WorldWideScience

Sample records for bagel assembler generation

  1. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins.

    Science.gov (United States)

    van Heel, Auke J; de Jong, Anne; Song, Chunxu; Viel, Jakob H; Kok, Jan; Kuipers, Oscar P

    2018-05-21

    Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster than its predecessor and is now fully independent from ORF-calling. Gene clusters of interest are discovered using the core-peptide database and/or through HMM motifs that are present in associated context genes. The databases used for mining have been updated and extended with literature references and links to UniProt and NCBI. Additionally, we have included automated promoter and terminator prediction and the option to upload RNA expression data, which can be displayed along with the identified clusters. Further improvements include the annotation of the context genes, which is now based on a fast blast against the prokaryote part of the UniRef90 database, and the improved web-BLAST feature that dynamically loads structural data such as internal cross-linking from UniProt. Overall BAGEL4 provides the user with more information through a user-friendly web-interface which simplifies data evaluation. BAGEL4 is freely accessible at http://bagel4.molgenrug.nl.

  2. Assembly delay line pulse generators

    CERN Multimedia

    CERN PhotoLab

    1971-01-01

    Assembly of six of the ten delay line pulse generators that will power the ten kicker magnet modules. One modulator part contains two pulse generators. Capacitors, inductances, and voltage dividers are in the oil tank on the left. Triggered high-pressure spark gap switches are on the platforms on the right. High voltage pulse cables to the kicker magnet emerge under the spark gaps. In the centre background are the assembled master gaps.

  3. Assembly and handling apparatus for the EBFA Marx generator

    International Nuclear Information System (INIS)

    Staller, G.E.; Hiett, G.E.; Hamilton, I.D.; Aker, M.F.; Daniels, G.A.

    1979-05-01

    Marx generators, a major slow-pulsed power component in Sandia Laboratories' Electron Beam Fusion Accelerator (EBFA), were assembled at a remote facility modified to utilize an assembly-line technique. Due to the size and weight of the various components, as well as the final Marx generator assembly, special handling apparatus was designed. Time and manpower constraints required that this assembly be done in parallel with the construction of the Electron Beam Fusion Facility (EBFF). The completed Marx generators were temporarily stored and then moved from the assembly building to the EBFF using special transportation racks designed specifically for this purpose

  4. A facility to remotely assemble radioisotope thermoelectric generators

    International Nuclear Information System (INIS)

    Engstrom, J.W.; Goldmann, L.H.; Truitt, R.W.

    1992-07-01

    Radioisotope Thermoelectric Generators (RTGs) are electrical power sources that use heat from decaying radioisotopes to directly generate electrical power. The RTG assembly process is performed in an inert atmosphere inside a large glovebox, which is surrounded by radiation shielding to reduce exposure to neutron and gamma radiation from the radioisotope heat source. In the past, allowable dose rate limits have allowed direct, manual assembly methods; however, current dose rate limits require a thicker radiation shielding that makes direct, manual assembly infeasible. To minimize RTG assembly process modifications, telerobotic systems are being investigated to perform remote assembly tasks. Telerobotic systems duplicate human arm motion and incorporate force feedback sensitivity to handle objects and tools in a human-like manner. A telerobotic system with two arms and a three-dimensional (3-D) vision system can be used to perform remote RTG assembly tasks inside gloveboxes and cells using unmodified, normal hand tools

  5. Tablet—next generation sequence assembly visualization

    Science.gov (United States)

    Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David

    2010-01-01

    Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Availability: Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions. Contact: tablet@scri.ac.uk PMID:19965881

  6. Electrode assemblies, plasma apparatuses and systems including electrode assemblies, and methods for generating plasma

    Science.gov (United States)

    Kong, Peter C; Grandy, Jon D; Detering, Brent A; Zuck, Larry D

    2013-09-17

    Electrode assemblies for plasma reactors include a structure or device for constraining an arc endpoint to a selected area or region on an electrode. In some embodiments, the structure or device may comprise one or more insulating members covering a portion of an electrode. In additional embodiments, the structure or device may provide a magnetic field configured to control a location of an arc endpoint on the electrode. Plasma generating modules, apparatus, and systems include such electrode assemblies. Methods for generating a plasma include covering at least a portion of a surface of an electrode with an electrically insulating member to constrain a location of an arc endpoint on the electrode. Additional methods for generating a plasma include generating a magnetic field to constrain a location of an arc endpoint on an electrode.

  7. INTEGRATED APPROACH TO GENERATION OF PRECEDENCE RELATIONS AND PRECEDENCE GRAPHS FOR ASSEMBLY SEQUENCE PLANNING

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    An integrated approach to generation of precedence relations and precedence graphs for assembly sequence planning is presented, which contains more assembly flexibility. The approach involves two stages. Based on the assembly model, the components in the assembly can be divided into partially constrained components and completely constrained components in the first stage, and then geometric precedence relation for every component is generated automatically. According to the result of the first stage, the second stage determines and constructs all precedence graphs. The algorithms of these two stages proposed are verified by two assembly examples.

  8. Advanced Stirling Radioisotope Generator Engineering Unit 2 (ASRG EU2) Final Assembly

    Science.gov (United States)

    Oriti, Salvatore M.

    2015-01-01

    NASA Glenn Research Center (GRC) has recently completed the assembly of a unique Stirling generator test article for laboratory experimentation. Under the Advanced Stirling Radioisotope Generator (ASRG) flight development contract, NASA GRC initiated a task to design and fabricate a flight-like generator for in-house testing. This test article was given the name ASRG Engineering Unit 2 (EU2) as it was effectively the second engineering unit to be built within the ASRG project. The intent of the test article was to duplicate Lockheed Martin's qualification unit ASRG design as much as possible to enable system-level tests not previously possible at GRC. After the cancellation of the ASRG flight development project, the decision was made to continue the EU2 build, and make use of a portion of the hardware from the flight development project. GRC and Lockheed Martin engineers collaborated to develop assembly procedures, leveraging the valuable knowledge gathered by Lockheed Martin during the ASRG development contract. The ASRG EU2 was then assembled per these procedures at GRC with Lockheed Martin engineers on site. The assembly was completed in August 2014. This paper details the components that were used for the assembly, and the assembly process itself.

  9. Verification of a Subgroup Generation Method for Thorium Fuel Assemblies

    International Nuclear Information System (INIS)

    Sim, Ohsung; Kim, Myunghyun

    2013-01-01

    Resonance parameter consists of subgroup level and weight. The subgroup weight is obtained by solving the ultrafine slowing down equation and fixed source problem. That means this cross section library procedure considers conservation of the shielded cross section for pin-cell in order to obtain subgroup parameters. There are some isotopes to be concerned for research such as actinides and thorium. Minor actinides(MA) are existing with very small amount in a spent fuel, but effect is not negligible in a high burnup fuel assemblies. Some MAs have high fission cross sections under thermal neutron spectrum. Thorium isotopes was not investigated as much as uranium, but it has high potential for future application. In this study, a new cross section library to be replaced with HELIOS library was generated and compared for the assembly calculation, specially for assembly with thorium. An average capture cross section value at a certain fuel pin and multiplication factor of assembly were compared with nTRACER calculation with HELIOS library and Monte Carlo calculation of MCNP with ENDF-B/II. The accuracy of library data generated for thorium isotope in nTRACER calculation was tested for WASB model. There was a great improvement in K-eff and capture cross section for this assembly compared with old library, HELIOS library

  10. Next-generation transcriptome assembly

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey A.; Wang, Zhong

    2011-09-01

    Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

  11. In Situ Generation of Two-Dimensional Au–Pt Core–Shell Nanoparticle Assemblies

    Directory of Open Access Journals (Sweden)

    Khalid Madiha

    2009-01-01

    Full Text Available Abstract Two-dimensional assemblies of Au–Pt bimetallic nanoparticles are generated in situ on polyethyleneimmine (PEI silane functionalized silicon and indium tin oxide (ITO coated glass surfaces. Atomic force microscopy (AFM, UV–Visible spectroscopy, and electrochemical measurements reveal the formation of core–shell structure with Au as core and Pt as shell. The core–shell structure is further supported by comparing with the corresponding data of Au nanoparticle assemblies. Static contact angle measurements with water show an increase in hydrophilic character due to bimetallic nanoparticle generation on different surfaces. It is further observed that these Au–Pt core–shell bimetallic nanoparticle assemblies are catalytically active towards methanol electro-oxidation, which is the key reaction for direct methanol fuel cells (DMFCs.

  12. Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data.

    Science.gov (United States)

    Jayakumar, Vasanthan; Sakakibara, Yasubumi

    2017-11-03

    Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms. © The Author 2017. Published by Oxford University Press.

  13. Generation of Supramolecular Chirality around Twofold Rotational or Helical Axes in Crystalline Assemblies of Achiral Components

    Directory of Open Access Journals (Sweden)

    Mikiji Miyata

    2015-10-01

    Full Text Available A multi-point approximation method clarifies supramolecular chirality of twofold rotational or helical assemblies as well as bundles of the one-dimensional (1D assemblies. While one-point approximation of materials claims no chirality generation of such assemblies, multi-point approximations do claim possible generation in the 1D assemblies of bars and plates. Such chirality derives from deformations toward three-axial directions around the helical axes. The chiral columns are bundled in chiral ways through symmetry operations. The preferable right- or left-handed columns are bundled together to yield chiral crystals with right- or left-handedness, respectively, indicating that twofold helix symmetry operations cause chiral crystals composed of achiral components via a three-stepwise and three-directional process.

  14. Characteristics of U-tube assembly design for CANDU 6 type steam generators

    International Nuclear Information System (INIS)

    Park, Jun Su; Jeong, Seung Ha

    1996-06-01

    Since the first operation of nuclear steam generator early 1960s, its performance requirements have been met but the steam generator problems have been met but the steam generator problems have been major cause of reducing the operational reliability, plant safety and availability. U-tube assembly of steam generator forms the primary system pressure boundary of the plant and have experienced several types of tube degradation problems. Tube failure and leakage resulting from the degradation will cause radioactive contamination of secondary system by the primary coolant, and this may lead to unplanned plant outages and costly repair operations such as tube plugging or steam generator replacement. For the case of steam generators for heavy water reactors, e.g. Wolsong 2, 3, and 4 NPP, a high cost of heavy water will be imposed additionally. During the plant operation, steam generator tubes can potentially be subject to adverse environmental conditions which will cause damages to U-tube assembly. Types of the damage depend upon the combined effects of design factors, materials and chemical environment of steam generator, and they are the pure water stress corrosion cracking, intergranular attack, pitting, wastage, denting, fretting and fatigue, etc. In this report, a comprehensive review of major design factors of recirculating steam generators has been performed against the potential tube damages. Then the design characteristics of CANDU-type Wolsong steam generator were investigated in detail, including tube material, thermalhydraulic aspects, tube-to-tubesheet joint, tube supports, water chemistry and sludge management. 9 tabs., 18 figs., 38 refs. (Author) .new

  15. Use of virtual steam generator cassette for tube spatial design and SGC assembling procedure

    International Nuclear Information System (INIS)

    Kim, Y. W.; Kim, J. I.; Ji, S. K.

    2003-01-01

    A method of determining spatial arrangement of tube connection and assembling procedure of once-through helical steam generator cassette utilizing three dimensional virtual steam generator cassette has been developed on the basis of recent 3-D modelling technology. One ends of the steam generator tubes are connected to the module feed water header and the other sides are connected to the module steam header. Due to the complex geometry of tube arrangement, it is very difficult to connect the tubes to the module headers without the help of a physical engineering mock up. A comparative study has been performed at each design step for the tube arrangement and heat transfer area. Heat transfer area computed from thermal sizing was 4% less than that of measured. Heat transfer area calculated from the virtual steam generator cassette mock up has only 0.2% difference with that of measured. Assembling procedure of the steam generator cassette also, can be developed in the design stage

  16. A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes.

    Science.gov (United States)

    Gopinath, G R; Cinar, H N; Murphy, H R; Durigan, M; Almeria, M; Tall, B D; DaSilva, A J

    2018-01-01

    Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations.

  17. Epoxy Adhesives for Stator Magnet Assembly in Stirling Radioisotope Generators (SRG)

    Science.gov (United States)

    Cater, George M.

    2004-01-01

    analysis was done as a function of cure time and temperatures. Adhesion bond strength was tested at various temperatures with lap shear samples using Hiperco 50 substrate to ensure that the proper adhesive is being used. To try and solve the problem of bondline thickness, micro glass beads of 0.0017" in diameter were investigated to see if any other physical properties of the epoxy were affected. Efforts will be made to develop a standard, optimized, fabrication process/procedure of sub-scale magnet-stator assemblies for various adhesive performance evaluation studies under simulated generator conditions. Also, accelerated aging testing will be done in a pressurized canister with stator assembly samples for three years to verify if any degassing or thermal degradation of the epoxy occurs. The necessity of verifying the correct epoxy adhesive system for the stator magnet in the SRG is crucial because failure of the stator assembly would jeopardize the electrical system, and thereby the entire mission itself. My work involves specimen fabrications, testing, and data analyses of the epoxy adhesive system for the stator magnet in the SRG is crucial because failure of the stator assembly would jeopardize the electrical system, and thereby the entire mission itself.

  18. Assembly of the Vivitron generator: State of the art on the 29th September 1989

    International Nuclear Information System (INIS)

    Heugel, J.

    1989-09-01

    The generator construction planning and the Van de Graaf components assembling are shown. The work performed since May 1989 and those in progress are described. The original design, the characteristics and performances, as well as the modifications carried out on the voltage divider are included. The charging system assembling is described [fr

  19. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Wenyu Zhang

    Full Text Available The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers.

  20. New tool to assemble repetitive regions using next-generation sequencing data

    Science.gov (United States)

    Kuśmirek, Wiktor; Nowak, Robert M.; Neumann, Łukasz

    2017-08-01

    The next generation sequencing techniques produce a large amount of sequencing data. Some part of the genome are composed of repetitive DNA sequences, which are very problematic for the existing genome assemblers. We propose a modification of the algorithm for a DNA assembly, which uses the relative frequency of reads to properly reconstruct repetitive sequences. The new approach was implemented and tested, as a demonstration of the capability of our software we present some results for model organisms. The new implementation, using a three-layer software architecture was selected, where the presentation layer, data processing layer, and data storage layer were kept separate. Source code as well as demo application with web interface and the additional data are available at project web-page: http://dnaasm.sourceforge.net.

  1. Peptide Assembly-Driven Metal-Organic Framework (MOF) Motors for Micro Electric Generator

    Science.gov (United States)

    Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L.; Uemura, Takashi; Zheng, Yongtai; Kitagawa, Susumu

    2014-01-01

    Peptide-MOF motors, whose motions are driven by anisotropic surface gradients created via peptide self-assembly around nanopores of MOFs, can rotate microscopic rotors and magnet fast enough to generate electric power of 0.1 µW. To make the peptide-MOF generator recyclable, a new MOF is applied as a host motor engine, which has a more rigid framework with higher H2O affinity so that peptide release occurs more efficiently via guest exchange without the destruction of MOF. PMID:25418936

  2. Methods for Generating Highly Magnetically Responsive Lanthanide-Chelating Phospholipid Polymolecular Assemblies.

    Science.gov (United States)

    Isabettini, Stéphane; Baumgartner, Mirjam E; Reckey, Pernille Q; Kohlbrecher, Joachim; Ishikawa, Takashi; Fischer, Peter; Windhab, Erich J; Kuster, Simon

    2017-06-27

    Mixtures of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and its lanthanide ion (Ln 3+ ) chelating phospholipid conjugate, 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA), assemble into highly magnetically responsive polymolecular assemblies such as DMPC/DMPE-DTPA/Ln 3+ (molar ratio 4:1:1) bicelles. Their geometry and magnetic alignability is enhanced by introducing cholesterol into the bilayer in DMPC/Cholesterol/DMPE-DTPA/Ln 3+ (molar ratio 16:4:5:5). However, the reported fabrication procedures remain tedious and limit the generation of highly magnetically alignable species. Herein, a simplified procedure where freeze thawing cycles and extrusion are replaced by gentle heating and cooling cycles for the hydration of the dry lipid film was developed. Heating above the phase transition temperature T m of the lipids composing the bilayer before cooling back below the T m was essential to guarantee successful formation of the polymolecular assemblies composed of DMPC/DMPE-DTPA/Ln 3+ (molar ratio 4:1:1). Planar polymolecular assemblies in the size range of hundreds of nanometers are achieved and deliver unprecedented gains in magnetic response. The proposed heating and cooling procedure further allowed to regenerate the highly magnetically alignable DMPC/Cholesterol/DMPE-DTPA/Ln 3+ (molar ratio 16:4:5:5) species after storage for one month frozen at -18 °C. The simplicity and viability of the proposed fabrication procedure offers a new set of highly magnetically responsive lanthanide ion chelating phospholipid polymolecular assemblies as building blocks for the smart soft materials of tomorrow.

  3. Graph mining for next generation sequencing: leveraging the assembly graph for biological insights.

    Science.gov (United States)

    Warnke-Sommer, Julia; Ali, Hesham

    2016-05-06

    The assembly of Next Generation Sequencing (NGS) reads remains a challenging task. This is especially true for the assembly of metagenomics data that originate from environmental samples potentially containing hundreds to thousands of unique species. The principle objective of current assembly tools is to assemble NGS reads into contiguous stretches of sequence called contigs while maximizing for both accuracy and contig length. The end goal of this process is to produce longer contigs with the major focus being on assembly only. Sequence read assembly is an aggregative process, during which read overlap relationship information is lost as reads are merged into longer sequences or contigs. The assembly graph is information rich and capable of capturing the genomic architecture of an input read data set. We have developed a novel hybrid graph in which nodes represent sequence regions at different levels of granularity. This model, utilized in the assembly and analysis pipeline Focus, presents a concise yet feature rich view of a given input data set, allowing for the extraction of biologically relevant graph structures for graph mining purposes. Focus was used to create hybrid graphs to model metagenomics data sets obtained from the gut microbiomes of five individuals with Crohn's disease and eight healthy individuals. Repetitive and mobile genetic elements are found to be associated with hybrid graph structure. Using graph mining techniques, a comparative study of the Crohn's disease and healthy data sets was conducted with focus on antibiotics resistance genes associated with transposase genes. Results demonstrated significant differences in the phylogenetic distribution of categories of antibiotics resistance genes in the healthy and diseased patients. Focus was also evaluated as a pure assembly tool and produced excellent results when compared against the Meta-velvet, Omega, and UD-IDBA assemblers. Mining the hybrid graph can reveal biological phenomena captured

  4. Drop performance test of conceptually designed control rod assembly for prototype generation IV sodium-cooled fast reactor

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Kyu; Lee, Jae Han; Kim, Hoe Woong; KIm, Sung Kyun; Kim, Jong Bum [Sodium-cooled Fast Reactor NSSS Design Division, Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2017-06-15

    The control rod assembly controls reactor power by adjusting its position during normal operation and shuts down chain reactions by its free drop under scram conditions. Therefore, the drop performance of the control rod assembly is important for the safety of a nuclear reactor. In this study, the drop performance of the conceptually designed control rod assembly for the prototype generation IV sodium-cooled fast reactor that is being developed at the Korea Atomic Energy Research Institute as a next-generation nuclear reactor was experimentally investigated. For the performance test, the test facility and test procedure were established first, and several free drop performance tests of the control rod assembly under different flow rate conditions were then carried out. Moreover, performance tests under several types and magnitudes of seismic loading conditions were also conducted to investigate the effects of seismic loading on the drop performance of the control rod assembly. The drop time of the conceptually designed control rod assembly for 0% of the tentatively designed flow rate was measured to be 1.527 seconds, and this agrees well with the analytically calculated drop time. It was also observed that the effect of seismic loading on the drop time was not significant.

  5. New self-assembly strategies for next generation lithography

    Science.gov (United States)

    Schwartz, Evan L.; Bosworth, Joan K.; Paik, Marvin Y.; Ober, Christopher K.

    2010-04-01

    Future demands of the semiconductor industry call for robust patterning strategies for critical dimensions below twenty nanometers. The self assembly of block copolymers stands out as a promising, potentially lower cost alternative to other technologies such as e-beam or nanoimprint lithography. One approach is to use block copolymers that can be lithographically patterned by incorporating a negative-tone photoresist as the majority (matrix) phase of the block copolymer, paired with photoacid generator and a crosslinker moiety. In this system, poly(α-methylstyrene-block-hydroxystyrene)(PαMS-b-PHOST), the block copolymer is spin-coated as a thin film, processed to a desired microdomain orientation with long-range order, and then photopatterned. Therefore, selfassembly of the block copolymer only occurs in select areas due to the crosslinking of the matrix phase, and the minority phase polymer can be removed to produce a nanoporous template. Using bulk TEM analysis, we demonstrate how the critical dimension of this block copolymer is shown to scale with polymer molecular weight using a simple power law relation. Enthalpic interactions such as hydrogen bonding are used to blend inorganic additives in order to enhance the etch resistance of the PHOST block. We demonstrate how lithographically patternable block copolymers might fit in to future processing strategies to produce etch-resistant self-assembled features at length scales impossible with conventional lithography.

  6. Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

    Science.gov (United States)

    Desai, Aarti; Marwah, Veer Singh; Yadav, Akshay; Jha, Vineet; Dhaygude, Kishor; Bangar, Ujwala; Kulkarni, Vivek; Jere, Abhay

    2013-01-01

    Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources.

  7. Families Finding the Balance: A Parent Handbook

    Science.gov (United States)

    ... Calories Bagel 3” diameter 140 Cheeseburger Spaghetti and meatballs Soda 1 1 cup spaghetti; 3 small meatballs 6.5 ounces 333 500 85 Blueberry muffin 1.5 ounces 210 Bagel Cheeseburger Spaghetti and meatballs Soda Blueberry muffin Today Portion Calories 6” diameter ...

  8. Layer-by-layer assembled biopolymer microcapsule with separate layer cavities generated by gas-liquid microfluidic approach.

    Science.gov (United States)

    Wang, Yifeng; Zhou, Jing; Guo, Xuecheng; Hu, Qian; Qin, Chaoran; Liu, Hui; Dong, Meng; Chen, Yanjun

    2017-12-01

    In this work, a layer-by-layer (LbL) assembled biopolymer microcapsule with separate layer cavities is generated by a novel and convenient gas-liquid microfluidic approach. This approach exhibits combined advantages of microfluidic approach and LbL assembly method, and it can straightforwardly build LbL-assembled capsules in mild aqueous environments at room temperature. In particular, using this approach we can build the polyelectrolyte multilayer capsule with favorable cavities in each layer, and without the need for organic solvent, emulsifying agent, or sacrificial template. Various components (e.g., drugs, proteins, fluorescent dyes, and nanoparticles) can be respectively encapsulated in the separate layer cavities of the LbL-assembled capsules. Moreover, the encapsulated capsules present the ability as colorimetric sensors, and they also exhibit the interesting release behavior. Therefore, the LbL-assembled biopolymer capsule is a promising candidate for biomedical applications in targeted delivery, controlled release, and bio-detection. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Self-assembly of the second-generation of nitroaryl-ended dendrons onto carbon

    International Nuclear Information System (INIS)

    Farías, E.D.; Paez, J.I.; Strumia, M.C.; Baruzzi, A.M.; Passeggi Jr, M.C.G.; Brunetti, V.

    2014-01-01

    Graphical abstract: - Abstract: We report the self-assembly of the second-generation of nitroaryl-ended dendrons onto carbon surfaces. The immobilized layer was characterized by cyclic voltammetry (CV), electrochemical impedance spectroscopy and atomic force microscopy (AFM). The response was analyzed in comparison to the first-generation dendron behavior. Reduction of both layers generates the hydroxylamine product. The resulting redox-active layer exhibits a well-behaved redox response for the adsorbed nitroso/hydroxylamine couple. The thermodynamic of the adsorption of both dendrons on glassy carbon electrodes was also studied by CV. The Frumkin adsorption isotherm was the best to describe the specific interactions. The AFM images showed a network film formation with embedded aggregates that completely covered the carbon surface. The average height suggests a tilted preferential adsorption for both molecules

  10. Protein Self-Assemblies That Can Generate, Hold, and Discharge Electric Potential in Response to Changes in Relative Humidity.

    Science.gov (United States)

    Carter, Nathan A; Grove, Tijana Z

    2018-05-30

    Generation of electric potential upon external stimulus has attracted much attention for the development of highly functional sensors and devices. Herein, we report large-displacement, fast actuation in the self-assembled engineered repeat protein Consensus Tetratricopeptide Repeat protein (CTPR18) materials. The ionic nature of the CTPR18 protein coupled to the long-range alignment upon self-assembly results in the measured conductivity of 7.1 × 10 -2 S cm -1 , one of the highest reported for protein materials. The change of through-thickness morphological gradient in the self-assembled materials provides the means to select between faster, highly water-sensitive actuation or vastly increased mechanical strength. Tuning of the mode of motion, e.g., bending, twisting, and folding, is achieved by changing the morphological director. We further show that the highly ionic character of CTPR18 gives rise to piezo-like behavior in these materials, exemplified by low-voltage, ionically driven actuation and mechanically driven generation/discharge of voltage. This work contributes to our understanding of the emergence of stimuli-responsiveness in biopolymer assemblies.

  11. SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.

    Science.gov (United States)

    Meng, Jintao; Wang, Bingqiang; Wei, Yanjie; Feng, Shengzhong; Balaji, Pavan

    2014-01-01

    There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. In this paper, we presented a highly scalable and efficient genome assembly software, SWAP-Assembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler.

  12. Self-assembly of highly efficient, broadband plasmonic absorbers for solar steam generation.

    Science.gov (United States)

    Zhou, Lin; Tan, Yingling; Ji, Dengxin; Zhu, Bin; Zhang, Pei; Xu, Jun; Gan, Qiaoqiang; Yu, Zongfu; Zhu, Jia

    2016-04-01

    The study of ideal absorbers, which can efficiently absorb light over a broad range of wavelengths, is of fundamental importance, as well as critical for many applications from solar steam generation and thermophotovoltaics to light/thermal detectors. As a result of recent advances in plasmonics, plasmonic absorbers have attracted a lot of attention. However, the performance and scalability of these absorbers, predominantly fabricated by the top-down approach, need to be further improved to enable widespread applications. We report a plasmonic absorber which can enable an average measured absorbance of ~99% across the wavelengths from 400 nm to 10 μm, the most efficient and broadband plasmonic absorber reported to date. The absorber is fabricated through self-assembly of metallic nanoparticles onto a nanoporous template by a one-step deposition process. Because of its efficient light absorption, strong field enhancement, and porous structures, which together enable not only efficient solar absorption but also significant local heating and continuous stream flow, plasmonic absorber-based solar steam generation has over 90% efficiency under solar irradiation of only 4-sun intensity (4 kW m(-2)). The pronounced light absorption effect coupled with the high-throughput self-assembly process could lead toward large-scale manufacturing of other nanophotonic structures and devices.

  13. Peptide assembly-driven metal-organic framework (MOF) motors for micro electric generators.

    Science.gov (United States)

    Ikezoe, Yasuhiro; Fang, Justin; Wasik, Tomasz L; Uemura, Takashi; Zheng, Yongtai; Kitagawa, Susumu; Matsui, Hiroshi

    2015-01-14

    Peptide-metal-organic framework (Pep-MOF) motors, whose motions are driven by anisotropic surface tension gradients created via peptide self-assembly around frameworks, can rotate microscopic rotors and magnets fast enough to generate an electric power of 0.1 μW. A new rigid Pep-MOF motor can be recycled by refilling the peptide fuel into the nanopores of the MOF. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. AutoAssemblyD: a graphical user interface system for several genome assemblers.

    Science.gov (United States)

    Veras, Adonney Allan de Oliveira; de Sá, Pablo Henrique Caracciolo Gomes; Azevedo, Vasco; Silva, Artur; Ramos, Rommel Thiago Jucá

    2013-01-01

    Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.

  15. Assembly of Repeat Content Using Next Generation Sequencing Data

    Energy Technology Data Exchange (ETDEWEB)

    labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex

    2014-03-17

    Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

  16. High conversion Th-U{sup 233} fuel assembly for current generation of PWRs

    Energy Technology Data Exchange (ETDEWEB)

    Baldova, D.; Fridman, E. [Reactor Safety Div., Helmholtz-Zentrum Dresden-Rossendorf, POB 510119, Dresden, 01314 (Germany)

    2012-07-01

    This paper presents a preliminary design of a high conversion Th-U{sup 233} fuel assembly applicable for current generation of Pressurized Water Reactor (PWRs). The considered fuel assembly has a typical 17 x 17 PWR lattice. However in order to increase the conversion of Th{sup 232} to U{sup 233}, the assembly was subdivided into the two regions called seed and blanket. The central seed region has a higher than blanket U{sup 233} content and acts as a neutron source for the peripheral blanket region. The latest acts as a U{sup 233} breeder. While the seed fuel pins have a standard dimensions the blanket fuel radius was increased in order to reduce the moderation and to facilitate the resonance neutron absorption in blanket Th{sup 232}. The U{sup 233} content in the seed and blanket regions was optimized to achieve maximal initial to discharged fissile inventory ratio (FIR) taking into account the target fuel cycle length of 12 months with 3-batch reloading scheme. In this study the neutronic calculations were performed on the fuel assembly level using Helios deterministic lattice transport code. The fuel cycle length and the core k{sub eff} were estimated by applying the Non Linear Reactivity Model. The applicability of the HELIOS code for the analysis of the Th-based high conversion designs was confirmed with the help of continuous-energy Monte-Carlo code SERPENT. The results of optimization studies show that for the heterogeneous seed and blanket (SB) fuel assembly the FIR of about 0.95 can be achieved. (authors)

  17. Ultraviolet Light Generation and Transport in the Final Optics Assembly of the National Ignition Facility

    Energy Technology Data Exchange (ETDEWEB)

    Wegner, P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hackel, L. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Feit, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Parham, T. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kozlowski, M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Whitman, P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-02-12

    The design of the National Ignition Facility (NIF) includes a Final Optics Assembly (FOA) subsystem for ultraviolet (UV) light generation and transport for each of the 192 beamlines. Analytical and experimental work has been done to help understand and predict the performance of FOA.

