and their in vitro anti-tumor activity towards the panel of human tumor cell line, such as, A549, A549/DPP, HepG2 and SMMC-7721 using MTT assay. We have also investigated the effect of galaxamide and its representative analogues on growth, cell-cycle phases, and induction of apoptosis in SMMC-7721 cells in vitro. Reckon with the significance of conformational space and N-Me aminoacid (aa) comprising this compound template, we designed the analogues with modification in N-Me-aa position, change in aa configuration from l to d aa and substitute one Leu-aa to d/l Phe-aa residue with respective to the parent structure. The efficient solid phase parallel synthesis approach is employed for the linear pentapeptide residue containing N-Me aa, followed by solution phase macrocyclisation to afford target cyclo pentapeptide compounds. In the present study, all galaxamide analogues exhibited growth inhibition in A549, A549/DPP, SMMC-7721 and HepG2 cell lines. Compounds 6, 18, and 22 exhibited interesting activities towards all cell line tested, while Compounds 1, 4, 15, and 22 showed strong activity towards SMMC-7221 cell line in the range of 1–2 μg/mL IC50. Flow cytometry experiment revealed that galaxamide analogues namely Compounds 6, 18, and 22 induced concentration dependent SMMC-7721 cell apoptosis after 48 h. These compounds induced G0/G1 phase cell-cycle arrest and morphological changes indicating induction of apoptosis. Thus, findings of our study suggest that the galaxamide and its analogues 6, 18 and 22 exerted growth inhibitory effect on SMMC-7721 cells by arresting the cell cycle in the G0/G1 phase and inducing apoptosis. Compound 1 showed promising anti-tumor activity towards SMMC-7721 cancer cell line, which is 9 and 10 fold higher than galaxamide and reference DPP (cisplatin), respectively. PMID:27598177

  6. Design and Synthesis of Analogues of Marine Natural Product Galaxamide, an N-methylated Cyclic Pentapeptide, as Potential Anti-Tumor Agent in Vitro.

    PubMed

    Lunagariya, Jignesh; Zhong, Shenghui; Chen, Jianwei; Bai, Defa; Bhadja, Poonam; Long, Weili; Liao, Xiaojian; Tang, Xiaoli; Xu, Shihai

    2016-09-03

    Herein, we report design and synthesis of novel 26 galaxamide analogues with N-methylated cyclo-pentapeptide, and their in vitro anti-tumor activity towards the panel of human tumor cell line, such as, A549, A549/DPP, HepG2 and SMMC-7721 using MTT assay. We have also investigated the effect of galaxamide and its representative analogues on growth, cell-cycle phases, and induction of apoptosis in SMMC-7721 cells in vitro. Reckon with the significance of conformational space and N-Me aminoacid (aa) comprising this compound template, we designed the analogues with modification in N-Me-aa position, change in aa configuration from l to d aa and substitute one Leu-aa to d/l Phe-aa residue with respective to the parent structure. The efficient solid phase parallel synthesis approach is employed for the linear pentapeptide residue containing N-Me aa, followed by solution phase macrocyclisation to afford target cyclo pentapeptide compounds. In the present study, all galaxamide analogues exhibited growth inhibition in A549, A549/DPP, SMMC-7721 and HepG2 cell lines. Compounds 6, 18, and 22 exhibited interesting activities towards all cell line tested, while Compounds 1, 4, 15, and 22 showed strong activity towards SMMC-7221 cell line in the range of 1-2 μg/mL IC50. Flow cytometry experiment revealed that galaxamide analogues namely Compounds 6, 18, and 22 induced concentration dependent SMMC-7721 cell apoptosis after 48 h. These compounds induced G0/G1 phase cell-cycle arrest and morphological changes indicating induction of apoptosis. Thus, findings of our study suggest that the galaxamide and its analogues 6, 18 and 22 exerted growth inhibitory effect on SMMC-7721 cells by arresting the cell cycle in the G0/G1 phase and inducing apoptosis. Compound 1 showed promising anti-tumor activity towards SMMC-7721 cancer cell line, which is 9 and 10 fold higher than galaxamide and reference DPP (cisplatin), respectively.