  18. Quasistationary magnetic field generation with a laser-driven capacitor-coil assembly.

    Science.gov (United States)

    Tikhonchuk, V T; Bailly-Grandvaux, M; Santos, J J; Poyé, A

    2017-08-01

    Recent experiments are showing possibilities to generate strong magnetic fields on the excess of 500 T with high-energy nanosecond laser pulses in a compact setup of a capacitor connected to a single turn coil. Hot electrons ejected from the capacitor plate (cathode) are collected at the other plate (anode), thus providing the source of a current in the coil. However, the physical processes leading to generation of currents exceeding hundreds of kiloamperes in such a laser-driven diode are not sufficiently understood. Here we present a critical analysis of previous results and propose a self-consistent model for the high current generation in a laser-driven capacitor-coil assembly. It accounts for three major effects controlling the diode current: the space charge neutralization, the plasma magnetization between the capacitor plates, and the Ohmic heating of the external circuit-the coil-shaped connecting wire. The model provides the conditions necessary for transporting strongly super-Alfvenic currents through the diode on the time scale of a few nanoseconds. The model validity is confirmed by a comparison with the available experimental data.

  19. Cholesterol-conjugated supramolecular assemblies of low generations polyamidoamine dendrimers for enhanced EGFP plasmid DNA transfection

    Energy Technology Data Exchange (ETDEWEB)

    Golkar, Nasim; Samani, Soliman Mohammadi; Tamaddon, Ali Mohammad, E-mail: amtamadon@gmail.com [Shiraz University of Medical Sciences, Department of Pharmaceutics, School of Pharmacy (Iran, Islamic Republic of)

    2016-05-15

    Aimed to prepare an enhanced gene delivery system with low cytotoxicity and high transfection efficiency, various cholesterol-conjugated derivates of low generation polyamidoamine (PAMAM) dendrimers were prepared. The conjugates were characterized by TNBS assay, FTIR, and {sup 1}H-NMR spectroscopy. Self-assembly of the dendrimer conjugates (G1-Chol, G2-Chol, and G3-Chol) was investigated by pyrene assay. Following formation of the complexes between enhanced green fluorescence protein plasmid and the dendrimer conjugates at various N (primary amine)/P (phosphate) mole ratios, plasmid condensation, biologic stability, cytotoxicity, and protein expression were investigated. The conjugates self-assembled into micellar dispersions with the critical micelle concentration values (<50 µg/ml) depending on the dendrimer generation and cholesterol/amine mole ratio. Cholesterol conjugation resulted in higher resistance of the condensed plasmid DNA in a competition assay with heparin sulfate. Also, the transfection efficiency was determined higher for the cholesterol conjugates than unmodified dendrimers in HepG2 cells, showing the highest for G2-Chol at 40 % degree of cholesterol modification (G2-Chol{sub 40 %}) among various dendrimer generations. Interestingly, such conjugate showed a complete protection of plasmid against serum nucleases. Our results confirmed that the cholesterol conjugation to PAMAM dendrimers of low generations bearing little cytotoxicity improves their several physicochemical and biological characteristics required for an enhanced delivery of plasmid DNA into cells.

  20. Operational experience for the latest generation of ATRIUM trademark 10 fuel assemblies

    International Nuclear Information System (INIS)

    Schoss, Volker; Hoffmann, Petra Britt; Schaefer, Jens

    2011-01-01

    AREVA NP's ATRIUM trademark 10 product family was first introduced to the BWR market in 1992. Lead test campaigns confirmed the outstanding product performance and justified introduction of reload quantities. Further development of particular product features was demonstrated and implemented in the fuel design to meet highest expectations for reliability and fuel economics. The latest generation called ATRIUM trademark 10XP and subsequently ATRIUM trademark 10XM was introduced in 2002 and 2005, respectively. The first lead test assemblies completed their operation successfully after seven cycles. (orig.)

  1. Two-level MOC calculation scheme in APOLLO2 for cross-section library generation for LWR hexagonal assemblies

    International Nuclear Information System (INIS)

    Petrov, Nikolay; Todorova, Galina; Kolev, Nikola; Damian, Frederic

    2011-01-01

    The accurate and efficient MOC calculation scheme in APOLLO2, developed by CEA for generating multi-parameterized cross-section libraries for PWR assemblies, has been adapted to hexagonal assemblies. The neutronic part of this scheme is based on a two-level calculation methodology. At the first level, a multi-cell method is used in 281 energy groups for cross-section definition and self-shielding. At the second level, precise MOC calculations are performed in a collapsed energy mesh (30-40 groups). In this paper, the application and validation of the two-level scheme for hexagonal assemblies is described. Solutions for a VVER assembly are compared with TRIPOLI4® calculations and direct 281g MOC solutions. The results show that the accuracy is close to that of the 281g MOC calculation while the CPU time is substantially reduced. Compared to the multi-cell method, the accuracy is markedly improved. (author)

  2. IEEE Std 317-1972: IEEE standard for electric penetration assemblies in containment structures for nuclear power generating stations

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    This standard prescribes the mechanical, electrical, and test requirements for the design, construction, and installation of electric penetration assemblies in containment structures for stationary nuclear power generating stations. The electric conductor and insulation characteristics of external circuits which connect to penetration assemblies are beyond the scope of these criteria. If there should be any conflict between this standard and those documents referenced herein, this standard shall take precedence over the referenced documents

  3. Fixture for aligning motor assembly

    Science.gov (United States)

    Shervington, Roger M.; Vaghani, Vallabh V.; Vanek, Laurence D.; Christensen, Scott A.

    2009-12-08

    An alignment fixture includes a rotor fixture, a stator fixture and a sensor system which measures a rotational displacement therebetween. The fixture precisely measures rotation of a generator stator assembly away from a NULL position referenced by a unique reference spline on the rotor shaft. By providing an adjustable location of the stator assembly within the housing, the magnetic axes within each generator shall be aligned to a predetermined and controlled tolerance between the generator interface mounting pin and the reference spline on the rotor shaft. Once magnetically aligned, each generator is essentially a line replaceable unit which may be readily mounted to any input of a multi-generator gearbox assembly with the assurance that the magnetic alignment will be within a predetermined tolerance.

  4. Self-assembling software generator

    Science.gov (United States)

    Bouchard, Ann M [Albuquerque, NM; Osbourn, Gordon C [Albuquerque, NM

    2011-11-25

    A technique to generate an executable task includes inspecting a task specification data structure to determine what software entities are to be generated to create the executable task, inspecting the task specification data structure to determine how the software entities will be linked after generating the software entities, inspecting the task specification data structure to determine logic to be executed by the software entities, and generating the software entities to create the executable task.

  5. Application of Carbon Nanotube Assemblies for Sound Generation and Heat Dissipation

    Science.gov (United States)

    Kozlov, Mikhail; Haines, Carter; Oh, Jiyoung; Lima, Marcio; Fang, Shaoli

    2011-03-01

    Nanotech approaches were explored for the efficient transformation of an electrical signal into sound, heat, cooling action, and mechanical strain. The studies are based on the aligned arrays of multi-walled carbon nanotubes (MWNT forests) that can be grown on various substrates using a conventional CVD technique. They form a three-dimensional conductive network that possesses uncommon electrical, thermal, acoustic and mechanical properties. When heated with an alternating current or a near-IR laser modulated in 0.01--20 kHz range, the nanotube forests produce loud, audible sound. High generated sound pressure and broad frequency response (beyond 20 kHz) show that the forests act as efficient thermo-acoustic (TA) transducers. They can generate intense third and fourth TA harmonics that reveal peculiar interference-like patterns from ac-dc voltage scans. A strong dependence of the patterns on forest height can be used for characterization of carbon nanotube assemblies and for evaluation of properties of thermal interfaces. Because of good coupling with surrounding air, the forests provide excellent dissipation of heat produced by IC chips. Thermoacoustic converters based on forests can be used for thermo- and photo-acoustic sound generation, amplification and noise cancellation.

  6. Generation of microfluidic flow using an optically assembled and magnetically driven microrotor

    International Nuclear Information System (INIS)

    Köhler, J; Ghadiri, R; Ksouri, S I; Guo, Q; Gurevich, E L; Ostendorf, A

    2014-01-01

    The key components in microfluidic systems are micropumps, valves and mixers. Depending on the chosen technology, the realization of these microsystems often requires rotational and translational control of subcomponents. The manufacturing of such active components as well as the driving principle are still challenging tasks. A promising all-optical approach could be the combination of laser direct writing and actuation based on optical forces. However, when higher actuation velocities are required, optical driving might be too slow. Hence, a novel approach based on optical assembling of microfluidic structures and subsequent magnetic actuation is proposed. By applying the optical assembly of microspherical building blocks as the manufacturing method and magnetic actuation, a microrotor was successfully fabricated and tested within a microfluidic channel. The resulting fluid flow was characterized by introducing an optically levitated measuring probe particle. Finally, a freely moving tracer particle visualizes the generated flow. The tracer particle analysis shows average velocities of 0.4–0.5 µm s −1 achieved with the presented technology. (paper)

  7. Experimental study of pressure drops through LOCA-generated debris deposited on a fuel assembly

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Jeong Kwan, E-mail: jksuh@khnp.co.kr [KHNP Central Research Institute, 1312-70 Yuseong-daero, Yuseong-gu, Daejeon 305-343 (Korea, Republic of); Kim, Jae Won; Kwon, Sun Guk; Lee, Jae Yong [KHNP Central Research Institute, 1312-70 Yuseong-daero, Yuseong-gu, Daejeon 305-343 (Korea, Republic of); Cho, Hyoung Kyu; Park, Goon Cherl [Department of Nuclear Engineering, Seoul National University, Seoul 151-742 (Korea, Republic of)

    2015-08-15

    Highlights: • In-vessel downstream effect tests were performed in the presence of LOCA-generated debris. • Available driving heads under each LOCA scenario were verified using experimental data. • Fibrous debris was prepared to satisfy the length distribution obtained from the bypass test. • Limiting test conditions were identified through sensitivity studies. - Abstract: Under post loss-of-coolant accident (LOCA) conditions, it is postulated that debris can be generated and transported to the containment sump strainer. Some of the debris may pass through the strainer and could challenge the long-term core cooling capability of the plant. To address this safety issue, in-vessel downstream effect tests for the advanced power reactor (APR) 1400 were performed. Fibrous debris is the most crucial material in terms of causing pressure drops, and was prepared in this study to satisfy the fiber length distribution obtained through a strainer bypass test. Sensitivity studies on pressure drops through LOCA-generated debris deposited on a fuel assembly were performed to evaluate the effects of water chemistry and fiber length distribution. The pressure drops with debris laden pure water were substantially less than those with debris laden ordinary tap water. The experiment with fiber length distribution suggested by WCAP-16793 showed lower pressure drops than those with the APR1400 specific fiber length distribution. All the experimental results showed that the pressure drops in the mock-up fuel assembly were less than the available driving head at each LOCA scenario.

  8. Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, Hiroshi

    2014-09-09

    Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

  9. Development of a novel miniature detonation-driven shock tube assembly that uses in situ generated oxyhydrogen mixture

    International Nuclear Information System (INIS)

    Janardhanraj, S.; Jagadeesh, G.

    2016-01-01

    A novel concept to generate miniature shockwaves in a safe, repeatable, and controllable manner in laboratory confinements using an in situ oxyhydrogen generator has been proposed and demonstrated. This method proves to be more advantageous than existing methods because there is flexibility to vary strength of the shockwave, there is no need for storage of high pressure gases, and there is minimal waste disposal. The required amount of oxyhydrogen mixture is generated using alkaline electrolysis that produces hydrogen and oxygen gases in stoichiometric quantity. The rate of oxyhydrogen mixture production for the newly designed oxyhydrogen generator is found to be around 8 ml/s experimentally. The oxyhydrogen generator is connected to the driver section of a specially designed 10 mm square miniature shock tube assembly. A numerical code that uses CANTERA software package is used to predict the properties of the driver gas in the miniature shock tube. This prediction along with the 1-D shock tube theory is used to calculate the properties of the generated shockwave and matches reasonably well with the experimentally obtained values for oxyhydrogen mixture fill pressures less than 2.5 bars. The miniature shock tube employs a modified tri-clover clamp assembly to facilitate quick changing of diaphragm and replaces the more cumbersome nut and bolt system of fastening components. The versatile nature of oxyhydrogen detonation-driven miniature shock tube opens up new horizons for shockwave-assisted interdisciplinary applications.

  10. Development of a novel miniature detonation-driven shock tube assembly that uses in situ generated oxyhydrogen mixture

    Energy Technology Data Exchange (ETDEWEB)

    Janardhanraj, S.; Jagadeesh, G., E-mail: jaggie@aero.iisc.ernet.in [Department of Aerospace Engineering, Indian Institute of Science, Bangalore 560012 (India)

    2016-08-15

    A novel concept to generate miniature shockwaves in a safe, repeatable, and controllable manner in laboratory confinements using an in situ oxyhydrogen generator has been proposed and demonstrated. This method proves to be more advantageous than existing methods because there is flexibility to vary strength of the shockwave, there is no need for storage of high pressure gases, and there is minimal waste disposal. The required amount of oxyhydrogen mixture is generated using alkaline electrolysis that produces hydrogen and oxygen gases in stoichiometric quantity. The rate of oxyhydrogen mixture production for the newly designed oxyhydrogen generator is found to be around 8 ml/s experimentally. The oxyhydrogen generator is connected to the driver section of a specially designed 10 mm square miniature shock tube assembly. A numerical code that uses CANTERA software package is used to predict the properties of the driver gas in the miniature shock tube. This prediction along with the 1-D shock tube theory is used to calculate the properties of the generated shockwave and matches reasonably well with the experimentally obtained values for oxyhydrogen mixture fill pressures less than 2.5 bars. The miniature shock tube employs a modified tri-clover clamp assembly to facilitate quick changing of diaphragm and replaces the more cumbersome nut and bolt system of fastening components. The versatile nature of oxyhydrogen detonation-driven miniature shock tube opens up new horizons for shockwave-assisted interdisciplinary applications.

  11. On the Automatic Generation of Plans for Life Cycle Assembly Processes

    Energy Technology Data Exchange (ETDEWEB)

    CALTON,TERRI L.

    2000-01-01

    Designing products for easy assembly and disassembly during their entire life cycles for purposes including product assembly, product upgrade, product servicing and repair, and product disposal is a process that involves many disciplines. In addition, finding the best solution often involves considering the design as a whole and by considering its intended life cycle. Different goals and manufacturing plan selection criteria, as compared to initial assembly, require re-visiting significant fundamental assumptions and methods that underlie current assembly planning techniques. Previous work in this area has been limited to either academic studies of issues in assembly planning or to applied studies of life cycle assembly processes that give no attention to automatic planning. It is believed that merging these two areas will result in a much greater ability to design for, optimize, and analyze the cycle assembly processes. The study of assembly planning is at the very heart of manufacturing research facilities and academic engineering institutions; and, in recent years a number of significant advances in the field of assembly planning have been made. These advances have ranged from the development of automated assembly planning systems, such as Sandia's Automated Assembly Analysis System Archimedes 3.0{copyright}, to the startling revolution in microprocessors and computer-controlled production tools such as computer-aided design (CAD), computer-aided manufacturing (CAM), flexible manufacturing systems (EMS), and computer-integrated manufacturing (CIM). These results have kindled considerable interest in the study of algorithms for life cycle related assembly processes and have blossomed into a field of intense interest. The intent of this manuscript is to bring together the fundamental results in this area, so that the unifying principles and underlying concepts of algorithm design may more easily be implemented in practice.

  12. Comparison of hydrogen generation for TVSM and TVSA fuel assemblies for water water energy reactor (VVER)-1000

    International Nuclear Information System (INIS)

    Stefanova, A.E.; Groudev, P.P.; Atanasova, B.P.

    2009-01-01

    This paper presents the results received during investigation of hydrogen generation for both types fuel assemblies-the old modernistic type of fuel assemblies (TVSM) and recently installed new one alternative type of fuel assemblies (TVSA) in case of severe accident. There are some differences between both types FAs. They have different geometry as well as different burnable poisons. To investigate behavior of new fuel assemblies during the severe conditions it have been performed comparison of fuel behavior of old type TVSM fuel assembly to new one TVSA. To perform this investigation it has been used MELCOR 'input model' for Kozloduy Nuclear Power Plant (KNPP) VVER 1000. The model was developed by Institute for Nuclear Research and Nuclear Energy-Bulgarian Academy of Sciences (INRNE-BAS) for investigation of severe accident scenarios and Probabilistic Safety Analyses (PSA) level 2. The model provides a significant analytical capability for the Bulgarian technical specialists, working in the field of the NPP safety, for analysis of core and containment damaged states and the estimation of radionuclides release outside fuel cladding. It was accepted criteria for vessel integrity about hydrogen concentration to be 8%. This criterion was based on the decision of RSK (Germany commission for reactor safety). Generally based on the received results it was made conclusion that using both types of fuel assemblies it was not disturbance safety conditions of NPP

  13. Highly stable and finely tuned magnetic fields generated by permanent magnet assemblies.

    Science.gov (United States)

    Danieli, E; Perlo, J; Blümich, B; Casanova, F

    2013-05-03

    Permanent magnetic materials are the only magnetic source that can be used to generate magnetic fields without power consumption or maintenance. Such stand-alone magnets are very attractive for many scientific and engineering areas, but they suffer from poor temporal field stability, which arises from the strong sensitivity of the magnetic materials and mechanical support to temperature variation. In this work, we describe a highly efficient method useful to cancel the temperature coefficient of permanent magnet assemblies in a passive and accurate way. It is based on the combination of at least two units made of magnetic materials with different temperature coefficients arranged in such a way that the ratio of the fields generated by each unit matches the ratio of their effective temperature coefficients defined by both the magnetic and mechanical contributions. Although typically available magnetic materials have negative temperature coefficients, the cancellation is achieved by aligning the fields generated by each unit in the opposite direction. We demonstrate the performance of this approach by stabilizing the field generated by a dipolar Halbach magnet, recently proposed to achieve high field homogeneity. Both the field drift and the homogeneity are monitored via nuclear magnetic resonance spectroscopy experiments. The results demonstrate the compatibility of the thermal compensation approach with existing strategies useful to fine-tune the spatial dependence of the field generated by permanent magnet arrays.

  14. Development and characterization of the control assembly system for the large 2400 MWth Generation IV gas-cooled fast reactor

    International Nuclear Information System (INIS)

    Girardin, G.; Rimpault, G.; Morin, F.; Bosq, J.C.; Coddington, P.; Mikityuk, K.; Chawla, R.

    2008-01-01

    The present paper is related to the design and neutronic characterization of the principal control assembly system for the reference large (2400 MWth) Generation IV gas-cooled fast reactor (GFR), which makes use of ceramic-ceramic (CERCER) plate-type fuel-elements with (U-Pu) carbide fuel contained within a SiC inert matrix. For the neutronic calculations, the deterministic code system ERANOS-2.0 has been used, in association with a full core model including a European fast reactor (EFR)-type pattern for the control assemblies as a starting point. More specifically, the core contains a total of 33 control (control system device: CSD) and safety (diverse safety device: DSD) assemblies implemented in three banks. In the design of the new control assembly system, particular attention was given to the heat generation within the assemblies, so that both neutronic and thermal-hydraulic constraints could be appropriately accounted for. The thermal-hydraulic calculations have been performed with the code COPERNIC, significant coolant mass flow rates being found necessary to maintain acceptable cladding temperatures of the absorber pins. Complementary to the design study, neutronic investigations have been performed to assess the impact of the control assemblies in the GFR core in greater detail (rod interactions, shift of the flux, peaking factors, etc.). Thus, considerable shadowing effects have been observed between the first bank and the safety bank, as also between individual assemblies within the first bank. Large anti-shadowing effects also occur, the most prominent being that between the two CSD banks, where the total assembly worth is almost doubled in comparison to the sum of the individual values. Additional investigations have been performed and, in this context, it has been found that computation of the first-order eigenvalue and the eigenvalue separation is a robust tool to anticipate control assembly interactions in a large fast-spectrum core. One interesting

  15. Monte Carlo Depletion with Critical Spectrum for Assembly Group Constant Generation

    International Nuclear Information System (INIS)

    Park, Ho Jin; Joo, Han Gyu; Shim, Hyung Jin; Kim, Chang Hyo

    2010-01-01

    The conventional two-step procedure has been used in practical nuclear reactor analysis. In this procedure, a deterministic assembly transport code such as HELIOS and CASMO is normally to generate multigroup flux distribution to be used in few-group cross section generation. Recently there are accuracy issues related with the resonance treatment or the double heterogeneity (DH) treatment for VHTR fuel blocks. In order to mitigate the accuracy issues, Monte Carlo (MC) methods can be used as an alternative way to generate few-group cross sections because the accuracy of the MC calculations benefits from its ability to use continuous energy nuclear data and detailed geometric information. In an earlier work, the conventional methods of obtaining multigroup cross sections and the critical spectrum are implemented into the McCARD Monte Carlo code. However, it was not complete in that the critical spectrum is not reflected in the depletion calculation. The purpose of this study is to develop a method to apply the critical spectrum to MC depletion calculations to correct for the leakage effect in the depletion calculation and then to examine the MC based group constants within the two-step procedure by comparing the two-step solution with the direct whole core MC depletion result

  16. Comparing de novo assemblers for 454 transcriptome data.

    Science.gov (United States)

    Kumar, Sujai; Blaxter, Mark L

    2010-10-16

    Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible

  17. Report of generation of the 'L1PG9321' nuclear bank of the CAORSO 3.26 collapsed assembly with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1991-03-01

    In this work it is described in a general way the form in that the collapsed bank of the CAORSO 3.26 fuel as possible reload fuel for Laguna Verde it was generated. The formation of the bank was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B codes of the FMS package installed in the VAX system of the offices of the National Commission of Nuclear Safety and Safeguards in Mexico City. The formed bank is denominated L 1PG9321 . All this one was carried out following the '6F3/I/CN029/90/P1' procedure. To generate the bank, the five RECORD cells that compose the one assemble its were 'collapsed' in one alone, representing this to the complete assemble in what refers to the fuel bar distribution and enrichment. The one collapsed of the it assemble it is made averaging the content of UO 2 and Gd 2 O 3 in each fuel bar of the one assemble. Of this way is conserved the arrangement x-y of fuel bars but a representative fuel cell is obtained of everything the one it assembles being this the studied RECORD cell. In accordance with the requirements of nuclear information of FCS-II the nuclear information generated with RECORD should be of the one defined type as series 1 in the generation procedure of '6F3/I/CN029/90/P1' nuclear banks. This means that only the nuclear information as function of the burnt one of the fuel and of the hole in the fuel cell is required; however the bank also contains information of the defined type as series 2 with the control bar present for possible analysis of the reactor under these conditions. (Author)

  18. Development of WWER-440 fuel. Use of fuel assemblies of 2-nd and 3-rd generations with increased enrichment

    International Nuclear Information System (INIS)

    Vasilchenko, I.; Lushin, V.; Ananev, U.; Baranov, A.; Kukushkin, U.

    2009-01-01

    The problem of increasing the power of units at NPPs with WWER-440 is of current importance. There are all the necessary prerequisites for the above-stated problem as a result of updating the design of fuel assemblies and codes. The decrease of power peaking factor in the core is achieved by using profiled fuel assemblies, fuel-integrated burning absorber, FAs with modernized docking unit, modern codes, which allows decreasing conservatism of RP safety substantiation. A wide range of experimental studies of fuel behaviour has been performed which has reached burn-up of (50-60) MW·day/kgU in transition and emergency conditions, post-reactor studies of fuel assemblies, fuel rods and fuel pellets with a 5-year operating period have been performed, which prove high reliability of fuel, presence of a large margin in the fuel pillar, which helps reactor operation at increased power. The results of the work performed on introduction of 5-6 fuel cycles show that the ultimate fuel state on operability in WWER-440 reactors is far from being achieved. Neutron-physical and thermal-hydraulic characteristics of the cores of working power units with RP V-213 are such that actual (design and measured) power peaking factors on fuel assemblies and fuel rods, as a rule, are smaller than the maximum design values. This factor is a real reserve for power forcing. There is experience of operating Units 1, 2, 4 of the Kola NPP and Unit 2 of the Rovno NPP at increased power. Units of the Loviisa NPP are operated at 109 % power. During transfer to work at increased power it is reasonable to use fuel assemblies with increased height of the fuel pillar, which allows decreasing medium linear power distribution. Further development of the 2-nd generation fuel assembly design and consequent transition to working fuel assemblies of the 3-rd generation provides significant improvement of fuel consumption under the conditions of WWER-440 reactors operation with more continuous fuel cycles and

  19. Supramolecular nanoparticles generated by the self-assembly of polyrotaxanes for antitumor drug delivery

    Directory of Open Access Journals (Sweden)

    Liu R

    2012-10-01

    Full Text Available Rong Liu,1,2,* Yusi Lai,1,* Bin He,1 Yuan Li,1 Gang Wang,1 Shuang Chang,1 Zhongwei Gu1 1National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, China; 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China*These authors contributed equally to this paperAbstract: A new approach of fabricating supramolecular nanoparticles generated by self-assembly polyrotaxanes for antitumor drug delivery has been reported. Cinnamic-acid-modified poly(ethylene glycol chains were threaded in a-cyclodextrins to form polyrotaxanes. The polyrotaxanes self-assembled supramolecular nanoparticles. The morphology of the nanoparticles was changed from nanovesicle to micelle after the antitumor drug, doxorubicin, was loaded. The release profile of the drug-loaded nanoparticles was investigated, and it was found that the sustaining release time could last for 32 hours. The drug-loaded nanoparticles were co-cultured with mouse 4T1 breast cancer cells with a drug concentration of 10 µg/mL; the cell survival rate was 3.3% after a 72-hour incubation. In an in vivo study of breast cancer in a mouse model, the drug-loaded nanoparticles were injected in the tail veins of mice with a dose of 5 mg/kg body weight. The tumor inhibition rate of drug-loaded nanoparticles was 53%, which was better than that of doxorubicin hydrochloride. The cardiac toxicity of doxorubicin was decreased greatly after the encapsulation into supramolecular polyrotaxane nanoparticles.Keywords: polyrotaxane, self-assembly, nanoparticle, doxorubicin, supermolecular

  20. Comparing de novo assemblers for 454 transcriptome data

    Directory of Open Access Journals (Sweden)

    Blaxter Mark L

    2010-10-01

    Full Text Available Abstract Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects, which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies

  1. High temperature technological heat exchangers and steam generators with helical coil assembly tube bundle

    International Nuclear Information System (INIS)

    Korotaev, O.J.; Mizonov, N.V.; Nikolaevsky, V.B.; Nazarov, E.K.

    1990-01-01

    Analysis of thermal hydraulics characteristics of nuclear steam generators with different tube bundle arrangements and waste heat boilers for ammonia production units was performed on the basis of operating experience results and research and development data. The present report involves the obtained information. The estimations of steam generator performances and repair-ability are given. The significant temperature profile of the primary and secondary coolant flows are attributed to all steam generator designs. The intermediate mixing is found to be an effective means of temperature profile overcoming. At present the only means to provide an effective mixing in heat exchangers of the following types: straight tubes, field tubes, platen tubes and multibank helical coil tubes (with complicated bend distribution along their length) are section arrangements in series in conjunction with forced and natural mixing in connecting lines. Development of the unificated system from mini helical coil assemblies allows to design and manufacture heat exchangers and steam generators within the wide range of operating conditions without additional expenses on the research and development work

  2. Illustrating how mechanical assemblies work

    KAUST Repository

    Mitra, Niloy J.; Yang, Yongliang; Yan, Dongming; Li, Wilmot; Agrawala, Maneesh

    2010-01-01

    How things work visualizations use a variety of visual techniques to depict the operation of complex mechanical assemblies. We present an automated approach for generating such visualizations. Starting with a 3D CAD model of an assembly, we first infer the motions of individual parts and the interactions between parts based on their geometry and a few user specified constraints. We then use this information to generate visualizations that incorporate motion arrows, frame sequences and animation to convey the causal chain of motions and mechanical interactions between parts. We present results for a wide variety of assemblies. © 2010 ACM.

  3. Illustrating how mechanical assemblies work

    KAUST Repository

    Mitra, Niloy J.

    2010-07-26

    How things work visualizations use a variety of visual techniques to depict the operation of complex mechanical assemblies. We present an automated approach for generating such visualizations. Starting with a 3D CAD model of an assembly, we first infer the motions of individual parts and the interactions between parts based on their geometry and a few user specified constraints. We then use this information to generate visualizations that incorporate motion arrows, frame sequences and animation to convey the causal chain of motions and mechanical interactions between parts. We present results for a wide variety of assemblies. © 2010 ACM.

  4. Evaluation of nine popular de novo assemblers in microbial genome assembly.

    Science.gov (United States)

    Forouzan, Esmaeil; Maleki, Masoumeh Sadat Mousavi; Karkhane, Ali Asghar; Yakhchali, Bagher

    2017-12-01

    Next generation sequencing (NGS) technologies are revolutionizing biology, with Illumina being the most popular NGS platform. Short read assembly is a critical part of most genome studies using NGS. Hence, in this study, the performance of nine well-known assemblers was evaluated in the assembly of seven different microbial genomes. Effect of different read coverage and k-mer parameters on the quality of the assembly were also evaluated on both simulated and actual read datasets. Our results show that the performance of assemblers on real and simulated datasets could be significantly different, mainly because of coverage bias. According to outputs on actual read datasets, for all studied read coverages (of 7×, 25× and 100×), SPAdes and IDBA-UD clearly outperformed other assemblers based on NGA50 and accuracy metrics. Velvet is the most conservative assembler with the lowest NGA50 and error rate. Copyright © 2017. Published by Elsevier B.V.

  5. IEEE C37.82-1987: IEEE standard for the qualification of switchgear assemblies for Class 1E applications in nuclear power generating stations

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    This document describes the methods and requirements for qualifying switchgear assemblies for indoor areas outside of the containment in nuclear power generating stations. These assemblies include (1) metal-enclosed low-voltage power circuit breaker switchgear assemblies, as defined in ANSI/IEEE C37.20.1-1987, (2) metal-clad switchgear assemblies, as defined in ANSI/IEEE C37.20.2-1987, (3) metal-enclosed bus, as defined in ANSI/IEEE C37.23-1987, and (4) metal-enclosed interrupter switchgear assemblies, as defined in ANSI/IEEE C37.20.3-1987. The purpose of this document is to provide amplification of the general requirements of ANSI/IEEE Std 323-1983 as they apply to the specific features of Class 1E switchgear assemblies. Where differences exist between this document and ANSI/IEEE Std 323-1983, this document takes precedence insofar as switchgear assemblies are concerned

  6. Experimental study of new generation WWER-1000 fuel assemblies at JSC NCCP

    International Nuclear Information System (INIS)

    Enin, A.; Rozhkov, V.; Sinikov, Y.; Ustimenko, A.; Shustov, M.

    2003-01-01

    An experimental program for the study of fuel assembly thermomechanical stability has been established together with RF SSC IPPE and Russian Scientific Center Kurchatov Institute. Assembly fragments and small dummy models of fuel assembly skeletons and fuel rod bundles have been used for the tests. The test results are used for the design selection, verification of the design codes and substantiation of operating capacity of fuel assemblies with a rigid skeleton. The mechanical characteristics of units make it possible to perform fuel assembly strength and rigidity calculations, including the cases of abnormal operation. The mechanical characteristics of the skeleton and fuel rod bundle dummy models make it possible to check for the adequacy of the fuel assembly design model. The mechanical characteristics obtained during fuel rods bundle push through experiments make it possible to substantiate the fuel assembly serviceability under the conditions of fuel rods bundle and skeleton interaction

  7. Results of trial operation of new generation assemblies with improved vibration stability for WWER-440 reactors of V-230 and V-213 plants

    International Nuclear Information System (INIS)

    Vasilchenko, I.; Lushin, V.; Shumeev, A.

    2006-01-01

    The main task in developing a fuel design of new generation for WWER-440 power units (particularly for power units of V-213 type) is to increase the effectiveness of fuel utilization. For this purpose the following design solutions were realized: 1) increase of fuel loading (increase of fuel stack in a fuel rod); 2) optimization of the water-uranium relation (at the cost of some decrease of outside diameter of a fuel rod from 9,1 mm to 9,07 mm and increase of fuel rod pitch in a bundle from 12,2 mm up to 12,3 mm); 3) decrease of harmful absorption of neutrons (due to decrease of hafnium content in zirconium materials from 0,05 % to 0,01 % and decrease of zirconium in transition to thickness of FA casing of ERC assembly - 1,5 mm). The parallel task is to increase vibration stability of fuel assemblies based on the verification and justification of the following technical solutions: 1)improvement of vibration stability due to SG rearrangement along the fuel rod bundle height and increasement of height of the first three grids along the course of coolant flow; 2) decreasement of backlashes in the assembly 'fuel rod - support grid' due to introduction of a new elastic tip of fuel rods; 3) introduction of a stiffening rib under the support grid and attachment of the central tube in the support grid by welding; 4) introduction of special sleeve in the protective grid, which permits to fasten a bundle against radial displacements in its upper part; 5) introduction of slots, located at different height marks of the central tube, permits to exclude distortion and destruction of spacing grids as a result of increase of fuel rod temperature; 6) installation of filters at the inlet. According to design considerations with due regard for statistics of fuel assemblies damage, the filters will be mounted at the working assembly (WA) inlet. In new generation fuel assemblies, the problem of decrease of local flash-up of neutrons in the WA peripheral fuel rods, surrounding the CPS

  8. Evaluation of Start Transient Oscillations with the J-2X Engine Gas Generator Assembly

    Science.gov (United States)

    Hulka, J. R.; Morgan, C. J.; Casiano, M. J.

    2015-01-01

    During development of the gas generator for the liquid oxygen/liquid hydrogen propellant J-2X rocket engine, distinctive and oftentimes high-amplitude pressure oscillations and hardware vibrations occurred during the start transient of nearly every workhorse gas generator assembly test, as well as during many tests of engine system hardware. These oscillations appeared whether the steady-state conditions exhibited stable behavior or not. They occurred similarly with three different injector types, and with every combustion chamber configuration tested, including chamber lengths ranging over a 5:1 range, several different nozzle types, and with or without a side branch line simulating a turbine spin start gas supply line. Generally, two sets of oscillations occurred, one earlier in the start transient and at higher frequencies, and the other almost immediately following and at lower frequencies. Multiple dynamic pressure measurements in the workhorse combustion chambers indicated that the oscillations were associated with longitudinal acoustic modes of the combustion chambers, with the earlier and higher frequency oscillation usually related to the second longitudinal acoustic mode and the later and lower frequency oscillation usually related to the first longitudinal acoustic mode. Given that several early development gas generator assemblies exhibited unstable behavior at frequencies near the first longitudinal acoustic modes of longer combustion chambers, the start transient oscillations are presumed to provide additional insight into the nature of the combustion instability mechanisms. Aspects of the steadystate oscillations and combustion instabilities from development and engine system test programs have been reported extensively in the three previous JANNAF Liquid Propulsion Subcommittee meetings (see references below). This paper describes the hardware configurations, start transient sequence operations, and transient and dynamic test data during the start

  9. Report of the generation of the nuclear bank 'L1PG9121' of the SVEA-96 'collapsed' assemble for the FCS-II program with the FMS codes

    International Nuclear Information System (INIS)

    Alonso V, G.

    1992-01-01

    In this work it is described in a general way the form in that was generated the collapsed bank of the SVEA-96 fuel for Laguna Verde. The formation of the bank it was carried out with the ECLIPSE 86-2D, RECORD 89-1A and POLGEN 88-1B codes of the FMS package installed in the VAX system of the office of the National Commission of Nuclear Safety and Safeguards in Mexico D.F. The formed bank is denominated 'LlPG9121'. All this one carries out following the procedure '6F3/I/CN029/90/P1'. To generate the bank, both RECORD 'cells' that compose the assemble its were 'collapsed' in an alone one, representing this, the complete assemble in what refers to the distribution of fuel bar and enrichment. The collapsed of the assemble was made averaging the content of UO 2 and Gd 2 O 3 in each fuel bar of the one assemble. By this way the x-y array of fuel bars is conserved but a representative fuel cell of all the one assemble is obtained, being this the studied RECORD cell. In accordance with the requirements of nuclear information of FCS-II, the nuclear information generated with RECORD only was of the defined type as series 1 in the generation procedure of nuclear banks '6F3/I/CN029/90/P1'. This only means that only was generated nuclear information as function of the fuel burnt and of the vacuum in the fuel cell. Although the nuclear bank (L1PG9121) it was generated in these circumstances, it was also generates information of the defined type as series 2 with the present control bar for possible reactor analysis under these conditions. (Author)

  10. Illustrating how mechanical assemblies work

    KAUST Repository

    Mitra, Niloy J.; Yang, Yongliang; Yan, Dongming; Li, Wilmot; Agrawala, Maneesh

    2013-01-01

    How-things-work visualizations use a variety of visual techniques to depict the operation of complex mechanical assemblies. We present an automated approach for generating such visualizations. Starting with a 3D CAD model of an assembly, we first infer the motions of the individual parts and the interactions across the parts based on their geometry and a few user-specified constraints. We then use this information to generate visualizations that incorporate motion arrows, frame sequences, and animation to convey the causal chain of motions and mechanical interactions across parts. We demonstrate our system on a wide variety of assemblies. © 2013 ACM 0001-0782/13/01.

  11. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo: genome assembly and analysis.

    Directory of Open Access Journals (Sweden)

    Rami A Dalloul

    2010-09-01

    Full Text Available A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo. Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (∼1.1 Gb includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.

  12. Assessment of metagenomic assembly using simulated next generation sequencing data

    DEFF Research Database (Denmark)

    Mende, Daniel R; Waller, Alison S; Sunagawa, Shinichi

    2012-01-01

    with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities. We first evaluated the effect of rigorous quality control on Illumina data. Although quality filtering removed a large proportion of the data, it greatly improved...... the accuracy and contig lengths of resulting assemblies. We then compared the quality-trimmed Illumina assemblies to those from Sanger and pyrosequencing. For the simple community (10 genomes) all sequencing technologies assembled a similar amount and accurately represented the expected functional composition...... the Sanger reads still represented the overall functional composition reasonably well. We further examined the effect of scaffolding of contigs using paired-end Illumina reads. It dramatically increased contig lengths of the simple community and yielded minor improvements to the more complex communities...

  13. Human Assisted Assembly Processes

    Energy Technology Data Exchange (ETDEWEB)

    CALTON,TERRI L.; PETERS,RALPH R.

    2000-01-01

    Automatic assembly sequencing and visualization tools are valuable in determining the best assembly sequences, but without Human Factors and Figure Models (HFFMs) it is difficult to evaluate or visualize human interaction. In industry, accelerating technological advances and shorter market windows have forced companies to turn to an agile manufacturing paradigm. This trend has promoted computerized automation of product design and manufacturing processes, such as automated assembly planning. However, all automated assembly planning software tools assume that the individual components fly into their assembled configuration and generate what appear to be a perfectly valid operations, but in reality the operations cannot physically be carried out by a human. Similarly, human figure modeling algorithms may indicate that assembly operations are not feasible and consequently force design modifications; however, if they had the capability to quickly generate alternative assembly sequences, they might have identified a feasible solution. To solve this problem HFFMs must be integrated with automated assembly planning to allow engineers to verify that assembly operations are possible and to see ways to make the designs even better. Factories will very likely put humans and robots together in cooperative environments to meet the demands for customized products, for purposes including robotic and automated assembly. For robots to work harmoniously within an integrated environment with humans the robots must have cooperative operational skills. For example, in a human only environment, humans may tolerate collisions with one another if they did not cause much pain. This level of tolerance may or may not apply to robot-human environments. Humans expect that robots will be able to operate and navigate in their environments without collisions or interference. The ability to accomplish this is linked to the sensing capabilities available. Current work in the field of cooperative

  14. Main results of post-irradiation examinations of new-generation fuel assemblies VVER-1000

    International Nuclear Information System (INIS)

    Zvir, E.; Markov, D.; Polenok, V.; Zhitelev, V.; Kobylyansky, G.

    2009-01-01

    To increase the competitiveness of Russian nuclear fuel at the foreign market and to improve its technical and economic performance in order to provide a necessary level of safety, it is necessary to solve certain important tasks: Increase of fuel burn-up; Extension of operational lifetime of fuel assemblies and operational reliability of nuclear fuel; Introduction of cost-beneficial and flexible fuel cycles. Alternative fuel assemblies TVSA VVER-1000 and TVS-2 are used as a basis to optimize the nuclear fuel and develop advanced fuel cycles for nuclear power plants with VVER-1000 reactor types. Four fuel assemblies TVSA operated during 1 and up to 6 reactor cycles, reference fuel assembly TVS-2 operated during three reactor cycles and achieved an average fuel burnup of 48MW·day/kgU as well as failed fuel assembly TVS-2 operated during one cycle were examined at RIAR in recent years. The main objectives of these examinations were to obtain experimental data in support of operational integrity of products or to find out reasons of their failure. The performed post-irradiation examinations confirmed the operational integrity of alternative fuel assemblies TVSA including their geometrical stability up to the average fuel burnup of 55 MW·day/kgU over the fuel assembly (FA) (up to the maximal fuel burnup of ∼73 MW·day/kgU in fuel rods) and of TVS-2 up to the average fuel burnup of 48 MW·day/kgU over the fuel assembly. The changes introduced in the design of VVER-1000 fuel assembly during the development of alternative fuel assembly TVSA and TVS-2 did not make any negative effect on fuel rods. It was proved that causes of fuel rod failure were not related to design features of fuel assemblies. The design features and operating conditions of fuel assemblies under examinations are briefly described. Post-irradiation examinations proved the geometrical stability of fuel assemblies TVSA and TVS-2 under operation up to the fuel burnup of ∼50 MW day/kgU, as for the

  15. Macro-assembler technique for generating control words for a micro-programmed processor

    International Nuclear Information System (INIS)

    Lesny, D.D.; Wray, J.J.

    1981-01-01

    To produce microcode for an experimental system, such as FASTBUS interfaces, with wide control words and many micro-fields, one needs a micro-assembler which (1) allows wide flexibility in defining defaults for microcode fields, (2) does a significant amount of error checking to prevent multiple or inconsistant definitions of fields, (3) allows macro expansions which define several microcode words for frequently used sequences, and (4) is easily modified as hardware definitions are refined. Using MACRO-11 on DEC PDP-11 computers, a library of macros has been created, which can be used to generate the 80-bit microcode words needed for a Unibus to FASTBUS micro-programmed interface and which meets the above requirements. The same technique could easily be used to develop libraries appropriate for other microcoded devices

  16. Selecting Operations for Assembler Encoding

    Directory of Open Access Journals (Sweden)

    Tomasz Praczyk

    2010-04-01

    Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
    The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper.

  17. One approach to accepting and transporting spent fuel from early-generation reactors with short fuel assemblies

    International Nuclear Information System (INIS)

    Peterson, R.W.; Bentz, E.J. Jr.; Bentz, C.B.

    1993-01-01

    In the early days of development of commercial nuclear power reactors in the U.S., the overall length and uranium loading of the fuel assemblies were considerably less than those of later generation facilities. In turn, some of these early facilities were designed for handling shorter casks than currently-certified casks. The spent fuel assemblies from these facilities are nearly all standard fuel within the definition in the Standard Contract (10 CFR 961) between the utilities and the U.S. Department of Energy (DOE) (the Big Rock Point fuel cross-section is outside the standard fuel dimension), and the utilities involved hold early delivery rights under DOE's oldest-fuel-first (OFF) allocation scenario. However, development of casks suitable for satisfying the acceptance and transportation requirements of some of these facilities is not currently underway in the DOE Cask System Development Program (CSDP). While the total MTU of these fuels is relatively small compared to the total program, the number of assemblies to be transported is significant, especially in the early years of operation according to the OFF allocation scenario. We therefore perceive a need for DOE to develop an approach and to implement plans to satisfy the unique acceptance and transportation requirements of these facilities. One such approach is outlined below. (author)

  18. Biomedical Applications of Self-Assembling Peptides

    NARCIS (Netherlands)

    Radmalekshahi, Mazda; Lempsink, Ludwijn; Amidi, Maryam; Hennink, Wim E.; Mastrobattista, Enrico

    2016-01-01

    Self-assembling peptides have gained increasing attention as versatile molecules to generate diverse supramolecular structures with tunable functionality. Because of the possibility to integrate a wide range of functional domains into self-assembling peptides including cell attachment sequences,

  19. Comparing memory-efficient genome assemblers on stand-alone and cloud infrastructures.

    Science.gov (United States)

    Kleftogiannis, Dimitrios; Kalnis, Panos; Bajic, Vladimir B

    2013-01-01

    A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memory by choosing suitable assembly methods. Our study reveals the minimum memory requirements for different assembly programs even when data volume exceeds memory capacity by orders of magnitude. By combining existing methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment on some findings regarding suitable computational resources for assembly.

  20. Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2013-09-27

    A fundamental problem in bioinformatics is genome assembly. Next-generation sequencing (NGS) technologies produce large volumes of fragmented genome reads, which require large amounts of memory to assemble the complete genome efficiently. With recent improvements in DNA sequencing technologies, it is expected that the memory footprint required for the assembly process will increase dramatically and will emerge as a limiting factor in processing widely available NGS-generated reads. In this report, we compare current memory-efficient techniques for genome assembly with respect to quality, memory consumption and execution time. Our experiments prove that it is possible to generate draft assemblies of reasonable quality on conventional multi-purpose computers with very limited available memory by choosing suitable assembly methods. Our study reveals the minimum memory requirements for different assembly programs even when data volume exceeds memory capacity by orders of magnitude. By combining existing methodologies, we propose two general assembly strategies that can improve short-read assembly approaches and result in reduction of the memory footprint. Finally, we discuss the possibility of utilizing cloud infrastructures for genome assembly and we comment on some findings regarding suitable computational resources for assembly.

  1. Fuel assembly

    International Nuclear Information System (INIS)

    Nomata, Terumitsu.

    1993-01-01

    Among fuel pellets to be loaded to fuel cans of a fuel assembly, fuel pellets having a small thermal power are charged in a region from the end of each of spacers up to about 50mm on the upstream of coolants that flow vertically at the periphery of fuel rods. Coolants at the periphery of fuel rods are heated by the heat generation, to result in voids. However, since cooling effect on the upstream of the spacers is low due to influences of the spacers. Further, since the fuel pellets disposed in the upstream region have small thermal power, a void coefficient is not increased. Even if a thermal power exceeding cooling performance should be generated, there is no worry of causing burnout in the upstream region. Even if burnout should be caused, safety margin and reliability relative to burnout are improved, to increase an allowable thermal power, thereby enabling to improve integrity and reliability of fuel rods and fuel assemblies. (N.H.)

  2. Self-assembled biomimetic nanoreactors I: Polymeric template

    Science.gov (United States)

    McTaggart, Matt; Malardier-Jugroot, Cecile; Jugroot, Manish

    2015-09-01

    The variety of nanoarchitectures made feasible by the self-assembly of alternating copolymers opens new avenues for biomimicry. Indeed, self-assembled structures allow the development of nanoreactors which combine the efficiency of high surface area metal active centres to the effect of confinement due to the very small cavities generated by the self-assembly process. A novel self-assembly of high molecular weight alternating copolymers is characterized in the present study. The self-assembly is shown to organize into nanosheets, providing a 2 nm hydrophobic cavity with a 1D confinement.

  3. Dynamic Multi-Component Hemiaminal Assembly

    Science.gov (United States)

    You, Lei; Long, S. Reid; Lynch, Vincent M.

    2012-01-01

    A simple approach to generating in situ metal templated tris-(2-picolyl)amine-like multi-component assemblies with potential applications in molecular recognition and sensing is reported. The assembly is based on the reversible covalent association between di-(2-picolyl)amine and aldehydes. Zinc ion is the best for inducing assembly among the metal salts investigated, while 2-picolinaldehyde is the best among the heterocyclic aldehydes studied. Although an equilibrium constant of 6.6 * 103 M-1 was measured for the assembly formed by 2-picolinaldehdye, di-(2-picolyl)amine, and zinc triflate, the equilibrium constants for other systems are in the 102 M-1 range. X-ray structural analysis revealed that zinc adopts a trigonal bipyramidal geometry within the assembled ligand. The diversity and equilibrium of the assemblies are readily altered by simply changing concentrations, varying components, or adding counter anions. PMID:21919095

  4. Automated ensemble assembly and validation of microbial genomes

    Science.gov (United States)

    2014-01-01

    Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to

  5. PAVE: Program for assembling and viewing ESTs

    Directory of Open Access Journals (Sweden)

    Bomhoff Matthew

    2009-08-01

    Full Text Available Abstract Background New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. Results The PAVE (Program for Assembling and Viewing ESTs assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. Conclusion The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

  6. PAVE: program for assembling and viewing ESTs.

    Science.gov (United States)

    Soderlund, Carol; Johnson, Eric; Bomhoff, Matthew; Descour, Anne

    2009-08-26

    New sequencing technologies are rapidly emerging. Many laboratories are simultaneously working with the traditional Sanger ESTs and experimenting with ESTs generated by the 454 Life Science sequencers. Though Sanger ESTs have been used to generate contigs for many years, no program takes full advantage of the 5' and 3' mate-pair information, hence, many tentative transcripts are assembled into two separate contigs. The new 454 technology has the benefit of high-throughput expression profiling, but introduces time and space problems for assembling large contigs. The PAVE (Program for Assembling and Viewing ESTs) assembler takes advantage of the 5' and 3' mate-pair information by requiring that the mate-pairs be assembled into the same contig and joined by n's if the two sub-contigs do not overlap. It handles the depth of 454 data sets by "burying" similar ESTs during assembly, which retains the expression level information while circumventing time and space problems. PAVE uses MegaBLAST for the clustering step and CAP3 for assembly, however it assembles incrementally to enforce the mate-pair constraint, bury ESTs, and reduce incorrect joins and splits. The PAVE data management system uses a MySQL database to store multiple libraries of ESTs along with their metadata; the management system allows multiple assemblies with variations on libraries and parameters. Analysis routines provide standard annotation for the contigs including a measure of differentially expressed genes across the libraries. A Java viewer program is provided for display and analysis of the results. Our results clearly show the benefit of using the PAVE assembler to explicitly use mate-pair information and bury ESTs for large contigs. The PAVE assembler provides a software package for assembling Sanger and/or 454 ESTs. The assembly software, data management software, Java viewer and user's guide are freely available.

  7. Shut-down margin study for the next generation VVER-1000 reactor including 13 x 13 hexagonal annular assemblies

    International Nuclear Information System (INIS)

    Faghihi, Farshad; Mirvakili, S. Mohammad

    2011-01-01

    Highlights: → Shut-Down Margin (SDM) for the next generation annular fuel core of typical VVER-1000, 13 x 13 assemblies are calculated. → The MCNP-5 code is run for many cases with different core burn up at various core temperatures. → There is a substantial drop in SDM in the case of annular fuel for the same power level. → SDM for our proposed VVER-1000 annular pins is calculated for specific average fuel burn up values at the BOC, MOC, and EOC. - Abstract: Shut-Down Margin (SDM) for the next generation annular fuel core of typical VVER-1000, 13 x 13 assemblies are calculated as the main aim of the present research. We have applied the MCNP-5 code for many cases with different values of core burn up at various core temperatures, and therefore their corresponding coolant densities and boric acid concentrations. There is a substantial drop in SDM in the case of annular fuel for the same power level. Specifically, SDM for our proposed VVER-1000 annular pins is calculated when the average fuel burn up values at the BOC, MOC, and EOC are 0.531, 11.5, and 43 MW-days/kg-U, respectively.

  8. Thermoelectric generator with hinged assembly for fins

    International Nuclear Information System (INIS)

    Purdy, D.L.; Shapiro, Z.M.; Hursen, T.F.; Maurer, G.W.

    1976-01-01

    A cylindrical casing has a central shielded capsule of radioisotope fuel. A plurality of thermonuclear modules are axially arranged with their hot junctions resiliently pressed toward the shield and with their cold junctions adjacent a transition member having fins radiating heat to the environment. For each module, the assembly of transition member and fins is hinged to the casing for swinging to permit access to and removal of such module. A ceramic plate having gold layers on opposite faces prevents diffusion bonding of the hot junction to the shield

  9. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  10. Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

    Directory of Open Access Journals (Sweden)

    Xianwen Ren

    Full Text Available Next generation sequencing (NGS technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.

  11. Hierarchical Self Assembly of Patterns from the Robinson Tilings: DNA Tile Design in an Enhanced Tile Assembly Model.

    Science.gov (United States)

    Padilla, Jennifer E; Liu, Wenyan; Seeman, Nadrian C

    2012-06-01

    We introduce a hierarchical self assembly algorithm that produces the quasiperiodic patterns found in the Robinson tilings and suggest a practical implementation of this algorithm using DNA origami tiles. We modify the abstract Tile Assembly Model, (aTAM), to include active signaling and glue activation in response to signals to coordinate the hierarchical assembly of Robinson patterns of arbitrary size from a small set of tiles according to the tile substitution algorithm that generates them. Enabling coordinated hierarchical assembly in the aTAM makes possible the efficient encoding of the recursive process of tile substitution.

  12. A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: Assembly of the duck (Anas platyrhynchos transcriptome.

    Directory of Open Access Journals (Sweden)

    Joanna eMoreton

    2014-06-01

    Full Text Available For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1 assessing the performance of three different assembly tools (2 using both single and multiple k-mer approaches (3 examining the influence of the number of reads used in the assembly (4 merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck. We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT and CEGMA (Core Eukaryotic Genes Mapping Approach provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of multiple k-mers in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi.org/10.6084/m9.figshare.1032613.

  13. Feasibility of sealed D-T neutron generator as neutron source for liver BNCT and its beam shaping assembly.

    Science.gov (United States)

    Liu, Zheng; Li, Gang; Liu, Linmao

    2014-04-01

    This paper involves the feasibility of boron neutron capture therapy (BNCT) for liver tumor with four sealed neutron generators as neutron source. Two generators are placed on each side of the liver. The high energy of these emitted neutrons should be reduced by designing a beam shaping assembly (BSA) to make them useable for BNCT. However, the neutron flux decreases as neutrons pass through different materials of BSA. Therefore, it is essential to find ways to increase the neutron flux. In this paper, the feasibility of using low enrichment uranium as a neutron multiplier is investigated to increase the number of neutrons emitted from D-T neutron generators. The neutron spectrum related to our system has a proper epithermal flux, and the fast and thermal neutron fluxes comply with the IAEA recommended values. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Hierarchical self-assembly of a bow-shaped molecule bearing self-complementary hydrogen bonding sites into extended supramolecular assemblies.

    Science.gov (United States)

    Ikeda, Masato; Nobori, Tadahito; Schmutz, Marc; Lehn, Jean-Marie

    2005-01-07

    The bow-shaped molecule 1 bearing a self-complementary DAAD-ADDA (D=donor A=acceptor) hydrogen-bonding array generates, in hydrocarbon solvents, highly ordered supramolecular sheet aggregates that subsequently give rise to gels by formation of an entangled network. The process of hierarchical self-assembly of compound 1 was investigated by the concentration and temperature dependence of UV-visible and (1)H NMR spectra, fluorescence spectra, and electron microscopy data. The temperature dependence of the UV-visible spectra indicates a highly cooperative process for the self-assembly of compound 1 in decaline. The electron micrograph of the decaline solution of compound 1 (1.0 mM) revealed supramolecular sheet aggregates forming an entangled network. The selected area electronic diffraction patterns of the supramolecular sheet aggregates were typical for single crystals, indicative of a highly ordered assembly. The results exemplify the generation, by hierarchical self-assembly, of highly organized supramolecular materials presenting novel collective properties at each level of organization.

  15. The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius with next generation sequencing.

    Directory of Open Access Journals (Sweden)

    Chih-Ming Hung

    Full Text Available The information from ancient DNA (aDNA provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome of two extinct passenger pigeons (Ectopistes migratorius using de novo assembly of massive short (90 bp, paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species.

  16. The De Novo Assembly of Mitochondrial Genomes of the Extinct Passenger Pigeon (Ectopistes migratorius) with Next Generation Sequencing

    Science.gov (United States)

    Hung, Chih-Ming; Lin, Rong-Chien; Chu, Jui-Hua; Yeh, Chia-Fen; Yao, Chiou-Ju; Li, Shou-Hsien

    2013-01-01

    The information from ancient DNA (aDNA) provides an unparalleled opportunity to infer phylogenetic relationships and population history of extinct species and to investigate genetic evolution directly. However, the degraded and fragmented nature of aDNA has posed technical challenges for studies based on conventional PCR amplification. In this study, we present an approach based on next generation sequencing to efficiently sequence the complete mitochondrial genome (mitogenome) of two extinct passenger pigeons (Ectopistes migratorius) using de novo assembly of massive short (90 bp), paired-end or single-end reads. Although varying levels of human contamination and low levels of postmortem nucleotide lesion were observed, they did not impact sequencing accuracy. Our results demonstrated that the de novo assembly of shotgun sequence reads could be a potent approach to sequence mitogenomes, and offered an efficient way to infer evolutionary history of extinct species. PMID:23437111

  17. GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.

    Directory of Open Access Journals (Sweden)

    Sebastian Jünemann

    Full Text Available De novo genome assembly is the process of reconstructing a complete genomic sequence from countless small sequencing reads. Due to the complexity of this task, numerous genome assemblers have been developed to cope with different requirements and the different kinds of data provided by sequencers within the fast evolving field of next-generation sequencing technologies. In particular, the recently introduced generation of benchtop sequencers, like Illumina's MiSeq and Ion Torrent's Personal Genome Machine (PGM, popularized the easy, fast, and cheap sequencing of bacterial organisms to a broad range of academic and clinical institutions. With a strong pragmatic focus, here, we give a novel insight into the line of assembly evaluation surveys as we benchmark popular de novo genome assemblers based on bacterial data generated by benchtop sequencers. Therefore, single-library assemblies were generated, assembled, and compared to each other by metrics describing assembly contiguity and accuracy, and also by practice-oriented criteria as for instance computing time. In addition, we extensively analyzed the effect of the depth of coverage on the genome assemblies within reasonable ranges and the k-mer optimization problem of de Bruijn Graph assemblers. Our results show that, although both MiSeq and PGM allow for good genome assemblies, they require different approaches. They not only pair with different assembler types, but also affect assemblies differently regarding the depth of coverage where oversampling can become problematic. Assemblies vary greatly with respect to contiguity and accuracy but also by the requirement on the computing power. Consequently, no assembler can be rated best for all preconditions. Instead, the given kind of data, the demands on assembly quality, and the available computing infrastructure determines which assembler suits best. The data sets, scripts and all additional information needed to replicate our results are freely

  18. Uracil Excision for Assembly of Complex Pathways

    DEFF Research Database (Denmark)

    Cavaleiro, Mafalda; Nielsen, Morten Thrane; Kim, Se Hyeuk

    2015-01-01

    Despite decreasing prices on synthetic DNA constructs, higher-order assembly of PCR-generated DNA continues to be an important exercise in molecular and synthetic biology. Simplicity and robustness are attractive features met by the uracil excision DNA assembly method, which is one of the most in...