  7. PISCES: An environment for parallel scientific computation

    NASA Technical Reports Server (NTRS)

    Pratt, T. W.

    1985-01-01

    The parallel implementation of scientific computing environment (PISCES) is a project to provide high-level programming environments for parallel MIMD computers. Pisces 1, the first of these environments, is a FORTRAN 77 based environment which runs under the UNIX operating system. The Pisces 1 user programs in Pisces FORTRAN, an extension of FORTRAN 77 for parallel processing. The major emphasis in the Pisces 1 design is in providing a carefully specified virtual machine that defines the run-time environment within which Pisces FORTRAN programs are executed. Each implementation then provides the same virtual machine, regardless of differences in the underlying architecture. The design is intended to be portable to a variety of architectures. Currently Pisces 1 is implemented on a network of Apollo workstations and on a DEC VAX uniprocessor via simulation of the task level parallelism. An implementation for the Flexible Computing Corp. FLEX/32 is under construction. An introduction to the Pisces 1 virtual computer and the FORTRAN 77 extensions is presented. An example of an algorithm for the iterative solution of a system of equations is given. The most notable features of the design are the provision for several granularities of parallelism in programs and the provision of a window mechanism for distributed access to large arrays of data.

  8. Equalizer: a scalable parallel rendering framework.

    PubMed

    Eilemann, Stefan; Makhinya, Maxim; Pajarola, Renato

    2009-01-01

    Continuing improvements in CPU and GPU performances as well as increasing multi-core processor and cluster-based parallelism demand for flexible and scalable parallel rendering solutions that can exploit multipipe hardware accelerated graphics. In fact, to achieve interactive visualization, scalable rendering systems are essential to cope with the rapid growth of data sets. However, parallel rendering systems are non-trivial to develop and often only application specific implementations have been proposed. The task of developing a scalable parallel rendering framework is even more difficult if it should be generic to support various types of data and visualization applications, and at the same time work efficiently on a cluster with distributed graphics cards. In this paper we introduce a novel system called Equalizer, a toolkit for scalable parallel rendering based on OpenGL which provides an application programming interface (API) to develop scalable graphics applications for a wide range of systems ranging from large distributed visualization clusters and multi-processor multipipe graphics systems to single-processor single-pipe desktop machines. We describe the system architecture, the basic API, discuss its advantages over previous approaches, present example configurations and usage scenarios as well as scalability results.

  9. A parallel algorithm for random searches

    NASA Astrophysics Data System (ADS)

    Wosniack, M. E.; Raposo, E. P.; Viswanathan, G. M.; da Luz, M. G. E.

    2015-11-01

    We discuss a parallelization procedure for a two-dimensional random search of a single individual, a typical sequential process. To assure the same features of the sequential random search in the parallel version, we analyze the former spatial patterns of the encountered targets for different search strategies and densities of homogeneously distributed targets. We identify a lognormal tendency for the distribution of distances between consecutively detected targets. Then, by assigning the distinct mean and standard deviation of this distribution for each corresponding configuration in the parallel simulations (constituted by parallel random walkers), we are able to recover important statistical properties, e.g., the target detection efficiency, of the original problem. The proposed parallel approach presents a speedup of nearly one order of magnitude compared with the sequential implementation. This algorithm can be easily adapted to different instances, as searches in three dimensions. Its possible range of applicability covers problems in areas as diverse as automated computer searchers in high-capacity databases and animal foraging.

  10. Parallel algorithms for the spectral transform method

    SciTech Connect

    Foster, I.T.; Worley, P.H.