  19. MITG test assembly design and fabrication

    International Nuclear Information System (INIS)

    Schock, A.

    1983-01-01

    The design, analysis, and evaluation of the Modular Isotopic Thermoelectric Generator (MITG), described in an earlier paper, led to a program to build and test prototypical, modules of that generator. Each test module duplicates the thermoelectric converters, thermal insulation, housing and radiator fins of a typical generator slice, and simulates its isotope heat source module by means of an electrical heater encased in a prototypical graphite box. Once the approx. 20-watt MITG module has been developed, it can be assembled in appropriate number to form a generator design yielding the desired power output. The present paper describes the design and fabrication of the MITG test assembly, which confirmed the fabricability of the multicouples and interleaved multifoil insulation called for by the design. Test plans, procedures, instrumentation, results, and post-test analyses, as well as revised designs, fabrication procedures, and performance estimates, are described in subsequent papers in these proceedings

  20. Determination of a representative volume element based on the variability of mechanical properties with sample size in bread.

    Science.gov (United States)

    Ramírez, Cristian; Young, Ashley; James, Bryony; Aguilera, José M

    2010-10-01

    Quantitative analysis of food structure is commonly obtained by image analysis of a small portion of the material that may not be the representative of the whole sample. In order to quantify structural parameters (air cells) of 2 types of bread (bread and bagel) the concept of representative volume element (RVE) was employed. The RVE for bread, bagel, and gelatin-gel (used as control) was obtained from the relationship between sample size and the coefficient of variation, calculated from the apparent Young's modulus measured on 25 replicates. The RVE was obtained when the coefficient of variation for different sample sizes converged to a constant value. In the 2 types of bread tested, the tendency of the coefficient of variation was to decrease as the sample size increased, while in the homogeneous gelatin-gel, it remained always constant around 2.3% to 2.4%. The RVE resulted to be cubes with sides of 45 mm for bread, 20 mm for bagels, and 10 mm for gelatin-gel (smallest sample tested). The quantitative image analysis as well as visual observation demonstrated that bread presented the largest dispersion of air-cell sizes. Moreover, both the ratio of maximum air-cell area/image area and maximum air-cell height/image height were greater for bread (values of 0.05 and 0.30, respectively) than for bagels (0.03 and 0.20, respectively). Therefore, the size and the size variation of air cells present in the structure determined the size of the RVE. It was concluded that RVE is highly dependent on the heterogeneity of the structure of the types of baked products.

  1. Physicochemical and biological properties of self-assembled antisense/poly(amidoamine) dendrimer nanoparticles: the effect of dendrimer generation and charge ratio

    OpenAIRE

    Nomani, Alireza; Haririan, Ismaeil; Rahimnia, Ramin; Fouladdel, Shamileh; Gazori, Tarane; Dinarvand, Rassoul; Omidi, Yadollah; Azizi, Ebrahim

    2010-01-01

    To gain a deeper understanding of the physicochemical phenomenon of self-assembled nanoparticles of different generations and ratios of poly (amidoamine) dendrimer (PAMAM) dendrimer and a short-stranded DNA (antisense oligonucleotide), multiple methods were used to characterize these nanoparticles including photon correlation spectroscopy (PCS); zeta potential measurement; and atomic force microscopy (AFM). PCS and AFM results revealed that, in contrast to larger molecules of DNA, smaller mol...

  2. Resistant starch intake at breakfast affects postprandial responses in type 2 diabetics and enhances the glucose-dependent insulinotropic polypeptide--insulin relationship following a second meal.

    Science.gov (United States)

    MacNeil, Stacey; Rebry, Rachel M; Tetlow, Ian J; Emes, Michael J; McKeown, Bruce; Graham, Terry E

    2013-12-01

    Resistant starch (RS) consumption can modulate postprandial metabolic responses, but its effects on carbohydrate (CHO) handling in type 2 diabetics (T2D) are unclear. It was hypothesized that a bagel high in RS would improve glucose and insulin homeostasis following the 1st meal, regardless of the amount of available CHO, and that in association with incretins, the effects would carry over to a 2nd meal. Using a randomized crossover design, 12 T2D ingested four different bagel treatments (their 1st meal) determined by available CHO and the weight or amount of bagel consumed: treatment A, without RS (50 g of available CHO); treatment B, with RS (same total CHO as in A); treatment C, with RS (same available CHO as in A); and treatment D, with the same RS as in B and available CHO as in A and C. A standard 2nd meal was ingested 3 h later. Following the first meal, B elicited a lower glucose incremental area under the curve (iAUC) than C (P portion of the available CHO, while ingesting more RS influenced the GIP-insulin axis following the 2nd meal.

  3. Parallel processing of neutron transport in fuel assembly calculation

    International Nuclear Information System (INIS)

    Song, Jae Seung

    1992-02-01

    Group constants, which are used for reactor analyses by nodal method, are generated by fuel assembly calculations based on the neutron transport theory, since one or a quarter of the fuel assembly corresponds to a unit mesh in the current nodal calculation. The group constant calculation for a fuel assembly is performed through spectrum calculations, a two-dimensional fuel assembly calculation, and depletion calculations. The purpose of this study is to develop a parallel algorithm to be used in a parallel processor for the fuel assembly calculation and the depletion calculations of the group constant generation. A serial program, which solves the neutron integral transport equation using the transmission probability method and the linear depletion equation, was prepared and verified by a benchmark calculation. Small changes from the serial program was enough to parallelize the depletion calculation which has inherent parallel characteristics. In the fuel assembly calculation, however, efficient parallelization is not simple and easy because of the many coupling parameters in the calculation and data communications among CPU's. In this study, the group distribution method is introduced for the parallel processing of the fuel assembly calculation to minimize the data communications. The parallel processing was performed on Quadputer with 4 CPU's operating in NURAD Lab. at KAIST. Efficiencies of 54.3 % and 78.0 % were obtained in the fuel assembly calculation and depletion calculation, respectively, which lead to the overall speedup of about 2.5. As a result, it is concluded that the computing time consumed for the group constant generation can be easily reduced by parallel processing on the parallel computer with small size CPU's

  4. Using the International Space Station (ISS) Oxygen Generation Assembly (OGA) Is Not Feasible for Mars Transit

    Science.gov (United States)

    Jones, Harry W.

    2016-01-01

    A review of two papers on improving the International Space Station (ISS) Oxygen Generation Assembly (OGA) shows that it would not save substantial mass on a Mars transit. The ISS OGA requires redesign for satisfactory operation, even for the ISS. The planned improvements of the OGA for ISS would not be sufficient to make it suitable for Mars, because Mars transit life support has significantly different requirements than ISS. The OGA for Mars should have lower mass, better reliability and maintainability, greater safety, radiation hardening, and capability for quiescent operation. NASA's methodical, disciplined systems engineering process should be used to develop the appropriate system.

  5. Meta-IDBA: a de Novo assembler for metagenomic data.

    Science.gov (United States)

    Peng, Yu; Leung, Henry C M; Yiu, S M; Chin, Francis Y L

    2011-07-01

    Next-generation sequencing techniques allow us to generate reads from a microbial environment in order to analyze the microbial community. However, assembling of a set of mixed reads from different species to form contigs is a bottleneck of metagenomic research. Although there are many assemblers for assembling reads from a single genome, there are no assemblers for assembling reads in metagenomic data without reference genome sequences. Moreover, the performances of these assemblers on metagenomic data are far from satisfactory, because of the existence of common regions in the genomes of subspecies and species, which make the assembly problem much more complicated. We introduce the Meta-IDBA algorithm for assembling reads in metagenomic data, which contain multiple genomes from different species. There are two core steps in Meta-IDBA. It first tries to partition the de Bruijn graph into isolated components of different species based on an important observation. Then, for each component, it captures the slight variants of the genomes of subspecies from the same species by multiple alignments and represents the genome of one species, using a consensus sequence. Comparison of the performances of Meta-IDBA and existing assemblers, such as Velvet and Abyss for different metagenomic datasets shows that Meta-IDBA can reconstruct longer contigs with similar accuracy. Meta-IDBA toolkit is available at our website http://www.cs.hku.hk/~alse/metaidba. chin@cs.hku.hk.

  6. Method and apparatus for assembling permanent magnet rotors

    Science.gov (United States)

    Hsu, J.S.; Adams, D.J.

    1999-06-22

    A permanent magnet assembly for assembly in large permanent magnet motors and generators includes a two-piece carrier that can be slid into a slot in the rotor and then secured in place using a set screw. The invention also provides an auxiliary carrier device with guide rails that line up with the teeth of the rotor, so that a permanent magnet assembly can be pushed first into a slot, and then down the slot to its proper location. An auxiliary tool is provided to move the permanent magnet assembly into position in the slot before it is secured in place. Methods of assembling and disassembling the magnet assemblies in the rotor are also disclosed. 2 figs.

  7. Deterministic nanoparticle assemblies: from substrate to solution

    International Nuclear Information System (INIS)

    Barcelo, Steven J; Gibson, Gary A; Yamakawa, Mineo; Li, Zhiyong; Kim, Ansoon; Norris, Kate J

    2014-01-01

    The deterministic assembly of metallic nanoparticles is an exciting field with many potential benefits. Many promising techniques have been developed, but challenges remain, particularly for the assembly of larger nanoparticles which often have more interesting plasmonic properties. Here we present a scalable process combining the strengths of top down and bottom up fabrication to generate deterministic 2D assemblies of metallic nanoparticles and demonstrate their stable transfer to solution. Scanning electron and high-resolution transmission electron microscopy studies of these assemblies suggested the formation of nanobridges between touching nanoparticles that hold them together so as to maintain the integrity of the assembly throughout the transfer process. The application of these nanoparticle assemblies as solution-based surface-enhanced Raman scattering (SERS) materials is demonstrated by trapping analyte molecules in the nanoparticle gaps during assembly, yielding uniformly high enhancement factors at all stages of the fabrication process. (paper)

  8. Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches.

    Science.gov (United States)

    Lin, Hsin-Hung; Liao, Yu-Chieh

    2015-01-01

    Despite the ever-increasing output of next-generation sequencing data along with developing assemblers, dozens to hundreds of gaps still exist in de novo microbial assemblies due to uneven coverage and large genomic repeats. Third-generation single-molecule, real-time (SMRT) sequencing technology avoids amplification artifacts and generates kilobase-long reads with the potential to complete microbial genome assembly. However, due to the low accuracy (~85%) of third-generation sequences, a considerable amount of long reads (>50X) are required for self-correction and for subsequent de novo assembly. Recently-developed hybrid approaches, using next-generation sequencing data and as few as 5X long reads, have been proposed to improve the completeness of microbial assembly. In this study we have evaluated the contemporary hybrid approaches and demonstrated that assembling corrected long reads (by runCA) produced the best assembly compared to long-read scaffolding (e.g., AHA, Cerulean and SSPACE-LongRead) and gap-filling (SPAdes). For generating corrected long reads, we further examined long-read correction tools, such as ECTools, LSC, LoRDEC, PBcR pipeline and proovread. We have demonstrated that three microbial genomes including Escherichia coli K12 MG1655, Meiothermus ruber DSM1279 and Pdeobacter heparinus DSM2366 were successfully hybrid assembled by runCA into near-perfect assemblies using ECTools-corrected long reads. In addition, we developed a tool, Patch, which implements corrected long reads and pre-assembled contigs as inputs, to enhance microbial genome assemblies. With the additional 20X long reads, short reads of S. cerevisiae W303 were hybrid assembled into 115 contigs using the verified strategy, ECTools + runCA. Patch was subsequently applied to upgrade the assembly to a 35-contig draft genome. Our evaluation of the hybrid approaches shows that assembling the ECTools-corrected long reads via runCA generates near complete microbial genomes, suggesting

  9. Onset of self-assembly

    International Nuclear Information System (INIS)

    Chitanvis, S.M.

    1998-01-01

    We have formulated a theory of self-assembly based on the notion of local gauge invariance at the mesoscale. Local gauge invariance at the mesoscale generates the required long-range entropic forces responsible for self-assembly in binary systems. Our theory was applied to study the onset of mesostructure formation above a critical temperature in estane, a diblock copolymer. We used diagrammatic methods to transcend the Gaussian approximation and obtain a correlation length ξ∼(c-c * ) -γ , where c * is the minimum concentration below which self-assembly is impossible, c is the current concentration, and γ was found numerically to be fairly close to 2/3. The renormalized diffusion constant vanishes as the critical concentration is approached, indicating the occurrence of critical slowing down, while the correlation function remains finite at the transition point. copyright 1998 The American Physical Society

  10. Orthology Guided Assembly in highly heterozygous crops

    DEFF Research Database (Denmark)

    Ruttink, Tom; Sterck, Lieven; Rohde, Antje

    2013-01-01

    to outbreeding crop species hamper De Bruijn Graph-based de novo assembly algorithms, causing transcript fragmentation and the redundant assembly of allelic contigs. If multiple genotypes are sequenced to study genetic diversity, primary de novo assembly is best performed per genotype to limit the level......Despite current advances in next-generation sequencing data analysis procedures, de novo assembly of a reference sequence required for SNP discovery and expression analysis is still a major challenge in genetically uncharacterized, highly heterozygous species. High levels of polymorphism inherent...... of polymorphism and avoid transcript fragmentation. Here, we propose an Orthology Guided Assembly procedure that first uses sequence similarity (tBLASTn) to proteins of a model species to select allelic and fragmented contigs from all genotypes and then performs CAP3 clustering on a gene-by-gene basis. Thus, we...

  11. De novo assembly and phasing of a Korean human genome.

    Science.gov (United States)

    Seo, Jeong-Sun; Rhie, Arang; Kim, Junsoo; Lee, Sangjin; Sohn, Min-Hwan; Kim, Chang-Uk; Hastie, Alex; Cao, Han; Yun, Ji-Young; Kim, Jihye; Kuk, Junho; Park, Gun Hwa; Kim, Juhyeok; Ryu, Hanna; Kim, Jongbum; Roh, Mira; Baek, Jeonghun; Hunkapiller, Michael W; Korlach, Jonas; Shin, Jong-Yeon; Kim, Changhoon

    2016-10-13

    Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of

  12. Oxford Nanopore MinION Sequencing and Genome Assembly

    Directory of Open Access Journals (Sweden)

    Hengyun Lu

    2016-10-01

    Full Text Available The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS technology. The third-generation sequencing (TGS technology, led by Pacific Biosciences (PacBio, is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT. MinION identifies DNA bases by measuring the changes in electrical conductivity generated as DNA strands pass through a biological pore. Its portability, affordability, and speed in data production makes it suitable for real-time applications, the release of the long read sequencer MinION has thus generated much excitement and interest in the genomics community. While de novo genome assemblies can be cheaply produced from SGS data, assembly continuity is often relatively poor, due to the limited ability of short reads to handle long repeats. Assembly quality can be greatly improved by using TGS long reads, since repetitive regions can be easily expanded into using longer sequencing lengths, despite having higher error rates at the base level. The potential of nanopore sequencing has been demonstrated by various studies in genome surveillance at locations where rapid and reliable sequencing is needed, but where resources are limited.

  13. An efficient approach to BAC based assembly of complex genomes.

    Science.gov (United States)

    Visendi, Paul; Berkman, Paul J; Hayashi, Satomi; Golicz, Agnieszka A; Bayer, Philipp E; Ruperao, Pradeep; Hurgobin, Bhavna; Montenegro, Juan; Chan, Chon-Kit Kenneth; Staňková, Helena; Batley, Jacqueline; Šimková, Hana; Doležel, Jaroslav; Edwards, David

    2016-01-01

    There has been an exponential growth in the number of genome sequencing projects since the introduction of next generation DNA sequencing technologies. Genome projects have increasingly involved assembly of whole genome data which produces inferior assemblies compared to traditional Sanger sequencing of genomic fragments cloned into bacterial artificial chromosomes (BACs). While whole genome shotgun sequencing using next generation sequencing (NGS) is relatively fast and inexpensive, this method is extremely challenging for highly complex genomes, where polyploidy or high repeat content confounds accurate assembly, or where a highly accurate 'gold' reference is required. Several attempts have been made to improve genome sequencing approaches by incorporating NGS methods, to variable success. We present the application of a novel BAC sequencing approach which combines indexed pools of BACs, Illumina paired read sequencing, a sequence assembler specifically designed for complex BAC assembly, and a custom bioinformatics pipeline. We demonstrate this method by sequencing and assembling BAC cloned fragments from bread wheat and sugarcane genomes. We demonstrate that our assembly approach is accurate, robust, cost effective and scalable, with applications for complete genome sequencing in large and complex genomes.

  14. PREP-PWR-1.0: a WIMS-D/4 pre-processor code for the generation of data for PWR fuel assemblies

    International Nuclear Information System (INIS)

    Ball, G.

    1991-06-01

    The PREP-PWR-1.0 computer code is a substantially modified version of the PREWIM code which formed part of the original MARIA System (Report J.E.N. 543). PREP-PWR-1.0 is a comprehensive pre-processor code which generates input data for the WIMS-D/4.1 code (Report PEL 294) for PWR fuel assemblies, with or without control and burnable poison rods. This data is generated at various base and off-base conditions. The overall cross section generation methodology is described, followed by a brief overview of the model. Aspects of the base/off-base calculational scheme are outlined. Additional features of the code are described while the input data format of PREP-PWR-1.0 is listed. The sample problems and suggestions for further improvements to the code are also described. 2 figs., 2 tabs., 12 refs

  15. Sambot II: A self-assembly modular swarm robot

    Science.gov (United States)

    Zhang, Yuchao; Wei, Hongxing; Yang, Bo; Jiang, Cancan

    2018-04-01

    The new generation of self-assembly modular swarm robot Sambot II, based on the original generation of self-assembly modular swarm robot Sambot, adopting laser and camera module for information collecting, is introduced in this manuscript. The visual control algorithm of Sambot II is detailed and feasibility of the algorithm is verified by the laser and camera experiments. At the end of this manuscript, autonomous docking experiments of two Sambot II robots are presented. The results of experiments are showed and analyzed to verify the feasibility of whole scheme of Sambot II.

  16. Neutronics assessment of thorium-based fuel assembly in SCWR

    International Nuclear Information System (INIS)

    Liu, Shichang; Cai, Jiejin

    2013-01-01

    Highlights: • A novel thorium-based fuel assembly for SCWR has been introduced and investigated. • Neutronic properties of three thorium fuels have been studied, compared with UO 2 fuel. • The thorium-based fuel has advantages on fuel utilization and lower MAs generation. -- Abstract: Aiming to take advantage of neutron spectrum of SCWR, a novel thorium-based fuel assembly for SCWR is introduced in this paper. The neutronic characteristics of the introduced fuel assembly with three different thorium fuel types have been investigated using the “dragon” codes. The parameters in different working conditions, such as infinite multiplication factors, radial power peaking factor, temperature coefficient of reactivity and their relation with the operation period have been assessed by comparing with conventional uranium assembly. Moreover, the moderator-to-fuel ratio (MFR) was changed in order to investigate its influence on the neutronic characteristics of fuel assembly. Results show that the thorium-based fuel has advantages on both efficient fuel utilization and lower minor actinide generation, with some similar neutronic properties to the uranium fuel

  17. Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.

    Science.gov (United States)

    Cerveau, Nicolas; Jackson, Daniel J

    2016-12-09

    Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be

  18. Syntactic sequencing in Hebbian cell assemblies.

    Science.gov (United States)

    Wennekers, Thomas; Palm, Günther

    2009-12-01

    Hebbian cell assemblies provide a theoretical framework for the modeling of cognitive processes that grounds them in the underlying physiological neural circuits. Recently we have presented an extension of cell assemblies by operational components which allows to model aspects of language, rules, and complex behaviour. In the present work we study the generation of syntactic sequences using operational cell assemblies timed by unspecific trigger signals. Syntactic patterns are implemented in terms of hetero-associative transition graphs in attractor networks which cause a directed flow of activity through the neural state space. We provide regimes for parameters that enable an unspecific excitatory control signal to switch reliably between attractors in accordance with the implemented syntactic rules. If several target attractors are possible in a given state, noise in the system in conjunction with a winner-takes-all mechanism can randomly choose a target. Disambiguation can also be guided by context signals or specific additional external signals. Given a permanently elevated level of external excitation the model can enter an autonomous mode, where it generates temporal grammatical patterns continuously.

  19. An assembly sequence planning method based on composite algorithm

    Directory of Open Access Journals (Sweden)

    Enfu LIU

    2016-02-01

    Full Text Available To solve the combination explosion problem and the blind searching problem in assembly sequence planning of complex products, an assembly sequence planning method based on composite algorithm is proposed. In the composite algorithm, a sufficient number of feasible assembly sequences are generated using formalization reasoning algorithm as the initial population of genetic algorithm. Then fuzzy knowledge of assembly is integrated into the planning process of genetic algorithm and ant algorithm to get the accurate solution. At last, an example is conducted to verify the feasibility of composite algorithm.

  20. Assembly of barcode-like nucleic acid nanostructures.

    Science.gov (United States)

    Wang, Pengfei; Tian, Cheng; Li, Xiang; Mao, Chengde

    2014-10-15

    Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. DNA fragments assembly based on nicking enzyme system.

    Directory of Open Access Journals (Sweden)

    Rui-Yan Wang

    Full Text Available A couple of DNA ligation-independent cloning (LIC methods have been reported to meet various requirements in metabolic engineering and synthetic biology. The principle of LIC is the assembly of multiple overlapping DNA fragments by single-stranded (ss DNA overlaps annealing. Here we present a method to generate single-stranded DNA overlaps based on Nicking Endonucleases (NEases for LIC, the method was termed NE-LIC. Factors related to cloning efficiency were optimized in this study. This NE-LIC allows generating 3'-end or 5'-end ss DNA overlaps of various lengths for fragments assembly. We demonstrated that the 10 bp/15 bp overlaps had the highest DNA fragments assembling efficiency, while 5 bp/10 bp overlaps showed the highest efficiency when T4 DNA ligase was added. Its advantage over Sequence and Ligation Independent Cloning (SLIC and Uracil-Specific Excision Reagent (USER was obvious. The mechanism can be applied to many other LIC strategies. Finally, the NEases based LIC (NE-LIC was successfully applied to assemble a pathway of six gene fragments responsible for synthesizing microbial poly-3-hydroxybutyrate (PHB.

  2. V-GAP: Viral genome assembly pipeline

    KAUST Repository

    Nakamura, Yoji

    2015-10-22

    Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.

  3. V-GAP: Viral genome assembly pipeline

    KAUST Repository

    Nakamura, Yoji; Yasuike, Motoshige; Nishiki, Issei; Iwasaki, Yuki; Fujiwara, Atushi; Kawato, Yasuhiko; Nakai, Toshihiro; Nagai, Satoshi; Kobayashi, Takanori; Gojobori, Takashi; Ototake, Mitsuru

    2015-01-01

    Next-generation sequencing technologies have allowed the rapid determination of the complete genomes of many organisms. Although shotgun sequences from large genome organisms are still difficult to reconstruct perfect contigs each of which represents a full chromosome, those from small genomes have been assembled successfully into a very small number of contigs. In this study, we show that shotgun reads from phage genomes can be reconstructed into a single contig by controlling the number of read sequences used in de novo assembly. We have developed a pipeline to assemble small viral genomes with good reliability using a resampling method from shotgun data. This pipeline, named V-GAP (Viral Genome Assembly Pipeline), will contribute to the rapid genome typing of viruses, which are highly divergent, and thus will meet the increasing need for viral genome comparisons in metagenomic studies.

  4. De novo assembly of a haplotype-resolved human genome.

    Science.gov (United States)

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

    2015-06-01

    The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

  5. A memory-efficient data structure representing exact-match overlap graphs with application for next-generation DNA assembly.

    Science.gov (United States)

    Dinh, Hieu; Rajasekaran, Sanguthevar

    2011-07-15

    Exact-match overlap graphs have been broadly used in the context of DNA assembly and the shortest super string problem where the number of strings n ranges from thousands to billions. The length ℓ of the strings is from 25 to 1000, depending on the DNA sequencing technologies. However, many DNA assemblers using overlap graphs suffer from the need for too much time and space in constructing the graphs. It is nearly impossible for these DNA assemblers to handle the huge amount of data produced by the next-generation sequencing technologies where the number n of strings could be several billions. If the overlap graph is explicitly stored, it would require Ω(n(2)) memory, which could be prohibitive in practice when n is greater than a hundred million. In this article, we propose a novel data structure using which the overlap graph can be compactly stored. This data structure requires only linear time to construct and and linear memory to store. For a given set of input strings (also called reads), we can informally define an exact-match overlap graph as follows. Each read is represented as a node in the graph and there is an edge between two nodes if the corresponding reads overlap sufficiently. A formal description follows. The maximal exact-match overlap of two strings x and y, denoted by ov(max)(x, y), is the longest string which is a suffix of x and a prefix of y. The exact-match overlap graph of n given strings of length ℓ is an edge-weighted graph in which each vertex is associated with a string and there is an edge (x, y) of weight ω=ℓ-|ov(max)(x, y)| if and only if ω ≤ λ, where |ov(max)(x, y)| is the length of ov(max)(x, y) and λ is a given threshold. In this article, we show that the exact-match overlap graphs can be represented by a compact data structure that can be stored using at most (2λ-1)(2⌈logn⌉+⌈logλ⌉)n bits with a guarantee that the basic operation of accessing an edge takes O(log λ) time. We also propose two algorithms for

  6. One step generation of customizable gRNA vectors for multiplex CRISPR approaches through string assembly gRNA cloning (STAgR).

    Science.gov (United States)

    Breunig, Christopher T; Durovic, Tamara; Neuner, Andrea M; Baumann, Valentin; Wiesbeck, Maximilian F; Köferle, Anna; Götz, Magdalena; Ninkovic, Jovica; Stricker, Stefan H

    2018-01-01

    Novel applications based on the bacterial CRISPR system make genetic, genomic, transcriptional and epigenomic engineering widely accessible for the first time. A significant advantage of CRISPR over previous methods is its tremendous adaptability due to its bipartite nature. Cas9 or its engineered variants define the molecular effect, while short gRNAs determine the targeting sites. A majority of CRISPR approaches depend on the simultaneous delivery of multiple gRNAs into single cells, either as an essential precondition, to increase responsive cell populations or to enhance phenotypic outcomes. Despite these requirements, methods allowing the efficient generation and delivery of multiple gRNA expression units into single cells are still sparse. Here we present STAgR (String assembly gRNA cloning), a single step gRNA multiplexing system, that obtains its advantages by employing the N20 targeting sequences as necessary homologies for Gibson assembly. We show that STAgR allows reliable and cost-effective generation of vectors with high numbers of gRNAs enabling multiplexed CRISPR approaches. Moreover, STAgR is easily customizable, as vector backbones as well as gRNA structures, numbers and promoters can be freely chosen and combined. Finally, we demonstrate STAgR's widespread functionality, its efficiency in multi-targeting approaches, using it for both, genome and transcriptome editing, as well as applying it in vitro and in vivo.

  7. SAGE: String-overlap Assembly of GEnomes.

    Science.gov (United States)

    Ilie, Lucian; Haider, Bahlul; Molnar, Michael; Solis-Oba, Roberto

    2014-09-15

    De novo genome assembly of next-generation sequencing data is one of the most important current problems in bioinformatics, essential in many biological applications. In spite of significant amount of work in this area, better solutions are still very much needed. We present a new program, SAGE, for de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an important number of new ideas, such as the efficient computation of the transitive reduction of the string overlap graph, the use of (generalized) edge multiplicity statistics for more accurate estimation of read copy counts, and the improved use of mate pairs and min-cost flow for supporting edge merging. The assemblies produced by SAGE for several short and medium-size genomes compared favourably with those of existing leading assemblers. SAGE benefits from innovations in almost every aspect of the assembly process: error correction of input reads, string-overlap graph construction, read copy counts estimation, overlap graph analysis and reduction, contig extraction, and scaffolding. We hope that these new ideas will help advance the current state-of-the-art in an essential area of research in genomics.