    1997-05-01

    The spectral transform method is a standard numerical technique for solving partial differential equations on a sphere and is widely used in atmospheric circulation models. Recent research has identified several promising algorithms for implementing this method on massively parallel computers; however, no detailed comparison of the different algorithms has previously been attempted. In this paper, the authors describe these different parallel algorithms and report on computational experiments that they have conducted to evaluate their efficiency on parallel computers. The experiments used a testbed code that solves the nonlinear shallow water equations on a sphere; considerable care was taken to ensure that the experiments provide a fair comparison of the different algorithms and that the results are relevant to global models. The authors focus on hypercube- and mesh-connected multicomputers with cut-through routing, such as the Intel iPSC/860, DELTA, and Paragon, and the nCUBE/2, but they also indicate how the results extend to other parallel computer architectures. The results of this study are relevant not only to the spectral transform method but also to multidimensional fast Fourier transforms (FFTs) and other parallel transforms.

  11. Iteration schemes for parallelizing models of superconductivity

    SciTech Connect

    Gray, P.A.

    1996-12-31

    The time dependent Lawrence-Doniach model, valid for high fields and high values of the Ginzburg-Landau parameter, is often used for studying vortex dynamics in layered high-T{sub c} superconductors. When solving these equations numerically, the added degrees of complexity due to the coupling and nonlinearity of the model often warrant the use of high-performance computers for their solution. However, the interdependence between the layers can be manipulated so as to allow parallelization of the computations at an individual layer level. The reduced parallel tasks may then be solved independently using a heterogeneous cluster of networked workstations connected together with Parallel Virtual Machine (PVM) software. Here, this parallelization of the model is discussed and several computational implementations of varying degrees of parallelism are presented. Computational results are also given which contrast properties of convergence speed, stability, and consistency of these implementations. Included in these results are models involving the motion of vortices due to an applied current and pinning effects due to various material properties.

  12. IMPAIR: massively parallel deconvolution on the GPU

    NASA Astrophysics Data System (ADS)

    Sherry, Michael; Shearer, Andy

    2013-02-01

    The IMPAIR software is a high throughput image deconvolution tool for processing large out-of-core datasets of images, varying from large images with spatially varying PSFs to large numbers of images with spatially invariant PSFs. IMPAIR implements a parallel version of the tried and tested Richardson-Lucy deconvolution algorithm regularised via a custom wavelet thresholding library. It exploits the inherently parallel nature of the convolution operation to achieve quality results on consumer grade hardware: through the NVIDIA Tesla GPU implementation, the multi-core OpenMP implementation, and the cluster computing MPI implementation of the software. IMPAIR aims to address the problem of parallel processing in both top-down and bottom-up approaches: by managing the input data at the image level, and by managing the execution at the instruction level. These combined techniques will lead to a scalable solution with minimal resource consumption and maximal load balancing. IMPAIR is being developed as both a stand-alone tool for image processing, and as a library which can be embedded into non-parallel code to transparently provide parallel high throughput deconvolution.

  13. Toward a science of parallel computation

    SciTech Connect

    Worlton, W.J.

    1986-01-01

    The evolution of parallel processing over the past several decades can be viewed as the development of a new scientific discipline. Parallel processing has been, and is, undergoing the same evolutionary stages that are common to the development of scientific disciplines in general: exploration, focusing, and maturity. That parallel processing is not yet a science can readily be appreciated by its lack of some of the characteristics typical of mature sciences, such as prescriptive terminology, comprehensive taxonomies, and authoritative fundamental principles. A great deal of outstanding work has been done and the field is experiencing the beginnings of its ''focusing'' phase, i.e., support is being concentrated in a set of the more promising approaches selected from among the larger set of exploratory projects. However, the possible set of parallel-processing concepts is so extensive that exploratory work will probably continue for one or two more decades. In the meantime, the growing maturity of the field will be reflected in the increasing clarity and precision of the terminology, the development of systematic classification of the domain of discourse, the development of basic principles, and the growing number of commercial products that are the outcome of the research and development projects on which support is being focused. In this paper we develop some generalizations of taxonomies and use basic principles to draw conclusions about the extensibility of parallel processor architectures. 7 refs., 5 figs., 2 tabs.