  8. Improvement of the Threespine Stickleback Genome Using a Hi-C-Based Proximity-Guided Assembly.

    Science.gov (United States)

    Peichel, Catherine L; Sullivan, Shawn T; Liachko, Ivan; White, Michael A

    2017-09-01

    Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs. Using Hi-C based PGA, we generated complete chromosome assemblies from a distribution of short contigs (20-100 kb). We found that 96.40% of contigs were correctly assigned to linkage groups (LGs), with ordering nearly identical to the previous genome assembly. Using available bacterial artificial chromosome (BAC) end sequences, we provide evidence that some of the few discrepancies between the Hi-C assembly and the existing assembly are due to structural variation between the populations used for the 2 assemblies or errors in the existing assembly. This Hi-C assembly also allowed us to improve the existing assembly, assigning over 60% (13.35 Mb) of the previously unassigned (~21.7 Mb) contigs to LGs. Together, our results highlight the potential of the Hi-C based PGA method to be used in combination with short read data to perform relatively inexpensive de novo genome assemblies. This approach will be particularly useful in organisms in which it is difficult to perform linkage mapping or to obtain high molecular weight DNA required for other scaffolding methods. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Toward a molecular programming language for algorithmic self-assembly

    Science.gov (United States)

    Patitz, Matthew John

    Self-assembly is the process whereby relatively simple components autonomously combine to form more complex objects. Nature exhibits self-assembly to form everything from microscopic crystals to living cells to galaxies. With a desire to both form increasingly sophisticated products and to understand the basic components of living systems, scientists have developed and studied artificial self-assembling systems. One such framework is the Tile Assembly Model introduced by Erik Winfree in 1998. In this model, simple two-dimensional square 'tiles' are designed so that they self-assemble into desired shapes. The work in this thesis consists of a series of results which build toward the future goal of designing an abstracted, high-level programming language for designing the molecular components of self-assembling systems which can perform powerful computations and form into intricate structures. The first two sets of results demonstrate self-assembling systems which perform infinite series of computations that characterize computably enumerable and decidable languages, and exhibit tools for algorithmically generating the necessary sets of tiles. In the next chapter, methods for generating tile sets which self-assemble into complicated shapes, namely a class of discrete self-similar fractal structures, are presented. Next, a software package for graphically designing tile sets, simulating their self-assembly, and debugging designed systems is discussed. Finally, a high-level programming language which abstracts much of the complexity and tedium of designing such systems, while preventing many of the common errors, is presented. The summation of this body of work presents a broad coverage of the spectrum of desired outputs from artificial self-assembling systems and a progression in the sophistication of tools used to design them. By creating a broader and deeper set of modular tools for designing self-assembling systems, we hope to increase the complexity which is

  10. Large branched self-assembled DNA complexes

    International Nuclear Information System (INIS)

    Tosch, Paul; Waelti, Christoph; Middelberg, Anton P J; Davies, A Giles

    2007-01-01

    Many biological molecules have been demonstrated to self-assemble into complex structures and networks by using their very efficient and selective molecular recognition processes. The use of biological molecules as scaffolds for the construction of functional devices by self-assembling nanoscale complexes onto the scaffolds has recently attracted significant attention and many different applications in this field have emerged. In particular DNA, owing to its inherent sophisticated self-organization and molecular recognition properties, has served widely as a scaffold for various nanotechnological self-assembly applications, with metallic and semiconducting nanoparticles, proteins, macromolecular complexes, inter alia, being assembled onto designed DNA scaffolds. Such scaffolds may typically contain multiple branch-points and comprise a number of DNA molecules selfassembled into the desired configuration. Previously, several studies have used synthetic methods to produce the constituent DNA of the scaffolds, but this typically constrains the size of the complexes. For applications that require larger self-assembling DNA complexes, several tens of nanometers or more, other techniques need to be employed. In this article, we discuss a generic technique to generate large branched DNA macromolecular complexes

  11. Reducing assembly complexity of microbial genomes with single-molecule sequencing

    Science.gov (United States)

    Genome assembly algorithms cannot fully reconstruct microbial chromosomes from the DNA reads output by first or second-generation sequencing instruments. Therefore, most genomes are left unfinished due to the significant resources required to manually close gaps left in the draft assemblies. Single-...

  12. Molecular engineering of lanthanide ion chelating phospholipids generating assemblies with a switched magnetic susceptibility.

    Science.gov (United States)

    Isabettini, Stéphane; Massabni, Sarah; Hodzic, Arnel; Durovic, Dzana; Kohlbrecher, Joachim; Ishikawa, Takashi; Fischer, Peter; Windhab, Erich J; Walde, Peter; Kuster, Simon

    2017-08-09

    Lanthanide ion (Ln 3+ ) chelating amphiphiles are powerful molecules for tailoring the magnetic response of polymolecular assemblies. Mixtures of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-ethanolamine-diethylene triaminepentaacetate (DMPE-DTPA) complexed to Ln 3+ deliver highly magnetically responsive bicelles. Their magnetic properties are readily tuned by changing the bicellar size or the magnetic susceptibility Δχ of the bilayer lipids. The former technique is intrinsically bound to the region of the phase diagram guarantying the formation of bicelles. Methods aiming towards manipulating the Δχ of the bilayer are comparatively more robust, flexible and lacking. Herein, we synthesized a new Ln 3+ chelating phospholipid using glutamic acid as a backbone: DMPE-Glu-DTPA. The chelate polyhedron was specifically engineered to alter the Δχ, whilst remaining geometrically similar to DMPE-DTPA. Planar asymmetric assemblies hundreds of nanometers in size were achieved presenting unprecedented magnetic alignments. The DMPE-Glu-DTPA/Ln 3+ complex switched the Δχ, achieving perpendicular alignment of assemblies containing Dy 3+ and parallel alignment of those containing Tm 3+ . Moreover, samples with chelated Yb 3+ were more alignable than the Tm 3+ chelating counterparts. Such a possibility has never been demonstrated for planar Ln 3+ chelating polymolecular assemblies. The physico-chemical properties of these novel assemblies were further studied by monitoring the alignment behavior at different temperatures and by including 16 mol% of cholesterol (Chol-OH) in the phospholipid bilayer. The DMPE-Glu-DTPA/Ln 3+ complex and the resulting assemblies are promising candidates for applications in numerous fields including pharmaceutical technologies, structural characterization of membrane biomolecules by NMR spectroscopy, as contrasting agents for magnetic resonance imaging, and for the development of smart optical gels.

  13. Fuel assembly

    International Nuclear Information System (INIS)

    Yokota, Tokunobu.

    1990-01-01

    A fuel assembly used in a FBR type nuclear reactor comprises a plurality of fuel rods and a moderator guide member (water rod). A moderator exit opening/closing mechanism is formed at the upper portion of the moderator guide member for opening and closing a moderator exit. In the initial fuel charging operation cycle to the reactor, the moderator exit is closed by the moderator exit opening/closing mechanism. Then, voids are accumulated at the inner upper portion of the moderator guide member to harden spectrum and a great amount of plutonium is generated and accumulated in the fuel assembly. Further, in the fuel re-charging operation cycle, the moderator guide member is used having the moderator exit opened. In this case, voids are discharged from the moderator guide member to decrease the ratio, and the plutonium accumulated in the initial charging operation cycle is burnt. In this way, the fuel economy can be improved. (I.N.)

  14. Micro Galvanic Cell To Generate PtO and Extend the Triple-Phase Boundary during Self-Assembly of Pt/C and Nafion for Catalyst Layers of PEMFC.

    Science.gov (United States)

    Long, Zhi; Gao, Liqin; Li, Yankai; Kang, Baotao; Lee, Jin Yong; Ge, Junjie; Liu, Changpeng; Ma, Shuhua; Jin, Zhao; Ai, Hongqi

    2017-11-08

    The self-assembly powder (SAP) with varying Nafion content was synthesized and characterized by XRD, XPS, HRTEM, and mapping. It is observed that the oxygen from oxygen functional groups transfers to the surface of Pt and generate PtO during the process of self-assembly with the mechanism of micro galvanic cell, where Pt, carbon black, and Nafion act as the anode, cathode and electrolyte, respectively. The appearance of PtO on the surface of Pt leads to a turnover of Nafion structure, and therefore more hydrophilic sulfonic groups directly contact with Pt, and thus the triple-phase boundary (TPB) has been expanded.

  15. Enabling Graph Appliance for Genome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Rina [ORNL; Graves, Jeffrey A [ORNL; Lee, Sangkeun (Matt) [ORNL; Sukumar, Sreenivas R [ORNL; Shankar, Mallikarjun [ORNL

    2015-01-01

    In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to store and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.

  16. Photovoltaic Assemblies for the Power Generation of the Exomars Missions

    Directory of Open Access Journals (Sweden)

    Ferrando Emanuele

    2017-01-01

    Finally the bio burden and planetary protection requirements are also not a standard in SA field. A special manufacturing, assembly and test sequence will be implemented to capitalize our previous experience on the Mars drill tool development. For both the arrays European PVA technology was exclusively used: more specifically high efficiency III-V compounds solar cells and a new glass grounding network.

  17. RGG: Reactor geometry (and mesh) generator

    International Nuclear Information System (INIS)

    Jain, R.; Tautges, T.

    2012-01-01

    The reactor geometry (and mesh) generator RGG takes advantage of information about repeated structures in both assembly and core lattices to simplify the creation of geometry and mesh. It is released as open source software as a part of the MeshKit mesh generation library. The methodology operates in three stages. First, assembly geometry models of various types are generated by a tool called AssyGen. Next, the assembly model or models are meshed by using MeshKit tools or the CUBIT mesh generation tool-kit, optionally based on a journal file output by AssyGen. After one or more assembly model meshes have been constructed, a tool called CoreGen uses a copy/move/merge process to arrange the model meshes into a core model. In this paper, we present the current state of tools and new features in RGG. We also discuss the parallel-enabled CoreGen, which in several cases achieves super-linear speedups since the problems fit in available RAM at higher processor counts. Several RGG applications - 1/6 VHTR model, 1/4 PWR reactor core, and a full-core model for Monju - are reported. (authors)

  18. Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology.

    Science.gov (United States)

    Judge, Kim; Hunt, Martin; Reuter, Sandra; Tracey, Alan; Quail, Michael A; Parkhill, Julian; Peacock, Sharon J

    2016-09-01

    Translating the Oxford Nanopore MinION sequencing technology into medical microbiology requires on-going analysis that keeps pace with technological improvements to the instrument and release of associated analysis software. Here, we use a multidrug-resistant Enterobacter kobei isolate as a model organism to compare open source software for the assembly of genome data, and relate this to the time taken to generate actionable information. Three software tools (PBcR, Canu and miniasm) were used to assemble MinION data and a fourth (SPAdes) was used to combine MinION and Illumina data to produce a hybrid assembly. All four had a similar number of contigs and were more contiguous than the assembly using Illumina data alone, with SPAdes producing a single chromosomal contig. Evaluation of the four assemblies to represent the genome structure revealed a single large inversion in the SPAdes assembly, which also incorrectly integrated a plasmid into the chromosomal contig. Almost 50 %, 80 % and 90 % of MinION pass reads were generated in the first 6, 9 and 12 h, respectively. Using data from the first 6 h alone led to a less accurate, fragmented assembly, but data from the first 9 or 12 h generated similar assemblies to that from 48 h sequencing. Assemblies were generated in 2 h using Canu, indicating that going from isolate to assembled data is possible in less than 48 h. MinION data identified that genes responsible for resistance were carried by two plasmids encoding resistance to carbapenem and to sulphonamides, rifampicin and aminoglycosides, respectively.

  19. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  20. Water box for steam generator

    International Nuclear Information System (INIS)

    Lecomte, Robert; Viaud, Michel.

    1975-01-01

    This invention relates to a water box for connecting an assembly composed of a vertical steam generator and a vertical pump to the vessel of the nuclear reactor, the assembly forming the primary cooling system of a pressurised water reactor. This invention makes it easy to dismantle the pump on the water box without significant loss of water in the primary cooling system of the reactor and particularly without it being necessary to drain the water contained in the steam generator beforehand. It makes it possible to shorten the time required for dismantling the primary pump in order to service or repair it and makes dismantling safer in that the dismantling does not involve draining the steam generator and therefore the critical storage of a large amount of cooling water that has been in contact with the fuel assemblies of the nuclear reactor core [fr

  1. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

    Directory of Open Access Journals (Sweden)

    Loren A Honaas

    Full Text Available Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1 proportion of reads mapping to an assembly 2 recovery of conserved, widely expressed genes, 3 N50 length statistics, and 4 the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation.

  2. A microwave powered sensor assembly for microwave ovens

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention relates to a microwave powered sensor assembly for micro- wave ovens. The microwave powered sensor assembly comprises a microwave antenna for generating an RF antenna signal in response to microwave radiation at a predetermined excitation frequency. A dc power supply circuit...... of the microwave powered sensor assembly is operatively coupled to the RF antenna signal for extracting energy from the RF antenna signal and produce a power supply voltage. A sensor is connected to the power supply voltage and configured to measure a physical or chemical property of a food item under heating...... in a microwave oven chamber....

  3. The sequence and de novo assembly of the giant panda genome

    Science.gov (United States)

    Li, Ruiqiang; Fan, Wei; Tian, Geng; Zhu, Hongmei; He, Lin; Cai, Jing; Huang, Quanfei; Cai, Qingle; Li, Bo; Bai, Yinqi; Zhang, Zhihe; Zhang, Yaping; Wang, Wen; Li, Jun; Wei, Fuwen; Li, Heng; Jian, Min; Li, Jianwen; Zhang, Zhaolei; Nielsen, Rasmus; Li, Dawei; Gu, Wanjun; Yang, Zhentao; Xuan, Zhaoling; Ryder, Oliver A.; Leung, Frederick Chi-Ching; Zhou, Yan; Cao, Jianjun; Sun, Xiao; Fu, Yonggui; Fang, Xiaodong; Guo, Xiaosen; Wang, Bo; Hou, Rong; Shen, Fujun; Mu, Bo; Ni, Peixiang; Lin, Runmao; Qian, Wubin; Wang, Guodong; Yu, Chang; Nie, Wenhui; Wang, Jinhuan; Wu, Zhigang; Liang, Huiqing; Min, Jiumeng; Wu, Qi; Cheng, Shifeng; Ruan, Jue; Wang, Mingwei; Shi, Zhongbin; Wen, Ming; Liu, Binghang; Ren, Xiaoli; Zheng, Huisong; Dong, Dong; Cook, Kathleen; Shan, Gao; Zhang, Hao; Kosiol, Carolin; Xie, Xueying; Lu, Zuhong; Zheng, Hancheng; Li, Yingrui; Steiner, Cynthia C.; Lam, Tommy Tsan-Yuk; Lin, Siyuan; Zhang, Qinghui; Li, Guoqing; Tian, Jing; Gong, Timing; Liu, Hongde; Zhang, Dejin; Fang, Lin; Ye, Chen; Zhang, Juanbin; Hu, Wenbo; Xu, Anlong; Ren, Yuanyuan; Zhang, Guojie; Bruford, Michael W.; Li, Qibin; Ma, Lijia; Guo, Yiran; An, Na; Hu, Yujie; Zheng, Yang; Shi, Yongyong; Li, Zhiqiang; Liu, Qing; Chen, Yanling; Zhao, Jing; Qu, Ning; Zhao, Shancen; Tian, Feng; Wang, Xiaoling; Wang, Haiyin; Xu, Lizhi; Liu, Xiao; Vinar, Tomas; Wang, Yajun; Lam, Tak-Wah; Yiu, Siu-Ming; Liu, Shiping; Zhang, Hemin; Li, Desheng; Huang, Yan; Wang, Xia; Yang, Guohua; Jiang, Zhi; Wang, Junyi; Qin, Nan; Li, Li; Li, Jingxiang; Bolund, Lars; Kristiansen, Karsten; Wong, Gane Ka-Shu; Olson, Maynard; Zhang, Xiuqing; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

    2013-01-01

    Using next-generation sequencing technology alone, we have successfully generated and assembled a draft sequence of the giant panda genome. The assembled contigs (2.25 gigabases (Gb)) cover approximately 94% of the whole genome, and the remaining gaps (0.05 Gb) seem to contain carnivore-specific repeats and tandem repeats. Comparisons with the dog and human showed that the panda genome has a lower divergence rate. The assessment of panda genes potentially underlying some of its unique traits indicated that its bamboo diet might be more dependent on its gut microbiome than its own genetic composition. We also identified more than 2.7 million heterozygous single nucleotide polymorphisms in the diploid genome. Our data and analyses provide a foundation for promoting mammalian genetic research, and demonstrate the feasibility for using next-generation sequencing technologies for accurate, cost-effective and rapid de novo assembly of large eukaryotic genomes. PMID:20010809

  4. Template Assembly for Detailed Urban Reconstruction

    KAUST Repository

    Nan, Liangliang

    2015-05-04

    We propose a new framework to reconstruct building details by automatically assembling 3D templates on coarse textured building models. In a preprocessing step, we generate an initial coarse model to approximate a point cloud computed using Structure from Motion and Multi View Stereo, and we model a set of 3D templates of facade details. Next, we optimize the initial coarse model to enforce consistency between geometry and appearance (texture images). Then, building details are reconstructed by assembling templates on the textured faces of the coarse model. The 3D templates are automatically chosen and located by our optimization-based template assembly algorithm that balances image matching and structural regularity. In the results, we demonstrate how our framework can enrich the details of coarse models using various data sets.

  5. DNAzyme-Based Logic Gate-Mediated DNA Self-Assembly.

    Science.gov (United States)

    Zhang, Cheng; Yang, Jing; Jiang, Shuoxing; Liu, Yan; Yan, Hao

    2016-01-13

    Controlling DNA self-assembly processes using rationally designed logic gates is a major goal of DNA-based nanotechnology and programming. Such controls could facilitate the hierarchical engineering of complex nanopatterns responding to various molecular triggers or inputs. Here, we demonstrate the use of a series of DNAzyme-based logic gates to control DNA tile self-assembly onto a prescribed DNA origami frame. Logic systems such as "YES," "OR," "AND," and "logic switch" are implemented based on DNAzyme-mediated tile recognition with the DNA origami frame. DNAzyme is designed to play two roles: (1) as an intermediate messenger to motivate downstream reactions and (2) as a final trigger to report fluorescent signals, enabling information relay between the DNA origami-framed tile assembly and fluorescent signaling. The results of this study demonstrate the plausibility of DNAzyme-mediated hierarchical self-assembly and provide new tools for generating dynamic and responsive self-assembly systems.

  6. Design of a mixed-oxide fuel assembly to be assessed as a lead test assembly in a BWR reactor

    International Nuclear Information System (INIS)

    Hernandez, H.; Alonso, G.

    2001-01-01

    The open and the close cycle are the two alternatives to pursue during power generation. The reprocessing is a mature process that now shows a more competitive economic aspect, making it more attractive than ever. Mexico has not decided what to do with the existing and future depleted fuel assemblies that will be generated from the power operation, thus the direct disposal and the reprocessing are still being considered. To have enough arguments in one or the other alternatives it is necessary to make an assessment of both. This investigation focus in the MOX fuel design assuming that the reprocessing is the option to follow and looking for the lowest impact in power generation. The first step in a reprocessing program is to analyze the performance of four lead test assemblies (LTA's), thus in this investigation we design the corresponding MOX to be used as LTA's and assess their performance through one operational cycle. (author)

  7. The United Nations General Assembly and Disarmament 1987

    International Nuclear Information System (INIS)

    1988-01-01

    The report offers a summary of the proposals made and action taken on disarmament issues by the Assembly at its forty-second regular session. It is published in the framework of the World Disarmament Campaign, which was launched by a unanimous decision of the Assembly in 1982 to inform, to educate and to generate public understanding and support for the objectives of the United Nations in the field of disarmament

  8. Self-supporting radioisotope generators with STC-55W Stirling converters

    International Nuclear Information System (INIS)

    Or, C.; Kumar, V.; Carpenter, R.; Schock, A.

    2000-01-01

    Previous Orbital Stirling generator designs rely on the spacecraft mounting structure to fasten the radiators, the converters, and the heat source assembly. This paper describes a self-supporting generator concept with a 1-piece honeycomb panel serving as a radiator and a rigid platform for the converters and the heat source assembly to be bolted on. This self-supporting generator allows for simpler mounting structure and more options on mounting location. Using this self-supporting generator concept, we derived four different design options to connect the converter pair rigidly to reduce vibration. This paper describes the four design options and their assembly procedure

  9. A novel design of beam shaping assembly to use D-T neutron generator for BNCT.

    Science.gov (United States)

    Kasesaz, Yaser; Karimi, Marjan

    2016-12-01

    In order to use 14.1MeV neutrons produced by d-T neutron generators, two special and novel Beam Shaping Assemblies (BSA), including multi-layer and hexagonal lattice have been suggested and the effect of them has been investigated by MCNP4C Monte Carlo code. The results show that the proposed BSA can provide the qualified epithermal neutron beam for BNCT. The final epithermal neutron flux is about 6e9 n/cm2.s. The final proposed BSA has some different advantages: 1) it consists of usual and well-known materials (Pb, Al, Fluental and Cd); 2) it has a simple geometry; 3) it does not need any additional gamma filter; 4) it can provide high flux of epithermal neutrons. As this type of neutron source is under development in the world, it seems that they can be used clinically in a hospital considering the proposed BSA. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Fluorescent Self-Assembled Polyphenylene Dendrimer Nanofibers

    NARCIS (Netherlands)

    Liu, Daojun; Feyter, Steven De; Cotlet, Mircea; Wiesler, Uwe-Martin; Weil, Tanja; Herrmann, Andreas; Müllen, Klaus; Schryver, Frans C. De

    2003-01-01

    A second-generation polyphenylene dendrimer 1 self-assembles into nanofibers on various substrates such as HOPG, silicon, glass, and mica from different solvents. The investigation with noncontact atomic force microscopy (NCAFM) and scanning electron microscopy (SEM) shows that the morphology of the

  11. Kid-Friendly Veggies and Fruits: 10 Tips for Making Healthy Food Choices More Fun for Children

    Science.gov (United States)

    ... Set up a pizza-making station in the kitchen. Use whole-wheat English muffins, bagels, or pita ... veggies or fruits into a fun shape or design. 5 fruity peanut butterfly Start with carrot sticks ...

  12. Assembly of viral genomes from metagenomes

    Directory of Open Access Journals (Sweden)

    Saskia L Smits

    2014-12-01

    Full Text Available Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes.

  13. Single molecule sequencing-guided scaffolding and correction of draft assemblies.

    Science.gov (United States)

    Zhu, Shenglong; Chen, Danny Z; Emrich, Scott J

    2017-12-06

    Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies. We propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm. Our experimental results show that our approach can improve the structural correctness of target assemblies in the cost of some contiguity, even with smaller amounts of long reads. In addition, our reassembling process can also serve as a competitive scaffolder relative to well-established assembly benchmarks.

  14. Preparation and self-assembly of amphiphilic polylysine dendrons

    DEFF Research Database (Denmark)

    Mirsharghi, Sahar; Knudsen, Kenneth D.; Bagherifam, Shahla

    2016-01-01

    Polylysine dendrons with lipid tails prepared by divergent solid-phase synthesis showed self-assembling properties in aqueous solutions., Herein, we present the synthesis of new amphiphilic polylysine dendrons with variable alkyl chain lengths (C1–C18) at the C-terminal. The dendrons were...... synthesized in moderate to quantitative yields by divergent solid-phase synthesis (SPS) employing an aldehyde linker. The self-assembling properties of the dendrons in aqueous solutions were studied by small angle neutron scattering (SANS) and dynamic light scattering (DLS). The self-assembling properties...... were influenced by the length of the alkyl chain and the generation number (Gn). Increasing the temperature and concentration did not have significant impact on the hydrodynamic diameter, but the self-assembling properties were influenced by the pH value. This demonstrated the need for positively...

  15. EXPERIMENTAL ANALYSES OF SPALLATION NEUTRONS GENERATED BY 100 MEV PROTONS AT THE KYOTO UNIVERSITY CRITICAL ASSEMBLY

    Directory of Open Access Journals (Sweden)

    CHEOL HO PYEON

    2013-02-01

    Full Text Available Neutron spectrum analyses of spallation neutrons are conducted in the accelerator-driven system (ADS facility at the Kyoto University Critical Assembly (KUCA. High-energy protons (100 MeV obtained from the fixed field alternating gradient accelerator are injected onto a tungsten target, whereby the spallation neutrons are generated. For neutronic characteristics of spallation neutrons, the reaction rates and the continuous energy distribution of spallation neutrons are measured by the foil activation method and by an organic liquid scintillator, respectively. Numerical calculations are executed by MCNPX with JENDL/HE-2007 and ENDF/B-VI libraries to evaluate the reaction rates of activation foils (bismuth and indium set at the target and the continuous energy distribution of spallation neutrons set in front of the target. For the reaction rates by the foil activation method, the C/E values between the experiments and the calculations are found around a relative difference of 10%, except for some reactions. For continuous energy distribution by the organic liquid scintillator, the spallation neutrons are observed up to 45 MeV. From these results, the neutron spectrum information on the spallation neutrons generated at the target are attained successfully in injecting 100 MeV protons onto the tungsten target.

  16. Dynamics of self-assembled cytosine nucleobases on graphene

    Science.gov (United States)

    Saikia, Nabanita; Johnson, Floyd; Waters, Kevin; Pandey, Ravindra

    2018-05-01

    Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.

  17. Patterning of self-assembled monolayers by phase-shifting mask and its applications in large-scale assembly of nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Fan; Zhang, Dakuan; Wang, Jianyu; Sheng, Yun; Wang, Xinran; Chen, Kunji; Zhou, Minmin [Key Laboratory of Advanced Photonic and Electronic Materials and School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Yan, Shancheng [Key Laboratory of Advanced Photonic and Electronic Materials and School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210046 (China); Shen, Jiancang; Pan, Lijia; Shi, Yi, E-mail: yshi@nju.edu.cn [Key Laboratory of Advanced Photonic and Electronic Materials and School of Electronic Science and Engineering, Nanjing University, Nanjing 210093 (China); Collaborative Innovation Center of Advanced Micro-structures, Nanjing University, Nanjing 210093 (China)

    2015-01-26

    A nonselective micropatterning method of self-assembled monolayers (SAMs) based on laser and phase-shifting mask (PSM) is demonstrated. Laser beam is spatially modulated by a PSM, and periodic SAM patterns are generated sequentially through thermal desorption. Patterned wettability is achieved with alternating hydrophilic/hydrophobic stripes on octadecyltrichlorosilane monolayers. The substrate is then used to assemble CdS semiconductor nanowires (NWs) from a solution, obtaining well-aligned NWs in one step. Our results show valuably the application potential of this technique in engineering SAMs for integration of functional devices.

  18. Wind turbine/generator set and method of making same

    Science.gov (United States)

    Bevington, Christopher M.; Bywaters, Garrett L.; Coleman, Clint C.; Costin, Daniel P.; Danforth, William L.; Lynch, Jonathan A.; Rolland, Robert H.

    2013-06-04

    A wind turbine comprising an electrical generator that includes a rotor assembly. A wind rotor that includes a wind rotor hub is directly coupled to the rotor assembly via a simplified connection. The wind rotor and generator rotor assembly are rotatably mounted on a central spindle via a bearing assembly. The wind rotor hub includes an opening having a diameter larger than the outside diameter of the central spindle adjacent the bearing assembly so as to allow access to the bearing assembly from a cavity inside the wind rotor hub. The spindle is attached to a turret supported by a tower. Each of the spindle, turret and tower has an interior cavity that permits personnel to traverse therethrough to the cavity of the wind rotor hub. The wind turbine further includes a frictional braking system for slowing, stopping or keeping stopped the rotation of the wind rotor and rotor assembly.

  19. Method of reducing multipole content in a conductor assembly during manufacture

    Science.gov (United States)

    Meinke, Rainer

    2013-08-20

    A method for manufacture of a conductor assembly. The assembly is of the type which, when conducting current, generates a magnetic field or in which, in the presence of a changing magnetic field, a voltage is induced. In an example embodiment one or more first coil rows are formed. The assembly has multiple coil rows about an axis with outer coil rows formed about inner coil rows. A determination is made of deviations from specifications associated with the formed one or more first coil rows. One or more deviations correspond to a magnitude of a multipole field component which departs from a field specification. Based on the deviations, one or more wiring patterns are generated for one or more second coil rows to be formed about the one or more first coil rows. The one or more second coil rows are formed in the assembly. The magnitude of each multipole field component that departs from the field specification is offset.

  20. Supracolloidal Architectures Self-Assembled in Microdroplets.

    Science.gov (United States)

    Xu, Xuejiao; Tian, Feng; Liu, Xin; Parker, Richard M; Lan, Yang; Wu, Yuchao; Yu, Ziyi; Scherman, Oren A; Abell, Chris

    2015-10-26

    We demonstrate a novel method for the formation of a library of structured colloidal assemblies by exploiting the supramolecular heteroternary host-guest interaction between cucurbit[8]uril (CB[8]) and methyl viologen- and naphthalene-functionalised particles. The approach is dependent upon compartmentalisation in microdroplets generated by a microfluidic platform. Though the distribution of colloidal particles encapsulated within each microdroplet followed a Poisson distribution, tuning the concentration of the initial colloidal particle suspensions provided some level of control over the structure of the formed colloidal assemblies. This ability to direct the assembly of complementarily-functionalised colloids through a supramolecular interaction, without the need for complex modification of the colloidal surface or external stimuli, presents an exciting new approach towards the design of structured colloidal materials with the potential to produce many challenging structures. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. An Improved Genome Assembly of Azadirachta indica A. Juss.