  14. Linear Bregman algorithm implemented in parallel GPU

    NASA Astrophysics Data System (ADS)

    Li, Pengyan; Ke, Jue; Sui, Dong; Wei, Ping

    2015-08-01

    At present, most compressed sensing (CS) algorithms have poor converging speed, thus are difficult to run on PC. To deal with this issue, we use a parallel GPU, to implement a broadly used compressed sensing algorithm, the Linear Bregman algorithm. Linear iterative Bregman algorithm is a reconstruction algorithm proposed by Osher and Cai. Compared with other CS reconstruction algorithms, the linear Bregman algorithm only involves the vector and matrix multiplication and thresholding operation, and is simpler and more efficient for programming. We use C as a development language and adopt CUDA (Compute Unified Device Architecture) as parallel computing architectures. In this paper, we compared the parallel Bregman algorithm with traditional CPU realized Bregaman algorithm. In addition, we also compared the parallel Bregman algorithm with other CS reconstruction algorithms, such as OMP and TwIST algorithms. Compared with these two algorithms, the result of this paper shows that, the parallel Bregman algorithm needs shorter time, and thus is more convenient for real-time object reconstruction, which is important to people's fast growing demand to information technology.

  15. A feasibility study of multiplexing parallel beam.

    PubMed

    Ma, Jiayi; Zhao, Jingwu; Shi, Xiaodong; Huang, Runshen

    2013-05-01

    Single-photon emission computed tomography (SPECT) is a suitable tool for clinically localizing deep-sited tumors; SPECT with high spatial resolution has the ability to localize deep-sited tumors precisely. However, because of its poor sensitivity, in China SPECT now only plays a complementary role. To improve the sensitivity of the parallel beam collimator mainly used in China, a multiplexing parallel beam collimator is proposed, which can improve sensitivity while maintaining higher spatial resolution by using theoretical prediction and Monte Carlo simulation. The improved sensitivity-to-spatial resolution ratio has an optimal value. In addition, a set of gamma ray channels, introduced only in the transverse direction, did not have any effect in the axial direction. In the transverse direction, the projection data are the sum of the parallel beam and two oblique parallel beams. From visual assessment obtained using computer simulations with equal sensitivity, the reconstructed image at deep-sited was noticeably better than that with the high sensitivity parallel beam.

  16. Parallel algorithms for the spectral transform method

    SciTech Connect

    Foster, I.T.; Worley, P.H.

    1994-04-01

    The spectral transform method is a standard numerical technique for solving partial differential equations on a sphere and is widely used in atmospheric circulation models. Recent research has identified several promising algorithms for implementing this method on massively parallel computers; however, no detailed comparison of the different algorithms has previously been attempted. In this paper, we describe these different parallel algorithms and report on computational experiments that we have conducted to evaluate their efficiency on parallel computers. The experiments used a testbed code that solves the nonlinear shallow water equations or a sphere; considerable care was taken to ensure that the experiments provide a fair comparison of the different algorithms and that the results are relevant to global models. We focus on hypercube- and mesh-connected multicomputers with cut-through routing, such as the Intel iPSC/860, DELTA, and Paragon, and the nCUBE/2, but also indicate how the results extend to other parallel computer architectures. The results of this study are relevant not only to the spectral transform method but also to multidimensional FFTs and other parallel transforms.

  17. Relative Debugging of Automatically Parallelized Programs

    NASA Technical Reports Server (NTRS)

    Jost, Gabriele; Hood, Robert; Biegel, Bryan (Technical Monitor)

    2002-01-01

    We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the computations begin to differ. If the original serial code is correct, errors due to parallelization will be isolated by the comparison. One of the primary goals of the system is to minimize the effort required of the user. To that end, the debugging system uses information produced by the parallelization tool to drive the comparison process. In particular, the debugging system relies on the parallelization tool to provide information about where variables may have been modified and how arrays are distributed across multiple processes. User effort is also reduced through the use of dynamic instrumentation. This allows us to modify, the program execution with out changing the way the user builds the executable. The use of dynamic instrumentation also permits us to compare the executions in a fine-grained fashion and only involve the debugger when a difference has been detected. This reduces the overhead of executing instrumentation.

  18. Support for Debugging Automatically Parallelized Programs

    NASA Technical Reports Server (NTRS)

    Jost, Gabriele; Hood, Robert; Biegel, Bryan (Technical Monitor)

    2001-01-01

    We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the computations begin to differ. If the original serial code is correct, errors due to parallelization will be isolated by the comparison. One of the primary goals of the system is to minimize the effort required of the user. To that end, the debugging system uses information produced by the parallelization tool to drive the comparison process. In particular the debugging system relies on the parallelization tool to provide information about where variables may have been modified and how arrays are distributed across multiple processes. User effort is also reduced through the use of dynamic instrumentation. This allows us to modify the program execution without changing the way the user builds the executable. The use of dynamic instrumentation also permits us to compare the executions in a fine-grained fashion and only involve the debugger when a difference has been detected. This reduces the overhead of executing instrumentation.

  19. A parallel adaptive mesh refinement algorithm

    NASA Technical Reports Server (NTRS)

    Quirk, James J.; Hanebutte, Ulf R.

    1993-01-01

    Over recent years, Adaptive Mesh Refinement (AMR) algorithms which dynamically match the local resolution of the computational grid to the numerical solution being sought have emerged as powerful tools for solving problems that contain disparate length and time scales. In particular, several workers have demonstrated the effectiveness of employing an adaptive, block-structured hierarchical grid system for simulations of complex shock wave phenomena. Unfortunately, from the parallel algorithm developer's viewpoint, this class of scheme is quite involved; these schemes cannot be distilled down to a small kernel upon which various parallelizing strategies may be tested. However, because of their block-structured nature such schemes are inherently parallel, so all is not lost. In this paper we describe the method by which Quirk's AMR algorithm has been parallelized. This method is built upon just a few simple message passing routines and so it may be implemented across a broad class of MIMD machines. Moreover, the method of parallelization is such that the original serial code is left virtually intact, and so we are left with just a single product to support. The importance of this fact should not be underestimated given the size and complexity of the original algorithm.

  20. Design, synthesis, and evaluation of an alpha-helix mimetic library targeting protein-protein interactions.

    PubMed

    Shaginian, Alex; Whitby, Landon R; Hong, Sukwon; Hwang, Inkyu; Farooqi, Bilal; Searcey, Mark; Chen, Jiandong; Vogt, Peter K; Boger, Dale L

    2009-04-22

    The design and solution-phase synthesis of an alpha-helix mimetic library as an integral component of a small-molecule library targeting protein-protein interactions are described. The iterative design, synthesis, and evaluation of the candidate alpha-helix mimetic was initiated from a precedented triaryl template and refined by screening the designs for inhibition of MDM2/p53 binding. Upon identifying a chemically and biologically satisfactory design and consistent with the screening capabilities of academic collaborators, the corresponding complete library was assembled as 400 mixtures of 20 compounds (20 x 20 x 20-mix), where the added subunits are designed to mimic all possible permutations of the naturally occurring i, i + 4, i + 7 amino acid side chains of an alpha-helix. The library (8000 compounds) was prepared using a solution-phase synthetic protocol enlisting acid/base liquid-liquid extractions for purification on a scale that insures its long-term availability for screening campaigns. Screening of the library for inhibition of MDM2/p53 binding not only identified the lead alpha-helix mimetic upon which the library was based, but also suggests that a digestion of the initial screening results that accompany the use of such a comprehensive library can provide insights into the nature of the interaction (e.g., an alpha-helix mediated protein-protein interaction) and define the key residues and their characteristics responsible for recognition.