    Directory of Open Access Journals (Sweden)

    Neeraja M. Krishnan

    2016-07-01

    Full Text Available Neem (Azadirachta indica A. Juss., an evergreen tree of the Meliaceae family, is known for its medicinal, cosmetic, pesticidal and insecticidal properties. We had previously sequenced and published the draft genome of a neem plant, using mainly short read sequencing data. In this report, we present an improved genome assembly generated using additional short reads from Illumina and long reads from Pacific Biosciences SMRT sequencer. We assembled short reads and error-corrected long reads using Platanus, an assembler designed to perform well for heterozygous genomes. The updated genome assembly (v2.0 yielded 3- and 3.5-fold increase in N50 and N75, respectively; 2.6-fold decrease in the total number of scaffolds; 1.25-fold increase in the number of valid transcriptome alignments; 13.4-fold less misassembly and 1.85-fold increase in the percentage repeat, over the earlier assembly (v1.0. The current assembly also maps better to the genes known to be involved in the terpenoid biosynthesis pathway. Together, the data represent an improved assembly of the A. indica genome.

  2. A Framework for Geometric Reasoning About Human Figures and Factors in Assembly Processes

    Energy Technology Data Exchange (ETDEWEB)

    Calton, Terri L.

    1999-07-20

    Automatic assembly sequencing and visualization tools are valuable in determining the best assembly sequences, but without Human Factors and Figure Models (HFFMs) it is difficult to evaluate or visualize human interaction. In industry, accelerating technological advances and shorter market windows have forced companies to turn to an agile manufacturing paradigm. This trend has promoted computerized automation of product design and manufacturing processes, such as automated assembly planning. However, all automated assembly planning software tools assume that the individual components fly into their assembled configuration and generate what appear to be perfectly valid operations, but in reality some operations cannot physically be carried out by a human. For example, the use of a ratchet may be reasoned feasible for an assembly operation; however, when a hand is placed on the tool the operation is no longer feasible, perhaps because of inaccessibility, insufficient strength or human interference with assembly components. Similarly, human figure modeling algorithms may indicate that assembly operations are not feasible and consequently force design modifications, however, if they had the capability to quickly generate alternative assembly sequences, they might have identified a feasible solution. To solve this problem, HFFMs must be integrated with automated assembly planning which allows engineers to quickly verify that assembly operations are possible and to see ways to make the designs even better. This paper presents a framework for integrating geometry-based assembly planning algorithms with commercially available human figure modeling software packages. Experimental results to selected applications along with lessons learned are presented.

  3. Impact Analysis for Fuel Assemblies in Spent Fuel Storage Rack

    International Nuclear Information System (INIS)

    Oh, Jinho

    2013-01-01

    The design and structural integrity evaluation of a spent fuel storage rack (SFSR) utilized for storing and protecting the spent fuel assemblies generated during the operation of a reactor are very important in terms of nuclear safety and waste management. The objective of this study is to show the validity of the SFSR design as well as fuel assembly through a structural integrity evaluation based on a numerical analysis. In particular, a dynamic time history analysis considering the gaps between the fuel assemblies and the walls of the storage cell pipes in the SFSR was performed to check the structural integrity of the fuel assembly and storage cell pipe

  4. Impact Analysis for Fuel Assemblies in Spent Fuel Storage Rack

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jinho [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-07-01

    The design and structural integrity evaluation of a spent fuel storage rack (SFSR) utilized for storing and protecting the spent fuel assemblies generated during the operation of a reactor are very important in terms of nuclear safety and waste management. The objective of this study is to show the validity of the SFSR design as well as fuel assembly through a structural integrity evaluation based on a numerical analysis. In particular, a dynamic time history analysis considering the gaps between the fuel assemblies and the walls of the storage cell pipes in the SFSR was performed to check the structural integrity of the fuel assembly and storage cell pipe.

  5. Nuclear fuel assembly with improved spectral shift-producing rods

    International Nuclear Information System (INIS)

    Ferrari, H.M.

    1987-01-01

    This patent describes a nuclear reactor having fuel assemblies and a moderator-coolant liquid flowing through the fuel assemblies, each fuel assembly including an organized array of nuclear fuel rods wherein the moderator-coolant liquid flows along the fuel rods, at least one improved spectral shift-producing rod disposed among the fuel rods. The spectra shift-producing rod consists of: (a) an elongated hollow hermetically-sealed tubular member; (b) a weakened region formed in a portion of the member, the portion being subject to rupture at a given level of internal pressure; and (c) burnable poison material contained in the member which generates gas in the member as operation of the reactor proceeds normally, the material being soluble in the moderator-coolant liquid when brought into contact therewith; (d) the given level of internal pressure being less than the maximum level of internal pressure normally expected to be generated within the member by the poison material by normal operation of the reactor

  6. Self-assembly strategies for the synthesis of functional nanostructured materials

    Science.gov (United States)

    Perego, M.; Seguini, G.

    2016-06-01

    Self-assembly is the autonomous organization of components into patterns or structures without human intervention. This is the approach followed by nature to generate living cells and represents one of the practical strategies to fabricate ensembles of nanostructures. In static self-assembly the formation of ordered structures could require energy but once formed the structures are stable. The introduction of additional regular features in the environment could be used to template the self-assembly guiding the organization of the components and determining the final structure they form. In this regard self-assembly of block copolymers represents a potent platform for fundamental studies at the nanoscale and for application-driven investigation as a tool to fabricate functional nanostructured materials. Block copolymers can hierarchically assemble into chemically distinct domains with size and periodicity on the order of 10nm or below, offering a potentially inexpensive route to generate large-area nanostructured materials. The final structure characteristics of these materials are dictated by the properties of the elementary block copolymers, like chain length, volume fraction or degree of block incompatibility. Modern synthetic chemistry offers the possibility to design these macromolecules with very specific length scales and geometries, directly embodying in the block copolymers the code that drives their self- assembling process. The understanding of the kinetics and thermodynamics of the block copolymer self-assembly process in the bulk phase as well as in thin films represents a fundamental prerequisite toward the exploitation of these materials. Incorporating block copolymer into device fabrication procedures or directly into devices, as active elements, will lead to the development of a new generation of devices fabricated using the fundamental law of nature to our advantage in order to minimize cost and power consumption in the fabrication process

  7. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 8 AND 9 CRYSTAL RIVER UNIT 3

    International Nuclear Information System (INIS)

    Wilson, Michael L.

    2001-01-01

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 8 and 9 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for Commercial Reactor Critical (CRC) evaluations to support the development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies

  8. Opto-electronic devices with nanoparticles and their assemblies

    Science.gov (United States)

    Nguyen, Chieu Van

    Nanotechnology is a fast growing field; engineering matters at the nano-meter scale. A key nanomaterial is nanoparticles (NPs). These sub-wavelength (background noise. The second device is based on a one-dimensional (1-D) self-directed self-assembly of Au NPs mediated by dielectric materials. Depending on the coverage density of the Au NPs assembly deposited on the device, electronic emission was observed at ultra-low bias of 40V, leading to low-power plasma generation in air at atmospheric pressure. Light emitted from the plasma is apparent to the naked eyes. Similarly, 1-D self-assembly of Au NPs mediated by iron oxide was fabricated and exhibits ferro-magnetic behavior. The multi-functional 1-D self-assembly of Au NPs has great potential in modern electronics such as solid state lighting, plasma-based nanoelectronics, and memory devices.

  9. Quality Assessment of Domesticated Animal Genome Assemblies

    DEFF Research Database (Denmark)

    Seemann, Stefan E; Anthon, Christian; Palasca, Oana

    2015-01-01

    affected by the lack of genomic sequence. Herein, we quantify the quality of the genome assemblies of 20 domesticated animals and related species by assessing a range of measurable parameters, and we show that there is a positive correlation between the fraction of mappable reads from RNAseq data...... domesticated animal genomes still need to be sequenced deeper in order to produce high-quality assemblies. In the meanwhile, ironically, the extent to which RNAseq and other next-generation data is produced frequently far exceeds that of the genomic sequence. Furthermore, basic comparative analysis is often...

  10. Analysis of reconfigurable assembly system framing systems in automotive industry

    Directory of Open Access Journals (Sweden)

    Md Zain Mohamad Zamri

    2017-01-01

    Full Text Available Current trend in automotive industry shows increasing demand for multiple models with lean production. Prior to that, automotive manufacturing systems evolved from mass production to flexible automation. Material handling systems and equipment in a single assembly line with multiple models require high investment but with low throughput thus making production cost relatively high. Current assembly process of side structure and undercarriage with downtime occurrence during assembly process affecting production performance (quality, cost and delivery. Manufacturing facilities should allow more flexibility and increase intelligence evolving toward novel reconfigurable assembly systems (RAS. RAS is envisaged capable of increasing factor flexibility and responsiveness by incorporating assembly jig, robot and framing, which could be next generation of world class automotive assembly systems. This project research proposes a new methodology of framework reconfigurable assembly systems principles in automotive framing systems i.e. enhance assembly process between side structure assembly and undercarriage assembly which a new RAS is capable to reconfigure the assembly processes of multiple model on a single assembly line. Simulation software (Witness will be used to simulate and validate current and proposed assembly process. RAS is expected to be a solution for rapid change in structure and for a responsively adjustable production capacity. Quality, cost and delivery are production key parameters that can be achieved by implementing RAS.

  11. FAITH – Fast Assembly Inhibitor Test for HIV

    Energy Technology Data Exchange (ETDEWEB)

    Hadravová, Romana [Institute of Organic Chemistry and Biochemistry IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague (Czech Republic); Rumlová, Michaela, E-mail: michaela.rumlova@vscht.cz [Institute of Organic Chemistry and Biochemistry IOCB Research Centre & Gilead Sciences, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague (Czech Republic); Department of Biotechnology, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague (Czech Republic); Ruml, Tomáš, E-mail: tomas.ruml@vscht.cz [Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Technická 3, 166 28 Prague (Czech Republic)

    2015-12-15

    Due to the high number of drug-resistant HIV-1 mutants generated by highly active antiretroviral therapy (HAART), there is continuing demand for new types of inhibitors. Both the assembly of the Gag polyprotein into immature and mature HIV-1 particles are attractive candidates for the blocking of the retroviral life cycle. Currently, no therapeutically-used assembly inhibitor is available. One possible explanation is the lack of a reliable and simple assembly inhibitor screening method. To identify compounds potentially inhibiting the formation of both types of HIV-1 particles, we developed a new fluorescent high-throughput screening assay. This assay is based on the quantification of the assembly efficiency in vitro in a 96-well plate format. The key components of the assay are HIV-1 Gag-derived proteins and a dual-labelled oligonucleotide, which emits fluorescence only when the assembly of retroviral particles is inhibited. The method was validated using three (CAI, BM2, PF74) reported assembly inhibitors. - Highlights: • Allows screening of assembly inhibitors of both mature and immature HIV-1 particles. • Based on Gag-derived proteins with CA in mature or immature conformation. • Simple and sensitive method suitable for high-throughput screening of inhibitors. • Unlike in other HIV assembly methods, works under physiological conditions. • No washing steps are necessary.

  12. FAITH – Fast Assembly Inhibitor Test for HIV

    International Nuclear Information System (INIS)

    Hadravová, Romana; Rumlová, Michaela; Ruml, Tomáš

    2015-01-01

    Due to the high number of drug-resistant HIV-1 mutants generated by highly active antiretroviral therapy (HAART), there is continuing demand for new types of inhibitors. Both the assembly of the Gag polyprotein into immature and mature HIV-1 particles are attractive candidates for the blocking of the retroviral life cycle. Currently, no therapeutically-used assembly inhibitor is available. One possible explanation is the lack of a reliable and simple assembly inhibitor screening method. To identify compounds potentially inhibiting the formation of both types of HIV-1 particles, we developed a new fluorescent high-throughput screening assay. This assay is based on the quantification of the assembly efficiency in vitro in a 96-well plate format. The key components of the assay are HIV-1 Gag-derived proteins and a dual-labelled oligonucleotide, which emits fluorescence only when the assembly of retroviral particles is inhibited. The method was validated using three (CAI, BM2, PF74) reported assembly inhibitors. - Highlights: • Allows screening of assembly inhibitors of both mature and immature HIV-1 particles. • Based on Gag-derived proteins with CA in mature or immature conformation. • Simple and sensitive method suitable for high-throughput screening of inhibitors. • Unlike in other HIV assembly methods, works under physiological conditions. • No washing steps are necessary.

  13. Prodrugs as self-assembled hydrogels: a new paradigm for biomaterials.

    Science.gov (United States)

    Vemula, Praveen Kumar; Wiradharma, Nikken; Ankrum, James A; Miranda, Oscar R; John, George; Karp, Jeffrey M

    2013-12-01

    Prodrug-based self-assembled hydrogels represent a new class of active biomaterials that can be harnessed for medical applications, in particular the design of stimuli responsive drug delivery devices. In this approach, a promoiety is chemically conjugated to a known-drug to generate an amphiphilic prodrug that is capable of forming self-assembled hydrogels. Prodrug-based self-assembled hydrogels are advantageous as they alter the solubility of the drug, enhance drug loading, and eliminate the use of harmful excipients. In addition, self-assembled prodrug hydrogels can be designed to undergo controlled drug release or tailored degradation in response to biological cues. Herein we review the development of prodrug-based self-assembled hydrogels as an emerging class of biomaterials that overcome several common limitations encountered in conventional drug delivery. Published by Elsevier Ltd.

  14. Fuel management inside the reactor. Project AZ-101 (ININ). Report of the generation of the nuclear bank 'L1PG3826' of the assemblies GE5 and GE9B 'collapsed' of the CNLV for the FCS-II program of the FMS system

    International Nuclear Information System (INIS)

    Alonso V, G.; Torres A, C.

    1991-06-01

    In order to be able to carry out studies but next to the operation of the reactor of the CNLV with the program FCS-II of the package of codes for the fuel management FMS, it was generated a 'collapsed' nuclear bank integrating the generated information with RECORD of each one of those assemblies of the initial load and of the first recharge. To generate the bank, the different ones RECORD 'cells' that compose each assemble were 'collapsed' to an alone one, representing this, to the one complete assemble in what refers to the fuel bars distribution and enrichments. The one collapsed of each assemble it is made averaging the content of UO 2 and Gd 2 O 3 in each fuel bar by the volumetric fraction occupied by each axial section of the fuel bar where the content of UO 2 and Gd 2 O 3 were constant, by this way the x-y fuel bars arrangement is conserved but a representative fuel cell of all the assemble is obtained. Of the five different assemblies that will be load in the reactor of the CNLV (3 of the initial load and 2 of the first recharge), only 4 were collapsed; the remaining one to be totally formed by natural uranium it was not necessary to collapse. From the collapsing process new enrichment values in U-235 and in content of Gd 2 O 3 for each fuel bar, for what according to the generation procedure of nuclear information it was generated the required information by RECORD for each fuel bar with Gd 2 O 3 with the ECLIPSE code. Once generated this information it was proceeded to generate the homogenized nuclear information, with RECORD, for the whole cell. According to the requirements of nuclear information of FCS-II, the nuclear Information generated with RECORD only was of the defined type as series 1 in the procedure of generation of nuclear banks '6F3/1/CN029/90/P1'; that which means that only it was generated nuclear information as function of the burnup of the fuel and of the vacuum in the fuel cell. Although the nuclear bank was generated (identified as 'L1

  15. Diabetes - when you are sick

    Science.gov (United States)

    ... check your urine ketones every time you urinate. Eat small meals often. Even if you are not eating as ... When you have an upset stomach, try to eat small meals. Try carbohydrates, such as: Bagels or bread Cooked ...

  16. Advanced fuel assemblies for economic and flexible operation of light water reactors

    International Nuclear Information System (INIS)

    Urban, P.; Bender, D.

    2001-01-01

    Increasing competition in the electricity market sets up a corresponding competition between the different electricity producing technologies. This makes further improvements in the economics of nuclear power generation a vital item for the future of nuclear energy. Though the costs for development, design and fabrication of fuel assemblies contribute only about 10% to the fuel cycle costs, the design and the performance of the fuel assemblies considerably influences total electricity generation cost. By the recent creation of Framatome ANP the nuclear activities of Framatome and Siemens were combined into one company. In the past, both had made considerable achievements in the development of fuel assemblies and related services supporting the goal of safe and economic electricity generation by light water reactors. The examples described in this paper cover former Siemens products and experience. In the future, our combined experience bases will be an ideal platform to offer further substantial improvements to our customers. (author)

  17. Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

    Directory of Open Access Journals (Sweden)

    Nobuyuki Uchikoga

    Full Text Available Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

  18. Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

    Science.gov (United States)

    Uchikoga, Nobuyuki; Matsuzaki, Yuri; Ohue, Masahito; Hirokawa, Takatsugu; Akiyama, Yutaka

    2013-01-01

    Interaction profile method is a useful method for processing rigid-body docking. After the docking process, the resulting set of docking poses could be classified by calculating similarities among them using these interaction profiles to search for near-native poses. However, there are some cases where the near-native poses are not included in this set of docking poses even when the bound-state structures are used. Therefore, we have developed a method for generating near-native docking poses by introducing a re-docking process. We devised a method for calculating the profile of interaction fingerprints by assembling protein complexes after determining certain core-protein complexes. For our analysis, we used 44 bound-state protein complexes selected from the ZDOCK benchmark dataset ver. 2.0, including some protein pairs none of which generated near-native poses in the docking process. Consequently, after the re-docking process we obtained profiles of interaction fingerprints, some of which yielded near-native poses. The re-docking process involved searching for possible docking poses in a restricted area using the profile of interaction fingerprints. If the profile includes interactions identical to those in the native complex, we obtained near-native docking poses. Accordingly, near-native poses were obtained for all bound-state protein complexes examined here. Application of interaction fingerprints to the re-docking process yielded structures with more native interactions, even when a docking pose, obtained following the initial docking process, contained only a small number of native amino acid interactions. Thus, utilization of the profile of interaction fingerprints in the re-docking process yielded more near-native poses.

  19. Redesigning assembly stations using ergonomic methods as a lean tool.

    Science.gov (United States)

    Eswaramoorthi, M; John, Mervyn; Rajagopal, C Arjun; Prasad, P S S; Mohanram, P V

    2010-01-01

    With the current state of the global economy, demand for various products plummeting. To sustain in the market, companies have to reduce cost and improve quality. Today, companies have started implementing new philosophies like TQM, TPM, six sigma and lean manufacturing techniques to remain competitive in the market. Lean manufacturing is an emerging philosophy which continuously strives to reduce waste. The main objective of analyzing the assembly line with a lean perspective is to identify the areas related to human interface with other systems that could lead to the generation of waste. Improper workplace design leads to unreasonable mental or physical burden and results in waste generation like slow work (delay and inventory), and defects, which is named as muri waste. An attempt has been made in this paper to locate muri waste and create a "Lean assembly line". The proposed method, based on the use of Rapid Upper Limb Assessment (RULA) with CATIA V5 platform, has allowed the measurement of a large set of operator posture parameters and assessment of ergonomic stresses. Based on the results, the process stations in the assembly line were redesigned to prevent the generation of waste.

  20. Development of a water boil-off spent-fuel calorimeter system. [To measure decay heat generation rate

    Energy Technology Data Exchange (ETDEWEB)

    Creer, J.M.; Shupe, J.W. Jr.

    1981-05-01

    A calorimeter system was developed to measure decay heat generation rates of unmodified spent fuel assemblies from commercial nuclear reactors. The system was designed, fabricated, and successfully tested using the following specifications: capacity of one BWR or PWR spent fuel assembly; decay heat generation range 0.1 to 2.5 kW; measurement time of < 12 h; and an accuracy of +-10% or better. The system was acceptance tested using a dc reference heater to simulate spent fuel assembly heat generation rates. Results of these tests indicated that the system could be used to measure heat generation rates between 0.5 and 2.5 kW within +- 5%. Measurements of heat generation rates of approx. 0.1 kW were obtained within +- 15%. The calorimeter system has the potential to permit measurements of heat generation rates of spent fuel assemblies and other devices in the 12- to 14-kW range. Results of calorimetry of a Turkey Point spent fuel assembly indicated that the assembly was generating approx. 1.55 kW.

  1. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 4 AND 5 OF CRYSTAL RIVER UNIT 3

    International Nuclear Information System (INIS)

    Wright, Kenneth D.

    1997-01-01

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 4 and 5 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for commercial Reactor Critical (CRC) evaluations to support the development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies

  2. Mobile assemblies of Bennett linkages from four-crease origami patterns

    Science.gov (United States)

    Zhang, Xiao; Chen, Yan

    2018-02-01

    This paper deals with constructing mobile assemblies of Bennett linkages inspired by four-crease origami patterns. A transition technique has been proposed by taking the thick-panel form of an origami pattern as an intermediate bridge. A zero-thickness rigid origami pattern and its thick-panel form share the same sector angles and folding behaviours, while the thick-panel origami and the mobile assembly of linkages are kinematically equivalent with differences only in link profiles. Applying this transition technique to typical four-crease origami patterns, we have found that the Miura-ori and graded Miura-ori patterns lead to assemblies of Bennett linkages with identical link lengths. The supplementary-type origami patterns with different mountain-valley crease assignments correspond to different types of Bennett linkage assemblies with negative link lengths. And the identical linkage-type origami pattern generates a new mobile assembly. Hence, the transition technique offers a novel approach to constructing mobile assemblies of spatial linkages from origami patterns.

  3. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.

    Science.gov (United States)

    Schneider, Valerie A; Graves-Lindsay, Tina; Howe, Kerstin; Bouk, Nathan; Chen, Hsiu-Chuan; Kitts, Paul A; Murphy, Terence D; Pruitt, Kim D; Thibaud-Nissen, Françoise; Albracht, Derek; Fulton, Robert S; Kremitzki, Milinn; Magrini, Vincent; Markovic, Chris; McGrath, Sean; Steinberg, Karyn Meltz; Auger, Kate; Chow, William; Collins, Joanna; Harden, Glenn; Hubbard, Timothy; Pelan, Sarah; Simpson, Jared T; Threadgold, Glen; Torrance, James; Wood, Jonathan M; Clarke, Laura; Koren, Sergey; Boitano, Matthew; Peluso, Paul; Li, Heng; Chin, Chen-Shan; Phillippy, Adam M; Durbin, Richard; Wilson, Richard K; Flicek, Paul; Eichler, Evan E; Church, Deanna M

    2017-05-01

    The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing assembly update since 2009; it reflects the resolution of roughly 1000 issues and encompasses modifications ranging from thousands of single base changes to megabase-scale path reorganizations, gap closures, and localization of previously orphaned sequences. We developed a new approach to sequence generation for targeted base updates and used data from new genome mapping technologies and single haplotype resources to identify and resolve larger assembly issues. For the first time, the reference assembly contains sequence-based representations for the centromeres. We also expanded the number of alternate loci to create a reference that provides a more robust representation of human population variation. We demonstrate that the updates render the reference an improved annotation substrate, alter read alignments in unchanged regions, and impact variant interpretation at clinically relevant loci. We additionally evaluated a collection of new de novo long-read haploid assemblies and conclude that although the new assemblies compare favorably to the reference with respect to continuity, error rate, and gene completeness, the reference still provides the best representation for complex genomic regions and coding sequences. We assert that the collected updates in GRCh38 make the newer assembly a more robust substrate for comprehensive analyses that will promote our understanding of human biology and advance our efforts to improve health. © 2017 Schneider et al.; Published by Cold Spring Harbor Laboratory Press.

  4. Shaft seal assembly for high speed and high pressure applications

    Science.gov (United States)

    Hadt, W. F.; Ludwig, L. P. (Inventor)

    1979-01-01

    A seal assembly is provided for reducing the escape of fluids from between a housing and a shaft rotably mounted in the housing. The seal assembly comprises a pair of seal rings resiliently connected to each other and disposed in side-by-side relationship. In each seal ring, both the internal bore surface and the radial face which faces away from the other seal ring are provided with a plurality of equi-spaced recesses. The seal faces referred to are located adjacent a seating surface of the housing. Under normal operating conditions, the seal assembly is stationary with respect to the housing, and the recesses generate life, keep the assembly spaced from the rotating shaft and allow slip therebetween. The seal assembly can seize on the shaft, and slip will then occur between the radial faces and the housing.

  5. Low Phosphorus Diet: Best for Kidney Disease?

    Science.gov (United States)

    ... cereal, rice and pasta White bread, crackers, cereals, rice and pasta Quick breads, biscuits, cornbread, muffins, pancakes or waffles White dinner rolls, bread, bagels or English muffins Dried peas (split, black-eyed), beans (black, garbanzo, lima, kidney, navy, pinto) ...

  6. Evaluation of efficiency of axial profiling in WWER-440 fuel assemblies

    International Nuclear Information System (INIS)

    Ananjev, Yu. A.; Kurakin, K. Yu.; Artemov, V.G.; Ivanov, A.S.

    2005-01-01

    The present report deals with consideration of fuel enrichment axial profiling in WWER-440 assemblies. The study is performed on improving the effectiveness of fuel utilization using the example of implementing the axial profiling in the assemblies of the second generation. For simulation of fuel loadings the computer code package SAPFIR 9 5 and RC is used that allows for correct consideration of specific features of assemblies design changes. The methodical approach to assessment of effectiveness of implementing the axial profiling is considered with the use of capabilities of the mentioned code package. In conclusion the recommendations are given on using the fuel enrichment axial profiling in WWER-440 assemblies (Authors)

  7. Assembly of the epithelial Na+ channel evaluated using sucrose gradient sedimentation analysis.

    Science.gov (United States)

    Cheng, C; Prince, L S; Snyder, P M; Welsh, M J

    1998-08-28

    Three subunits, alpha, beta, and gamma, contribute to the formation of the epithelial Na+ channel. To investigate the oligomeric assembly of the channel complex, we used sucrose gradient sedimentation analysis to determine the sedimentation properties of individual subunits and heteromultimers comprised of multiple subunits. When the alpha subunit was expressed alone, it first formed an oligomeric complex with a sedimentation coefficient of 11 S, and then generated a higher order multimer of 25 S. In contrast, individual beta and gamma subunits predominately assembled into 11 S complexes. We obtained similar results with expression in cells and in vitro. When we co-expressed beta with alpha or with alpha plus gamma, the beta subunit assembled into a 25 S complex. Glycosylation of the alpha subunit was not required for assembly into a 25 S complex. We found that the alpha subunit formed intra-chain disulfide bonds. Although such bonds were not required to generate an oligomeric complex, under nonreducing conditions the alpha subunit formed a complex that migrated more homogeneously at 25 S. This suggests that intra-chain disulfide bonds may stabilize the complex. These data suggest that the epithelial Na+ channel subunits form high order oligomeric complexes and that the alpha subunit contains the information that facilitates such formation. Interestingly, the ability of the alpha, but not the beta or gamma, subunit to assemble into a 25 S homomeric complex correlates with the ability of these subunits to generate functional channels when expressed alone.

  8. Gas recombination assembly for electrochemical cells

    Science.gov (United States)

    Levy, Isaac; Charkey, Allen

    1989-01-01

    An assembly for recombining gases generated in electrochemical cells wherein a catalyst strip is enveloped within a hydrophobic, gas-porous film which, in turn, is encased between gas-porous, metallic layers. The sandwich construction of metallic layers and film is formed into a spiral with a tab for connection to the cell.

  9. Temperature rise of the mask-resist assembly during LIGA exposure

    International Nuclear Information System (INIS)

    Ting, Aili

    2004-01-01

    Deep X-ray lithography on PMMA resist is used in the LIGA process. The resist is exposed to synchrotron X-rays through a patterned mask and then is developed in a liquid developer to make high aspect ratio microstructures. The limitations in dimensional accuracies of the LIGA generated microstructure originate from many sources, including synchrotron and X-ray physics, thermal and mechanical properties of mask and resist, and from the kinetics of the developer. This work addresses the thermal analysis and temperature rise of the mask-resist assembly during exposure in air at the Advanced Light Source (ALS) synchrotron. The concern is that dimensional errors generated at the mask and the resist due to thermal expansion will lower the accuracy of the lithography. We have developed a three-dimensional finite-element model of the mask and resist assembly that includes a mask with absorber, a resist with substrate, three metal holders, and a water-cooling block. We employed the LIGA exposure-development software LEX-D to calculate volumetric heat sources generated in the assembly by X-ray absorption and the commercial software ABAQUS to calculate heat transfer including thermal conduction inside the assembly, natural and forced convection, and thermal radiation. at assembly outer and/or inner surfaces. The calculations of assembly maximum temperature. have been compared with temperature measurements conducted at ALS. In some of these experiments, additional cooling of the assembly was produced by forced nitrogen flow ('nitrogen jets') directed at the mask surface. The temperature rise in the silicon mask and the mask holder comes directly from the X-ray absorption, but nitrogen jets carry away a significant portion of heat energy from the mask surface, while natural convection carries away negligibly small amounts energy from the holder. The temperature rise in PMMA resist is mainly from heat conducted from the silicon substrate backward to the resist and from the inner

  10. Self-assembly strategies for the synthesis of functional nanostructured materials

    International Nuclear Information System (INIS)

    Perego, M.; Seguini, G.

    2016-01-01

    Self-assembly is the autonomous organization of components into patterns or structures without human intervention. This is the approach followed by nature to generate living cells and represents one of the practical strategies to fabricate ensembles of nanostructures. In static self-assembly the formation of ordered structures could require energy but once formed the structures are stable. The introduction of additional regular features in the environment could be used to template the self-assembly guiding the organization of the components and determining the final structure they form. In this regard self-assembly of block copolymers represents a potent platform for fundamental studies at the nanoscale and for application-driven investigation as a tool to fabricate functional nanostructured materials. Block copolymers can hierarchically assemble into chemically distinct domains with size and periodicity on the order of 10 nm or below, offering a potentially inexpensive route to generate large-area nanostructured materials. The final structure characteristics of these materials are dictated by the properties of the elementary block copolymers, like chain length, volume fraction or degree of block incompatibility. Modern synthetic chemistry offers the possibility to design these macromolecules with very specific length scales and geometries, directly embodying in the block copolymers the code that drives their self- assembling process. The understanding of the kinetics and thermodynamics of the block copolymer selfassembly process in the bulk phase as well as in thin films represents a fundamental prerequisite toward the exploitation of these materials. Incorporating block copolymer into device fabrication procedures or directly into devices, as active elements, will lead to the development of a new generation of devices fabricated using the fundamental law of nature to our advantage in order to minimize cost and power consumption in the fabrication process

  11. Verification of FA2D Prediction Capability Using Fuel Assembly Benchmark

    International Nuclear Information System (INIS)

    Jecmenica, R.; Pevec, D.; Grgic, D.; Konjarek, D.

    2008-01-01

    FA2D is 2D transport collision probability code developed at Faculty of Electrical Engineering and Computing, University Zagreb. It is used for calculation of cross section data at fuel assembly level. Main objective of its development was capability to generate cross section data to be used for fuel management and safety analyses of PWR reactors. Till now formal verification of code predictions capability is not performed at fuel assembly level, but results of fuel management calculations obtained using FA2D generated cross sections for NPP Krsko and IRIS reactor are compared against Westinghouse calculations. Cross section data were used within NRC's PARCS code and satisfactory preliminary results were obtained. This paper presents results of calculations performed for Nuclear Fuel Industries, Ltd., benchmark using FA2D, and SCALE5 TRITON calculation sequence (based on discrete ordinates code NEWT). Nuclear Fuel Industries, Ltd., Japan, released LWR Next Generation Fuels Benchmark with the aim to verify prediction capability in nuclear design for extended burnup regions. We performed calculations for two different Benchmark problem geometries - UO 2 pin cell and UO 2 PWR fuel assembly. The results obtained with two mentioned 2D spectral codes are presented for burnup dependency of infinite multiplication factor, isotopic concentration of important materials and for local peaking factor vs. burnup (in case of fuel assembly calculation).(author)

  12. A new building block for DNA network formation by self-assembly and polymerase chain reaction.

    Science.gov (United States)

    Bußkamp, Holger; Keller, Sascha; Robotta, Marta; Drescher, Malte; Marx, Andreas

    2014-01-01

    The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.

  13. Chitosan Based Self-Assembled Nanoparticles in Drug Delivery

    Directory of Open Access Journals (Sweden)

    Javier Pérez Quiñones

    2018-02-01

    Full Text Available Chitosan is a cationic polysaccharide that is usually obtained by alkaline deacetylation of chitin poly(N-acetylglucosamine. It is biocompatible, biodegradable, mucoadhesive, and non-toxic. These excellent biological properties make chitosan a good candidate for a platform in developing drug delivery systems having improved biodistribution, increased specificity and sensitivity, and reduced pharmacological toxicity. In particular, chitosan nanoparticles are found to be appropriate for non-invasive routes of drug administration: oral, nasal, pulmonary and ocular routes. These applications are facilitated by the absorption-enhancing effect of chitosan. Many procedures for obtaining chitosan nanoparticles have been proposed. Particularly, the introduction of hydrophobic moieties into chitosan molecules by grafting to generate a hydrophobic-hydrophilic balance promoting self-assembly is a current and appealing approach. The grafting agent can be a hydrophobic moiety forming micelles that can entrap lipophilic drugs or it can be the drug itself. Another suitable way to generate self-assembled chitosan nanoparticles is through the formation of polyelectrolyte complexes with polyanions. This paper reviews the main approaches for preparing chitosan nanoparticles by self-assembly through both procedures, and illustrates the state of the art of their application in drug delivery.

  14. Electrostatic Self-Assembly of Polysaccharides into Nanofibers

    DEFF Research Database (Denmark)

    Mendes, Ana Carina Loureiro; Strohmenger, Timm; Goycoolea, Francisco

    2017-01-01

    In this study, the anionic polysaccharide Xanthan gum (X) was mixed with positively charged Chitosan oligomers (ChO), and used as building blocks, to generate novel nanofibers by electrostatic self-assembly in aqueous conditions. Different concentrations, ionic strength and order of mixing of both...

  15. Guide to Eating for Sports

    Medline Plus

    Full Text Available ... ultimately affects performance. Good sources of carbohydrates include fruits, vegetables, and grains. Choose whole grains (such as brown ... have a light snack such as low-fiber fruits or vegetables (like plums, melons, cherries, carrots), crackers, a bagel, ...

  16. DNA-directed self-assembly of gold nanoparticles into binary and ternary nanostructures

    International Nuclear Information System (INIS)

    Yao Hui; Yi Changqing; Tzang Chihung; Zhu Junjie; Yang Mengsu

    2007-01-01

    The assembly and characterization of gold nanoparticle-based binary and ternary structures are reported. Two strategies were used to assemble gold nanoparticles into ordered nanoscale architectures: in strategy 1, gold nanoparticles were functionalized with single-strand DNA (ssDNA) first, and then hybridized with complementary ssDNA-labelled nanoparticles to assemble designed architectures. In strategy 2, the designed architectures were constructed through hybridization between complementary ssDNA first, then by assembling gold nanoparticles to the scaffolding through gold-sulfur bonds. Both TEM measurements and agarose gel electrophoresis confirmed that the latter strategy is more efficient in generating the designed nanostructures

  17. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 4 AND 5 OF CRYSTAL RIVER UNIT 3

    Energy Technology Data Exchange (ETDEWEB)

    Kenneth D. Wright

    1997-07-30

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 4 and 5 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for commercial Reactor Critical (CRC) evaluations to support the development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies.

  18. Device Assembly Facility (DAF) Glovebox Radioactive Waste Characterization

    International Nuclear Information System (INIS)

    Dominick, J L

    2001-01-01

    The Device Assembly Facility (DAF) at the Nevada Test Site (NTS) provides programmatic support to the Joint Actinide Shock Physics Experimental Research (JASPER) Facility in the form of target assembly. The target assembly activities are performed in a glovebox at DAF and include Special Nuclear Material (SNM). Currently, only activities with transuranic SNM are anticipated. Preliminary discussions with facility personnel indicate that primarily two distributions of SNM will be used: Weapons Grade Plutonium (WG-Pu), and Pu-238 enhanced WG-Pu. Nominal radionuclide distributions for the two material types are included in attachment 1. Wastes generated inside glove boxes is expected to be Transuranic (TRU) Waste which will eventually be disposed of at the Waste Isolation Pilot Plant (WIPP). Wastes generated in the Radioactive Material Area (RMA), outside of the glove box is presumed to be low level waste (LLW) which is destined for disposal at the NTS. The process knowledge quantification methods identified herein may be applied to waste generated anywhere within or around the DAF and possibly JASPER as long as the fundamental waste stream boundaries are adhered to as outlined below. The method is suitable for quantification of waste which can be directly surveyed with the Blue Alpha meter or swiped. An additional quantification methodology which requires the use of a high resolution gamma spectroscopy unit is also included and relies on the predetermined radionuclide distribution and utilizes scaling to measured nuclides for quantification

  19. Ultrasonic Examination of Jet Pump Diffuser Assemblies

    International Nuclear Information System (INIS)

    Hacker, M.; Levesque, M.; Whitman, G.

    1998-01-01

    In October 1997 the Boiling Water REactor Vessel and Internals Project (BWRVIP) issued the BWR Jet Pump Assembly Inspection and Flaw Evaluation Guidelines (BWRVIP-41). This document identified several welds on the jet pump diffuser assembly that are susceptible to Intergranular Stress Corrosion Cracking (IGSCC) or fatigue, and whose failure could result in jet pump disassembly. Based on the potential for failures, the document recommends inspection of 50% of the high priority welds at the next refueling outage for each BWR, with 100% expansion if flaws are identified. Because each diffuser assembly contains as many as six high priority welds, and access to these welds from the annulus is very restricted, implementing these recommendations can have a significant impact on outage critical path. In an effort to minimize the impact of implementing these recommendations, Framatome Technologies, Inc (FTI) developed a method to perform ultrasonic examinations of the jet pump diffuser assembly welds utilizing remotely operated equipment from the inner diameter (ID) of the diffuser assembly. This paper will discuss the tooling, ultrasonic methods, and delivery techniques used to perform the examinations, as well as the results obtained from a spring 1998 deployment of the system at a U.S. Nuclear Generating Plant. (Author)

  20. Plantagora: modeling whole genome sequencing and assembly of plant genomes.

    Directory of Open Access Journals (Sweden)

    Roger Barthelson

    Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

  1. CRC DEPLETION CALCULATIONS FOR THE NON-RODDED ASSEMBLIES IN BATCHES 1, 2, AND 3 OF CRYSTAL RIVER UNIT 3

    International Nuclear Information System (INIS)

    Wright, Kenneth D.

    1997-01-01

    The purpose of this design analysis is to document the SAS2H depletion calculations of certain non-rodded fuel assemblies from batches 1, 2, and 3 of the Crystal River Unit 3 pressurized water reactor (PWR) that are required for Commercial Reactor Critical (CRC) evaluations to support development of the disposal criticality methodology. A non-rodded assembly is one which never contains a control rod assembly (CRA) or an axial power shaping rod assembly (APSRA) during its irradiation history. The objective of this analysis is to provide SAS2H generated isotopic compositions for each fuel assembly's depleted fuel and depleted burnable poison materials. These SAS2H generated isotopic compositions are acceptable for use in CRC benchmark reactivity calculations containing the various fuel assemblies

  2. Self assembled temperature responsive surfaces for generation of cell patches for bone tissue engineering

    International Nuclear Information System (INIS)

    Valmikinathan, Chandra M; ChangWei; Xu Jiahua; Yu Xiaojun

    2012-01-01

    One of the major challenges in the fabrication of tissue engineered scaffolds is the ability of the scaffold to biologically mimic autograft-like tissues. One of the alternate approaches to achieve this is by the application of cell seeded scaffolds with optimal porosity and mechanical properties. However, the current approaches for seeding cells on scaffolds are not optimal in terms of seeding efficiencies, cell penetration into the scaffold and more importantly uniform distribution of cells on the scaffold. Also, recent developments in scaffold geometries to enhance surface areas, pore sizes and porosities tend to further complicate the scenario. Cell sheet-based approaches for cell seeding have demonstrated a successful approach to generate scaffold-free tissue engineering approaches. However, the method of generating the temperature responsive surface is quite challenging and requires carcinogenic reagents and gamma rays. Therefore, here, we have developed temperature responsive substrates by layer-by-layer self assembly of smart polymers. Multilayer thin films prepared from tannic acid and poly N-isopropylacrylamide were fabricated based on their electrostatic and hydrogen bonding interactions. Cell attachment and proliferation studies on these thin films showed uniform cell attachment on the substrate, matching tissue culture plates. Also, the cells could be harvested as cell patches and sheets from the scaffolds, by reducing the temperature for a short period of time, and seeded onto porous scaffolds for tissue engineering applications. An enhanced cell seeding efficiency on scaffolds was observed using the cell patch-based technique as compared to seeding cells in suspension. Owing to the already pre-existent cell–cell and cell–extracellular matrix interactions, the cell patch showed the ability to reattach rapidly onto scaffolds and showed enhanced ability to proliferate and differentiate into a bone-like matrix. (paper)

  3. Assaying Used Nuclear Fuel Assemblies Using Lead Slowing-Down Spectroscopy and Singular Value Decomposition

    International Nuclear Information System (INIS)

    Kulisek, Jonathan A.; Anderson, Kevin K.; Casella, Andrew M.; Gesh, Christopher J.; Warren, Glen A.

    2013-01-01

    This study investigates the use of a Lead Slowing-Down Spectrometer (LSDS) for the direct and independent measurement of fissile isotopes in light-water nuclear reactor fuel assemblies. The current study applies MCNPX, a Monte Carlo radiation transport code, to simulate the measurement of the assay of the used nuclear fuel assemblies in the LSDS. An empirical model has been developed based on the calibration of the LSDS to responses generated from the simulated assay of six well-characterized fuel assemblies. The effects of self-shielding are taken into account by using empirical basis vectors calculated from the singular value decomposition (SVD) of a matrix containing the self-shielding functions from the assay of assemblies in the calibration set. The performance of the empirical algorithm was tested on version 1 of the Next-Generation Safeguards Initiative (NGSI) used fuel library consisting of 64 assemblies, as well as a set of 27 diversion assemblies, both of which were developed by Los Alamos National Laboratory. The potential for direct and independent assay of the sum of the masses of Pu-239 and Pu-241 to within 2%, on average, has been demonstrated

  4. Comparison of de novo assembly statistics of Cucumis sativus L.

    Science.gov (United States)

    Wojcieszek, Michał; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

    2017-08-01

    Genome sequencing is the core of genomic research. With the development of NGS and lowering the cost of procedure there is another tight gap - genome assembly. Developing the proper tool for this task is essential as quality of genome has important impact on further research. Here we present comparison of several de Bruijn assemblers tested on C. sativus genomic reads. The assessment shows that newly developed software - dnaasm provides better results in terms of quantity and quality. The number of generated sequences is lower by 5 - 33% with even two fold higher N50. Quality check showed reliable results were generated by dnaasm. This provides us with very strong base for future genomic analysis.

  5. De novo assembly of highly diverse viral populations

    Directory of Open Access Journals (Sweden)

    Yang Xiao

    2012-09-01

    Full Text Available Abstract Background Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. Results We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/ viral-genomics-analysis-software. Conclusions We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research.

  6. DOWNHOLE POWER GENERATION AND WIRELESS COMMUNICATIONS FOR INTELLIGENT COMPLETIONS APPLICATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Paul Tubel

    2003-10-14

    The fourth quarter of the project was dedicated to the manufacturing of the mechanical system for wireless communications and the power generation module and inspection pre assembly of the mechanical components. Another emphasis for the quarter was the development of filter control and signal detection software. The tasks accomplished during this report period were: (1) Dimensional issues were resolved and revised drawings for manufacturing of the wireless communications gauge and power generator were completed and sent to a machine shop for manufacturing. (2) Finalized the requirements and fittings and connections for testing the tool in the Halliburton flow loop. (3) The new acoustic generator was manufactured successfully and it was delivered during this quarter. The assembly will be outsourced for plastic coating in preparation for hostile environment use. (4) The acoustic two-way communications development continued to progress. The real time firmware for the surface system was developed and the processor was able to detect and process the data frame transmitted from downhole. The analog section of the tool was also developed and it is being tested for filtering capabilities and signal detection and amplification. (5) The new transformer to drive the acoustic generator assembly was manufactured and was successfully tested. Spring mandrel design showed increased acoustic output on the pipe and was implemented. (6) PCBA board carrier with board set was tested for function and fit and is 100% complete. (7) Filter control software is complete and software to allow modification of communication parameters dynamically is 50% complete. (8) All mechanical parts to assemble the wireless gauge and power generator have been received and verified to be within specification. (9) Acoustic generator has been assembled in the tool mandrel and tested successfully. (10) The circuit required to harvest the power generated downhole has been designed and the power generator

  7. Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

    Science.gov (United States)

    Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

    2017-01-01

    This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called "digital materials." We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

  8. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  9. The mathematics of virus shell assembly. Progress report 1995--1996

    Energy Technology Data Exchange (ETDEWEB)

    Berger, B.

    1996-08-01

    This research focuses on applying computational and mathematical techniques to problems in biology, and more specifically to problems in protein folding. Significant progress has been made in the following areas relating to virus shell assembly: the local rules theory has been further developed; development has begun on a second-generation simulator which provides a more physically realistic model of assembly, collaborative efforts have continued with an experimental biologist to verify and inspire the local rules theory; an investigation has been initiated into the mechanics of virus shell assembly; laboratory experiments have been conducted on bacteriophage T4 which verify that the previously believed structure for the core may be incorrect.

  10. Nanomaterial processing using self-assembly-bottom-up chemical and biological approaches

    International Nuclear Information System (INIS)

    Thiruvengadathan, Rajagopalan; Gangopadhyay, Keshab; Gangopadhyay, Shubhra; Korampally, Venumadhav; Ghosh, Arkasubhra; Chanda, Nripen

    2013-01-01

    Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle–polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly. (review article)

  11. Self-Assembled Polyelectrolyte Nanoparticles as Fluorophore-Free Contrast Agents for Multicolor Optical Imaging

    Directory of Open Access Journals (Sweden)

    Da Hye Shin

    2015-03-01

    Full Text Available In this work, we describe the fabrication of self-assembled polyelectrolyte nanoparticles that provide a multicolor optical imaging modality. Poly(γ-glutamic acid(γ-PGA formed self-assembled nanoparticles through electrostatic interactions with two different cationic polymers: poly(L-lysine(PLL and chitosan. The self-assembled γ-PGA/PLL and γ-PGA/chitosan nanoparticles were crosslinked by glutaraldehyde. Crosslinking of the ionic self-assembled nanoparticles with glutaraldehyde not only stabilized the nanoparticles but also generated a strong autofluorescence signal. Fluorescent Schiff base bonds (C=N and double bonds (C=C were generated simultaneously by crosslinking of the amine moiety of the cationic polyelectrolytes with monomeric glutaraldehyde or with polymeric glutaraldehyde. The unique optical properties of the nanoparticles that resulted from the crosslinking by glutaraldehyde were analyzed using UV/Vis and fluorescence spectroscopy. We observed that the fluorescence intensity of the nanoparticles could be regulated by adjusting the crosslinker concentration and the reaction time. The nanoparticles also exhibited high performance in the labeling and monitoring of therapeutic immune cells (macrophages and dendritic cells. These self-assembled nanoparticles are expected to be a promising multicolor optical imaging contrast agent for the labeling, detection, and monitoring of cells.

  12. Single Day Construction of Multigene Circuits with 3G Assembly.

    Science.gov (United States)

    Halleran, Andrew D; Swaminathan, Anandh; Murray, Richard M

    2018-05-18

    The ability to rapidly design, build, and test prototypes is of key importance to every engineering discipline. DNA assembly often serves as a rate limiting step of the prototyping cycle for synthetic biology. Recently developed DNA assembly methods such as isothermal assembly and type IIS restriction enzyme systems take different approaches to accelerate DNA construction. We introduce a hybrid method, Golden Gate-Gibson (3G), that takes advantage of modular part libraries introduced by type IIS restriction enzyme systems and isothermal assembly's ability to build large DNA constructs in single pot reactions. Our method is highly efficient and rapid, facilitating construction of entire multigene circuits in a single day. Additionally, 3G allows generation of variant libraries enabling efficient screening of different possible circuit constructions. We characterize the efficiency and accuracy of 3G assembly for various construct sizes, and demonstrate 3G by characterizing variants of an inducible cell-lysis circuit.

  13. De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

    Science.gov (United States)

    Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

    2015-09-21

    Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

  14. Tailoring luminescence color conversion via affinitive co-assembly of glutamates appended with pyrene and naphthalene dicarboximide units.

    Science.gov (United States)

    Xing, Pengyao; Zhao, Zhuo; Hao, Aiyou; Zhao, Yanli

    2016-01-21

    Structural matching of two organic building blocks bearing glutamate units and different luminophores assembled into unilamellar nanovesicles in aqueous media through a co-assembly process. Aggregation-induced energy transfer took place in the co-assembled system, leading to controllable generation of multiple luminescence colors including white light.

  15. Bacteriophage Assembly

    Directory of Open Access Journals (Sweden)

    Anastasia A. Aksyuk

    2011-02-01

    Full Text Available Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.

  16. The Automated Assembly Team contributions to the APRIMED Agile Manufacturing Project

    International Nuclear Information System (INIS)

    Jones, R.E.; Ames, A.L.; Calton, T.L.

    1995-06-01

    The Automated Assembly Team of the APRIMED Project (abbreviated as A') consists of two parts: the Archimedes Project, which is an ongoing project developing automated assembly technology, and the A' Robot Team. Archimedes is a second generation assembly planning system that both provides a general high-level assembly sequencing capability and, for a smaller class of products, facilitates automatic programming of a robotic workcell to assemble them. The A' robot team designed, developed, and implemented a flexible robot workcell which served as the automated factory of the A' project. In this document we briefly describe the role of automated assembly planning in agile manufacturing, and specifically describe the contributions of the Archimedes project and the A' robot team to the A' project. We introduce the concepts of the Archimedes automated assembly planning project, and discuss the enhancements to Archimedes which were developed in response to the needs of the A' project. We also present the work of the A' robot team in designing and developing the A' robot workcell, including all tooling and programming to support assembly of the A' discriminator devices. Finally, we discuss the process changes which these technologies have enabled in the A' project

  17. Removable bearing arrangement for a wind turbine generator

    Science.gov (United States)

    Bagepalli, Bharat Sampathkumaran; Jansen, Patrick Lee; Gadre, Aniruddha Dattatraya

    2010-06-15

    A wind generator having removable change-out bearings includes a rotor and a stator, locking bolts configured to lock the rotor and stator, a removable bearing sub-assembly having at least one shrunk-on bearing installed, and removable mounting bolts configured to engage the bearing sub-assembly and to allow the removable bearing sub-assembly to be removed when the removable mounting bolts are removed.

  18. Combinatorial Models for Assembly and Decomposition of Products

    Directory of Open Access Journals (Sweden)

    A. N. Bojko

    2015-01-01

    Full Text Available The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the entry of parts into the assembly unit. The asymmetric part is a partial order. It specifies part- ordering time in in the course of the assembly process. The structure of preferences is a minimal description of the restrictions and constraints in the assembly process. It can serve as a source for generating multiple assembly sequences of a product and its components, which are allowed by design. This multiplicity increases the likelihood of rational choice under uncertainty, unpredictable changes in the properties of technological or industrial systems.Incomplete dominance relation gives grounds for further examination and better understanding of the project situation. Operation field of the study is limited to a set of disparate elements of the partial order. Different strategies for processing the disparate elements may be offered, e.g. selection of the most informative pairs, comparison of which foremost linearizes the original partial order.

  19. Controlled short-linkage assembly of functional nano-objects

    Energy Technology Data Exchange (ETDEWEB)

    Chaudhary, Shilpi; Kamra, Tripta [Division of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund (Sweden); ENI AB, Malmö (Sweden); Division of Synchrotron Radiation Research, Lund University, Box 118, 221 00 Lund (Sweden); Uddin, Khan Mohammad Ahsan [Division of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund (Sweden); Snezhkova, Olesia [Division of Synchrotron Radiation Research, Lund University, Box 118, 221 00 Lund (Sweden); Jayawardena, H. Surangi N. [Department of Chemistry, University of Massachusetts Lowell, 1 University Ave., Lowell, MA 01854 (United States); Yan, Mingdi [Department of Chemistry, University of Massachusetts Lowell, 1 University Ave., Lowell, MA 01854 (United States); Department of Chemistry, KTH – Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm (Sweden); Montelius, Lars [ENI AB, Malmö (Sweden); Schnadt, Joachim, E-mail: joachim.schnadt@sljus.lu.se [Division of Synchrotron Radiation Research, Lund University, Box 118, 221 00 Lund (Sweden); Ye, Lei, E-mail: lei.ye@tbiokem.lth.se [Division of Pure and Applied Biochemistry, Lund University, Box 124, 221 00 Lund (Sweden)

    2014-05-01

    Graphical abstract: - Highlights: • Fast photoconjugation of nanoparticles on surface. • Non-destructive feature guarantees intact function of nanoparticles. • Direct contact between nano-objects allows efficient photon and electron transfer. • Possibility of generating patterned nanoparticle assemblies on surface. • Open new opportunities for assembling chemical sensors. - Abstract: In this work, we report a method that allows the deterministic, photo-controlled covalent assembly of nanoparticles directly on surface. As a model system, we study the conjugation of molecularly imprinted polymer (MIP) nanoparticles on a glass surface and confirm that the immobilized nanoparticles maintain their molecular recognition functionality. The glass slide was first modified with perfluorophenylazide and then used to bind MIP nanoparticles under UV irradiation. After each step the surface was analyzed by water contact angle measurement, fluorescence microscopy, scanning electron microscopy, and/or synchrotron-based X-ray photoelectron spectroscopy. The MIP nanoparticles immobilized on the glass surface remained stable and maintained specific binding for the template molecule, propranolol. The method developed in this work allows MIP nanoparticles to be directly coupled to a flat surface, offering a straightforward means to construct robust chemical sensors. Using the reported photo conjugation method, it is possible to generate patterned assembly of nanoparticles using a photomask. Since perfluorophenylazide-based photochemistry works with all kinds of organic material, the method developed in this work is expected to enable immobilization of not only MIPs but also other kinds of organic and inorganic–organic core–shell particles for various applications involving photon or electron transfer.

  20. Controlled short-linkage assembly of functional nano-objects

    International Nuclear Information System (INIS)

    Chaudhary, Shilpi; Kamra, Tripta; Uddin, Khan Mohammad Ahsan; Snezhkova, Olesia; Jayawardena, H. Surangi N.; Yan, Mingdi; Montelius, Lars; Schnadt, Joachim; Ye, Lei

    2014-01-01

    Graphical abstract: - Highlights: • Fast photoconjugation of nanoparticles on surface. • Non-destructive feature guarantees intact function of nanoparticles. • Direct contact between nano-objects allows efficient photon and electron transfer. • Possibility of generating patterned nanoparticle assemblies on surface. • Open new opportunities for assembling chemical sensors. - Abstract: In this work, we report a method that allows the deterministic, photo-controlled covalent assembly of nanoparticles directly on surface. As a model system, we study the conjugation of molecularly imprinted polymer (MIP) nanoparticles on a glass surface and confirm that the immobilized nanoparticles maintain their molecular recognition functionality. The glass slide was first modified with perfluorophenylazide and then used to bind MIP nanoparticles under UV irradiation. After each step the surface was analyzed by water contact angle measurement, fluorescence microscopy, scanning electron microscopy, and/or synchrotron-based X-ray photoelectron spectroscopy. The MIP nanoparticles immobilized on the glass surface remained stable and maintained specific binding for the template molecule, propranolol. The method developed in this work allows MIP nanoparticles to be directly coupled to a flat surface, offering a straightforward means to construct robust chemical sensors. Using the reported photo conjugation method, it is possible to generate patterned assembly of nanoparticles using a photomask. Since perfluorophenylazide-based photochemistry works with all kinds of organic material, the method developed in this work is expected to enable immobilization of not only MIPs but also other kinds of organic and inorganic–organic core–shell particles for various applications involving photon or electron transfer

  1. Automated and model-based assembly of an anamorphic telescope

    Science.gov (United States)

    Holters, Martin; Dirks, Sebastian; Stollenwerk, Jochen; Loosen, Peter

    2018-02-01

    Since the first usage of optical glasses there has been an increasing demand for optical systems which are highly customized for a wide field of applications. To meet the challenge of the production of so many unique systems, the development of new techniques and approaches has risen in importance. However, the assembly of precision optical systems with lot sizes of one up to a few tens of systems is still dominated by manual labor. In contrast, highly adaptive and model-based approaches may offer a solution for manufacturing with a high degree of automation and high throughput while maintaining high precision. In this work a model-based automated assembly approach based on ray-tracing is presented. This process runs autonomously, and accounts for a wide range of functionality. It firstly identifies the sequence for an optimized assembly and secondly, generates and matches intermediate figures of merit to predict the overall optical functionality of the optical system. This process also takes into account the generation of a digital twin of the optical system, by mapping key-performance-indicators like the first and the second momentum of intensity into the optical model. This approach is verified by the automatic assembly of an anamorphic telescope within an assembly cell. By continuous measuring and mapping the key-performance-indicators into the optical model, the quality of the digital twin is determined. Moreover, by measuring the optical quality and geometrical parameters of the telescope, the precision of this approach is determined. Finally, the productivity of the process is evaluated by monitoring the speed of the different steps of the process.

  2. Solving Vertex Cover Problem Using DNA Tile Assembly Model

    Directory of Open Access Journals (Sweden)

    Zhihua Chen

    2013-01-01

    Full Text Available DNA tile assembly models are a class of mathematically distributed and parallel biocomputing models in DNA tiles. In previous works, tile assembly models have been proved be Turing-universal; that is, the system can do what Turing machine can do. In this paper, we use tile systems to solve computational hard problem. Mathematically, we construct three tile subsystems, which can be combined together to solve vertex cover problem. As a result, each of the proposed tile subsystems consists of Θ(1 types of tiles, and the assembly process is executed in a parallel way (like DNA’s biological function in cells; thus the systems can generate the solution of the problem in linear time with respect to the size of the graph.

  3. Electrodynamic tailoring of self-assembled three-dimensional electrospun constructs

    Science.gov (United States)

    Reis, Tiago C.; Correia, Ilídio J.; Aguiar-Ricardo, Ana

    2013-07-01

    The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive electrostatic forces between the positively charged aerial fibers and the already collected ones, which tend to acquire a negatively charged network oriented towards the nozzle. The in situ polarization degree is strengthened by higher amounts of clustered fibers, and therefore the initial high density fibrous regions are the preliminary motifs for the self-assembly mechanism. As such regions increase their in situ polarization electrostatic repulsive forces will appear, favoring a competitive growth of these self-assembled fibrous clusters. Highly polarized regions will evidence higher distances between consecutive micro-assembled fibers (MAFs). Different processing parameters - deposition time, electric field intensity, concentration of polymer solution, environmental temperature and relative humidity - were evaluated in an attempt to control material's design.The rational design of three-dimensional electrospun constructs (3DECs) can lead to striking topographies and tailored shapes of electrospun materials. This new generation of materials is suppressing some of the current limitations of the usual 2D non-woven electrospun fiber mats, such as small pore sizes or only flat shaped constructs. Herein, we pursued an explanation for the self-assembly of 3DECs based on electrodynamic simulations and experimental validation. We concluded that the self-assembly process is driven by the establishment of attractive

  4. Metrology for ITER Assembly

    International Nuclear Information System (INIS)

    Bogusch, E.

    2006-01-01

    The overall dimensions of the ITER Tokamak and the particular assembly sequence preclude the use of conventional optical metrology, mechanical jigs and traditional dimensional control equipment, as used for the assembly of smaller, previous generation, fusion devices. This paper describes the state of the art of the capabilities of available metrology systems, with reference to the previous experience in Fusion engineering and in other industries. Two complementary procedures of transferring datum from the primary datum network on the bioshield to the secondary datum s inside the VV with the desired accuracy of about 0.1 mm is described, one method using the access directly through the ports and the other using transfer techniques, developed during the co-operation with ITER/EFDA. Another important task described is the development of a method for the rapid and easy measurement of the gaps between sectors, required for the production of the customised splice plates between them. The scope of the paper includes the evaluation of the composition and cost of the systems and team of technical staff required to meet the requirements of the assembly procedure. The results from a practical, full-scale demonstration of the methodologies used, using the proposed equipment, is described. This work has demonstrated the feasibility of achieving the necessary accuracies for the successful building of ITER. (author)

  5. Development of ORIGEN libraries for mixed oxide (MOX) fuel assembly designs

    International Nuclear Information System (INIS)

    Mertyurek, Ugur; Gauld, Ian C.

    2016-01-01

    Highlights: • ORIGEN MOX library generation process is described. • SCALE burnup calculations are validated against measured MOX fuel samples from the MALIBU program. • ORIGEN MOX libraries are verified using the OECD Phase IV-B benchmark. • There is good agreement for calculated-to-measured isotopic distributions. - Abstract: ORIGEN cross section libraries for reactor-grade mixed oxide (MOX) fuel assembly designs have been developed to provide fast and accurate depletion calculations to predict nuclide inventories, radiation sources and thermal decay heat information needed in safety evaluations and safeguards verification measurements of spent nuclear fuel. These ORIGEN libraries are generated using two-dimensional lattice physics assembly models that include enrichment zoning and cross section data based on ENDF/B-VII.0 evaluations. Using the SCALE depletion sequence, burnup-dependent cross sections are created for selected commercial reactor assembly designs and a representative range of reactor operating conditions, fuel enrichments, and fuel burnup. The burnup dependent cross sections are then interpolated to provide problem-dependent cross sections for ORIGEN, avoiding the need for time-consuming lattice physics calculations. The ORIGEN libraries for MOX assembly designs are validated against destructive radiochemical assay measurements of MOX fuel from the MALIBU international experimental program. This program included measurements of MOX fuel from a 15 × 15 pressurized water reactor assembly and a 9 × 9 boiling water reactor assembly. The ORIGEN MOX libraries are also compared against detailed assembly calculations from the Phase IV-B numerical MOX fuel burnup credit benchmark coordinated by the Nuclear Energy Agency within the Organization for Economic Cooperation and Development. The nuclide compositions calculated by ORIGEN using the MOX libraries are shown to be in good agreement with other physics codes and with experimental data.

  6. Optimizing Transcriptome Assemblies for Eleusine indica Leaf and Seedling by Combining Multiple Assemblies from Three De Novo Assemblers

    Directory of Open Access Journals (Sweden)

    Shu Chen

    2015-03-01

    Full Text Available Due to rapid advances in sequencing technology, increasing amounts of genomic and transcriptomic data are available for plant species, presenting enormous challenges for biocomputing analysis. A crucial first step for a successful transcriptomics-based study is the building of a high-quality assembly. Here, we utilized three different de novo assemblers (Trinity, Velvet, and CLC and the EvidentialGene pipeline tr2aacds to assemble two optimized transcript sets for the notorious weed species, . Two RNA sequencing (RNA-seq datasets from leaf and aboveground seedlings were processed using three assemblers, which resulted in 20 assemblies for each dataset. The contig numbers and N50 values of each assembly were compared to study the effect of read number, k-mer size, and in silico normalization on assembly output. The 20 assemblies were then processed through the tr2aacds pipeline to remove redundant transcripts and to select the transcript set with the best coding potential. Each assembly contributed a considerable proportion to the final transcript combination with the exception of the CLC-k14. Thus each assembler and parameter set did assemble better contigs for certain transcripts. The redundancy, total contig number, N50, fully assembled contig number, and transcripts related to target-site herbicide resistance were evaluated for the EvidentialGene and Trinity assemblies. Comparing the EvidentialGene set with the Trinity assembly revealed improved quality and reduced redundancy in both leaf and seedling EvidentialGene sets. The optimized transcriptome references will be useful for studying herbicide resistance in and the evolutionary process in the three allotetraploid offspring.

  7. Blockages in LMFBR fuel assemblies: a review

    International Nuclear Information System (INIS)

    Han, J.T.; Fontana, M.H.

    1977-01-01

    Experimental and analytical investigations performed in the United States, Germany, Great Britain, and Japan on the effects of partial flow blockages in liquid-metal fast breeder reactor fuel assemblies are reviewed and the results presented. Generalized models are developed from experimental data obtained for blockages of various sizes, shapes, and porosity, with and without pins, utilizing water and sodium as the coolant. Generally, the recirculating flow in the wake behind a blockage is a relatively effective heat transfer mechanism. Experiments where sodium boiling was made to occur behind the blockages indicate that boiling is stable for the configurations tested; these results are predicted by analytical models. Blockages at the inlet of fuel assemblies tend to have insignificant effects in the fuel assembly unless flow is reduced grossly and therefore would be detectable. Blockages in the heat generating zone have to be quite large to cause sodium boiling under normal reactor operating conditions

  8. Blockages in LMFBR fuel assemblies: a review

    Energy Technology Data Exchange (ETDEWEB)

    Han, J T; Fontana, M H

    1977-01-01

    Experimental and analytical investigations performed in the United States, Germany, Great Britain, and Japan on the effects of partial flow blockages in liquid-metal fast breeder reactor fuel assemblies are reviewed and the results presented. Generalized models are developed from experimental data obtained for blockages of various sizes, shapes, and porosity, with and without pins, utilizing water and sodium as the coolant. Generally, the recirculating flow in the wake behind a blockage is a relatively effective heat transfer mechanism. Experiments where sodium boiling was made to occur behind the blockages indicate that boiling is stable for the configurations tested; these results are predicted by analytical models. Blockages at the inlet of fuel assemblies tend to have insignificant effects in the fuel assembly unless flow is reduced grossly and therefore would be detectable. Blockages in the heat generating zone have to be quite large to cause sodium boiling under normal reactor operating conditions.

  9. Genomes correction and assembling: present methods and tools

    Science.gov (United States)

    Wojcieszek, Michał; Pawełkowicz, Magdalena; Nowak, Robert; Przybecki, Zbigniew

    2014-11-01

    Recent rapid development of next generation sequencing (NGS) technologies provided significant impact into genomics field of study enabling implementation of many de novo sequencing projects of new species which was previously confined by technological costs. Along with advancement of NGS there was need for adjustment in assembly programs. New algorithms must cope with massive amounts of data computation in reasonable time limits and processing power and hardware is also an important factor. In this paper, we address the issue of assembly pipeline for de novo genome assembly provided by programs presently available for scientist both as commercial and as open - source software. The implementation of four different approaches - Greedy, Overlap - Layout - Consensus (OLC), De Bruijn and Integrated resulting in variation of performance is the main focus of our discussion with additional insight into issue of short and long reads correction.

  10. Assembly of cells and vesicles for organ engineering

    International Nuclear Information System (INIS)

    Taguchi, Tetsushi

    2011-01-01

    The development of materials and technologies for the assembly of cells and/or vesicles is a key for the next generation of tissue engineering. Since the introduction of the tissue engineering concept in 1993, various types of scaffolds have been developed for the regeneration of connective tissues in vitro and in vivo. Cartilage, bone and skin have been successfully regenerated in vitro, and these regenerated tissues have been applied clinically. However, organs such as the liver and pancreas constitute numerous cell types, contain small amounts of extracellular matrix, and are highly vascularized. Therefore, organ engineering will require the assembly of cells and/or vesicles. In particular, adhesion between cells/vesicles will be required for regeneration of organs in vitro. This review introduces and discusses the key technologies and materials for the assembly of cells/vesicles for organ regeneration. (topical review)

  11. Coordination in the Decentralized Assembly System with Dual Supply Modes

    Directory of Open Access Journals (Sweden)

    Xu Guan

    2013-01-01

    Full Text Available This paper investigates a decentralized assembly system that consists of one assembler and two independent suppliers; wherein one supplier is perfectly reliable for the production, while the other generates yield uncertainty. Facing the random market demand, the assembler has to order the components from one supplier in advance and meanwhile requires the other supplier to deliver the components under VMI mode. We construct a Nash game between the supplier and the assembler so as to derive their equilibrium procurement/production strategies. The results show that the channel’s performance is highly undermined by the decentralization between players and also the combination of two supply modes. Compared to the centralized system, we propose an advance payment contract to perfectly coordinate the supply chain performance. The numerical examples indicate some management implications on the supply mode comparison and sensitivity analysis.

  12. Self-assembly of silver nanoparticles and bacteriophage

    Directory of Open Access Journals (Sweden)

    Santi Scibilia

    2016-03-01

    Full Text Available Biohybrid nanostructured materials, composed of both inorganic nanoparticles and biomolecules, offer prospects for many new applications in extremely diverse fields such as chemistry, physics, engineering, medicine and nanobiotechnology. In the recent years, Phage display technique has been extensively used to generate phage clones displaying surface peptides with functionality towards organic materials. Screening and selection of phage displayed material binding peptides has attracted great interest because of their use for development of hybrid materials with multiple functionalities. Here, we present a self-assembly approach for the construction of hybrid nanostructured networks consisting of M13 P9b phage clone, specific for Pseudomonas aeruginosa, selected by Phage display technology, directly assembled with silver nanoparticles (AgNPs, previously prepared by pulsed laser ablation. These networks are characterized by UV–vis optical spectroscopy, scanning/transmission electron microscopies and Raman spectroscopy. We investigated the influence of different ions and medium pH on self-assembly by evaluating different phage suspension buffers. The assembly of these networks is controlled by electrostatic interactions between the phage pVIII major capsid proteins and the AgNPs. The formation of the AgNPs-phage networks was obtained only in two types of tested buffers at a pH value near the isoelectric point of each pVIII proteins displayed on the surface of the clone. This systematic study allowed to optimize the synthesis procedure to assembly AgNPs and bacteriophage. Such networks find application in the biomedical field of advanced biosensing and targeted gene and drug delivery. Keywords: Phage display, Silver nanoparticles, Self-assembly, Hybrid architecture, Raman spectroscopy

  13. Extensive error in the number of genes inferred from draft genome assemblies.

    Directory of Open Access Journals (Sweden)

    James F Denton

    2014-12-01

    Full Text Available Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

  14. Fuel assemblies

    International Nuclear Information System (INIS)

    Nakatsuka, Masafumi.

    1979-01-01

    Purpose: To prevent scattering of gaseous fission products released from fuel assemblies stored in an fbr type reactor. Constitution; A cap provided with means capable of storing gas is adapted to amount to the assembly handling head, for example, by way of threading in a storage rack of spent fuel assemblies consisting of a bottom plate, a top plate and an assembly support mechanism. By previously eliminating the gas inside of the assembly and the cap in the storage rack, gaseous fission products upon loading, if released from fuel rods during storage, are stored in the cap and do not scatter in the storage rack. (Horiuchi, T.)

  15. Tritium breeding experiments in a fusion blanket assembly using a low-intensity neutron generator

    International Nuclear Information System (INIS)

    Dalton, A.W.; Woodley, H.J.; McGregor, B.J.

    1987-01-01

    Experiments have been carried out to determine the accuracy with which tritium production rates (TPRs) can be measured in a fusion blanket assembly of non-spherical geometry by a non-central low intensity D-T neutron source (2x10 10 neutrons per second). The tritium production was determined for samples of lithium carbonate containing high enrichments of 6 Li(96%) and 7 Li(99.9%). The measured data were used to check the accuracy with which the TPRs could be numerically predicted using current nuclear data and calculational methods. The numerical predictions from tritium production from the 7 Li samples agreed within the experimental errors of the measurements, but 6 Li measurements which differ by more than 20 per cent from the predicted values were observed in the lower half of the assembly

  16. Advanced Engineering Methods for Assessing Welding Distortion in Aero-Engine Assemblies

    International Nuclear Information System (INIS)

    Jackson, Kathryn; Darlington, Roger

    2011-01-01

    Welding remains an attractive fabrication method for aero-engine assemblies, offering high production rates and reduced total cost, particularly for large complex assemblies. However, distortion generated during the welding process continues to provide a major challenge in terms of the control of geometric tolerances and residual stress. The welding distortion is influenced by the sequence and position of joints, the clamping configuration and the design of the assembly. For large complex assemblies the range of these options may be large. Hence the use of numerical simulation at an early stage of the product development process is valuable to enable a wide range of these factors to be explored with the aim of minimising welding distortions before production commences, and thereby reducing the product development time. In this paper, a new technique for simulation of welding distortions based on a shrinkage analysis is evaluated for an aero-engine assembly. The shrinkage simulations were built and solved using the ESI Group software Weld Planner. The rapid simulation speed enabled a wide range of welding plans to be explored, leading to recommendations for the fabrication process. The sensitivity of the model to mesh size and material properties is reported. The results of the shrinkage analysis were found to be similar to those of a transient analysis generated using ESI Group software SysWeld. The solution times were found to be significantly lower for the shrinkage analysis than the transient analysis. Hence it has been demonstrated that shrinkage analysis is a valuable tool for exploring the fabrication process of a welded assembly at an early stage of the product development process.

  17. Thermal Hydraulic Analysis Of Thorium-Based Annular Fuel Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Han, Kyu Hyun [Korea Institute of Nuclear Safety, 19, Guseong-dong, Yuseong-gu, Daejeon, 305-338 (Korea, Republic of)

    2008-07-01

    Thermal hydraulic characteristics of thorium-based fuel assemblies loaded with annular seed pins have been analyzed using AMAP combined with MATRA, and compared with those of the existing thorium-based assemblies. MATRA and AMAP showed good agreements for the pressure drops at the internal sub-channels. The pressure drop generally increased in the cases of the assemblies loaded with annular seed pins due to the larger wetted perimeter, but an exception existed. In the inner sub-channels of the seed pins, mass fluxes were high due to the grid form losses in the outer sub-channels. About 43% of the heat generated from the seed pin flowed into the inner sub-channel and the rest into the outer sub-channel, which implies the inner to outer wall heat flux ratio was approximately 1.2. The maximum temperatures of the annular seed pins were slightly above 500 deg. C. The MDNBRs of the assemblies loaded with annular seed pins were higher than those of the existing assemblies. Due to the fact that inter-channel mixing cannot occur in the inner sub-channels, temperatures and enthalpies were higher in the inner sub-channels. (author)

  18. Helmet-Mounted Displays: Sensation, Perception and Cognition Issues

    Science.gov (United States)

    2009-01-01

    bagels, pretzels, fig or fruit bars, granola bars, yogurt , milk, fresh fruits and vegetables. The bottom line on nutrition and combat is to eat sensible...carcinogens in tobacco are the tobacco-specific nitrosamines. They are formed during the growing, curing, fermenting , and aging of tobacco. Other

  19. Books,Writers,Translators

    Institute of Scientific and Technical Information of China (English)

    Nicholas; Richards

    2011-01-01

    Our editor Liz baked Sidney Shapiro an apple pie.The next day she ran across the city to buy him bagels,cream cheese and lox,and then at the arranged time she telephoned him from outside his home:a courtyard nestled by the Houhai lakes dug

  20. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

    Science.gov (United States)

    Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

    2012-01-01

    The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

  1. Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

    2016-12-16

    Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.

  2. Comprehensive transcriptome assembly of Chickpea (Cicer arietinum L. using sanger and next generation sequencing platforms: development and applications.

    Directory of Open Access Journals (Sweden)

    Himabindu Kudapa

    Full Text Available A comprehensive transcriptome assembly of chickpea has been developed using 134.95 million Illumina single-end reads, 7.12 million single-end FLX/454 reads and 139,214 Sanger expressed sequence tags (ESTs from >17 genotypes. This hybrid transcriptome assembly, referred to as Cicer arietinumTranscriptome Assembly version 2 (CaTA v2, available at http://data.comparative-legumes.org/transcriptomes/cicar/lista_cicar-201201, comprising 46,369 transcript assembly contigs (TACs has an N50 length of 1,726 bp and a maximum contig size of 15,644 bp. Putative functions were determined for 32,869 (70.8% of the TACs and gene ontology assignments were determined for 21,471 (46.3%. The new transcriptome assembly was compared with the previously available chickpea transcriptome assemblies as well as to the chickpea genome. Comparative analysis of CaTA v2 against transcriptomes of three legumes - Medicago, soybean and common bean, resulted in 27,771 TACs common to all three legumes indicating strong conservation of genes across legumes. CaTA v2 was also used for identification of simple sequence repeats (SSRs and intron spanning regions (ISRs for developing molecular markers. ISRs were identified by aligning TACs to the Medicago genome, and their putative mapping positions at chromosomal level were identified using transcript map of chickpea. Primer pairs were designed for 4,990 ISRs, each representing a single contig for which predicted positions are inferred and distributed across eight linkage groups. A subset of randomly selected ISRs representing all eight chickpea linkage groups were validated on five chickpea genotypes and showed 20% polymorphism with average polymorphic information content (PIC of 0.27. In summary, the hybrid transcriptome assembly developed and novel markers identified can be used for a variety of applications such as gene discovery, marker-trait association, diversity analysis etc., to advance genetics research and breeding

  3. Physicochemical and biological properties of self-assembled antisense/poly(amidoamine dendrimer nanoparticles: the effect of dendrimer generation and charge ratio

    Directory of Open Access Journals (Sweden)

    Alireza Nomani

    2010-05-01

    Full Text Available Alireza Nomani1,6, Ismaeil Haririan1,5, Ramin Rahimnia2,4, Shamileh Fouladdel2, Tarane Gazori1, Rassoul Dinarvand1, Yadollah Omidi3, Ebrahim Azizi2,41Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; 2Molecular Research Lab, Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; 3Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; 4Department of Medical Biotechnology, School of Advanced Medical Technologies, Tehran University of Medical Sciences, Tehran, Iran; 5Biomaterials Research Center (BRC Tehran, Iran; 6Department of Pharmaceutics, Faculty of Pharmacy, Zanjan University of Medical Sciences, Zanjan, IranAbstract: To gain a deeper understanding of the physicochemical phenomenon of self-assembled nanoparticles of different generations and ratios of poly (amidoamine dendrimer (PAMAM dendrimer and a short-stranded DNA (antisense oligonucleotide, multiple methods were used to characterize these nanoparticles including photon correlation spectroscopy (PCS; zeta potential measurement; and atomic force microscopy (AFM. PCS and AFM results revealed that, in contrast to larger molecules of DNA, smaller molecules produce more heterodisperse and large nanoparticles when they are condensed with a cationic dendrimer. AFM images also showed that such nanoparticles were spherical. The stability of the antisense content of the nanoparticles was investigated over different charge ratios using polyacrylamide gel electrophoresis. It was clear from such analyses that much more than charge neutrality point was required to obtain stable nanoparticles. For cell uptake, self-assembled nanoparticles were prepared with PAMAM G5 and 5’-FITC labeled antisense and the uptake experiment was carried out in T47D cell culture. This investigation also shows that the cytotoxicity of the nanoparticles was

  4. Self-assembled fluorescent organic nanoparticles for live cell imaging

    NARCIS (Netherlands)

    Fischer, I.; Petkau, K.; Dorland, Y.L.; Schenning, A.P.H.J.; Brunsveld, L.

    2013-01-01

    Fluorescent, cell-permeable, organic nanoparticles based on self-assembled p-conjugated oligomers with high absorption cross-sections and high quantum yields have been developed. The nanoparticles are generated with a tuneable density of amino groups for charge-mediated cellular uptake by a

  5. Directed assembly of functional light harvesting antenna complexes onto chemically patterned surfaces

    International Nuclear Information System (INIS)

    Escalante, Maryana; Maury, Pascale; Bruinink, Christiaan M; Werf, Kees van der; Olsen, John D; Timney, John A; Huskens, Jurriaan; Hunter, C Neil; Subramaniam, Vinod; Otto, Cees

    2008-01-01

    We report the directed assembly of the photosynthetic membrane proteins LH1 and LH2 isolated from the purple bacterium Rhodobacter sphaeroides onto chemically patterned substrates. Nanoimprint lithography was used to pattern discrete regions of amino- and fluoro-terminated or poly(ethylene glycol) self-assembled monolayers onto a glass substrate. Densely packed layers of assembled protein complexes were observed with atomic force microscopy. The protein complexes attached selectively to the amino-terminated regions by electrostatic interactions. Spectral images generated with a hybrid scanning probe and fluorescence microscope confirmed that the patterned proteins retained their native optical signatures

  6. Directed assembly of functional light harvesting antenna complexes onto chemically patterned surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Escalante, Maryana [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Maury, Pascale [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Bruinink, Christiaan M [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Werf, Kees van der [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Olsen, John D [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Timney, John A [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Huskens, Jurriaan [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Hunter, C Neil [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Subramaniam, Vinod [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Otto, Cees [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands)

    2008-01-16

    We report the directed assembly of the photosynthetic membrane proteins LH1 and LH2 isolated from the purple bacterium Rhodobacter sphaeroides onto chemically patterned substrates. Nanoimprint lithography was used to pattern discrete regions of amino- and fluoro-terminated or poly(ethylene glycol) self-assembled monolayers onto a glass substrate. Densely packed layers of assembled protein complexes were observed with atomic force microscopy. The protein complexes attached selectively to the amino-terminated regions by electrostatic interactions. Spectral images generated with a hybrid scanning probe and fluorescence microscope confirmed that the patterned proteins retained their native optical signatures.

  7. Sensor mount assemblies and sensor assemblies

    Science.gov (United States)

    Miller, David H [Redondo Beach, CA

    2012-04-10

    Sensor mount assemblies and sensor assemblies are provided. In an embodiment, by way of example only, a sensor mount assembly includes a busbar, a main body, a backing surface, and a first finger. The busbar has a first end and a second end. The main body is overmolded onto the busbar. The backing surface extends radially outwardly relative to the main body. The first finger extends axially from the backing surface, and the first finger has a first end, a second end, and a tooth. The first end of the first finger is disposed on the backing surface, and the tooth is formed on the second end of the first finger.

  8. Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

    Science.gov (United States)

    Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud

    2018-04-24

    Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

  9. Improving Phrap-based assembly of the rat using "reliable" overlaps.

    Directory of Open Access Journals (Sweden)

    Michael Roberts

    2008-03-01

    Full Text Available The assembly methods used for whole-genome shotgun (WGS data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.

  10. Benchmark problem suite for reactor physics study of LWR next generation fuels

    International Nuclear Information System (INIS)

    Yamamoto, Akio; Ikehara, Tadashi; Ito, Takuya; Saji, Etsuro

    2002-01-01

    This paper proposes a benchmark problem suite for studying the physics of next-generation fuels of light water reactors. The target discharge burnup of the next-generation fuel was set to 70 GWd/t considering the increasing trend in discharge burnup of light water reactor fuels. The UO 2 and MOX fuels are included in the benchmark specifications. The benchmark problem consists of three different geometries: fuel pin cell, PWR fuel assembly and BWR fuel assembly. In the pin cell problem, detailed nuclear characteristics such as burnup dependence of nuclide-wise reactivity were included in the required calculation results to facilitate the study of reactor physics. In the assembly benchmark problems, important parameters for in-core fuel management such as local peaking factors and reactivity coefficients were included in the required results. The benchmark problems provide comprehensive test problems for next-generation light water reactor fuels with extended high burnup. Furthermore, since the pin cell, the PWR assembly and the BWR assembly problems are independent, analyses of the entire benchmark suite is not necessary: e.g., the set of pin cell and PWR fuel assembly problems will be suitable for those in charge of PWR in-core fuel management, and the set of pin cell and BWR fuel assembly problems for those in charge of BWR in-core fuel management. (author)

  11. Method of using infrared radiation for assembling a first component with a second component

    Science.gov (United States)

    Sikka, Vinod K.; Whitson, Barry G.; Blue, Craig A.

    1999-01-01

    A method of assembling a first component for assembly with a second component involves a heating device which includes an enclosure having a cavity for inserting a first component. An array of infrared energy generators is disposed within the enclosure. At least a portion of the first component is inserted into the cavity, exposed to infrared energy and thereby heated to a temperature wherein the portion of the first component is sufficiently softened and/or expanded for assembly with a second component.

  12. A SCWR core design with a conceptual fuel assembly using a cruciform moderator

    International Nuclear Information System (INIS)

    Bae, Kang Mok; Joo, Hyung Kook; Lee, Hyun Chul; Noh, Jae Man; Bae, Yoon Yong

    2005-01-01

    A super critical water cooled reactor (SCWR) system has a potential to compete with the advanced fossil plant by achieving a high thermal efficiency up to 44% and a plant simplification by eliminating steam generators, steam dryers, steam separators, and recirculation pumps. Due to these advantages, a SCWR is considered as one of the most promising nuclear plants for the Generation-IV (Gen-IV) system. As a first step of a feasibility study a rectangular fuel assembly with a cruciform solid moderator was suggested as a conceptual assembly design at the Korea Atomic Energy Research Institute (KAERI) for the SCWR on a thermal neutron spectrum. In this paper, based on the system parameters proposed by the Gen-IV road map, a preliminary SCWR core design was performed using a conceptual assembly design focused on the power shape control, reactivity coefficients, and cladding temperature limit

  13. Smart human serum albumin-indocyanine green nanoparticles generated by programmed assembly for dual-modal imaging-guided cancer synergistic phototherapy.

    Science.gov (United States)

    Sheng, Zonghai; Hu, Dehong; Zheng, Mingbin; Zhao, Pengfei; Liu, Huilong; Gao, Duyang; Gong, Ping; Gao, Guanhui; Zhang, Pengfei; Ma, Yifan; Cai, Lintao

    2014-12-23

    Phototherapy, including photodynamic therapy (PDT) and photothermal therapy (PTT), is a light-activated local treatment modality that is under intensive preclinical and clinical investigations for cancer. To enhance the treatment efficiency of phototherapy and reduce the light-associated side effects, it is highly desirable to improve drug accumulation and precision guided phototherapy for efficient conversion of the absorbed light energy to reactive oxygen species (ROS) and local hyperthermia. In the present study, a programmed assembly strategy was developed for the preparation of human serum albumin (HSA)-indocyanine green (ICG) nanoparticles (HSA-ICG NPs) by intermolecular disulfide conjugations. This study indicated that HSA-ICG NPs had a high accumulation with tumor-to-normal tissue ratio of 36.12±5.12 at 24 h and a long-term retention with more than 7 days in 4T1 tumor-bearing mice, where the tumor and its margin, normal tissue were clearly identified via ICG-based in vivo near-infrared (NIR) fluorescence and photoacoustic dual-modal imaging and spectrum-resolved technology. Meanwhile, HSA-ICG NPs efficiently induced ROS and local hyperthermia simultaneously for synergetic PDT/PTT treatments under a single NIR laser irradiation. After an intravenous injection of HSA-ICG NPs followed by imaging-guided precision phototherapy (808 nm, 0.8 W/cm2 for 5 min), the tumor was completely suppressed, no tumor recurrence and treatments-induced toxicity were observed. The results suggest that HSA-ICG NPs generated by programmed assembly as smart theranostic nanoplatforms are highly potential for imaging-guided cancer phototherapy with PDT/PTT synergistic effects.

  14. Ultra-Precise Assembly of Micro-Electromechanical Systems (MEMS) Components

    Energy Technology Data Exchange (ETDEWEB)

    Feddema, J.T.; Simon, R.; Polosky, M.; Christenson, T.

    1999-04-01

    This report summarizes a three year effort to develop an automated microassembly workcell for the assembly of LIGA (Lithography Galvonoforming Abforming) parts. Over the last several years, Sandia has developed processes for producing surface machined silicon and LIGA parts for use in weapons surety devices. Some of these parts have outside dimensions as small as 100 micron, and most all have submicron tolerances. Parts this small and precise are extremely difficult to assembly by hand. Therefore, in this project, we investigated the technologies required to develop a robotic workcell to assembly these parts. In particular, we concentrated on micro-grippers, visual servoing, micro-assembly planning, and parallel assembly. Three different micro-grippers were tested: a pneumatic probe, a thermally actuated polysilicon tweezer, and a LIGA fabricated tweezer. Visual servoing was used to accuracy position two parts relative to one another. Fourier optics methods were used to generate synthetic microscope images from CAD drawings. These synthetic images are used off-line to test image processing routines under varying magnifications and depths of field. They also provide reference image features which are used to visually servo the part to the desired position. We also investigated a new aspect of fine motion planning for the micro-domain. As parts approach 1-10 {micro}m or less in outside dimensions, interactive forces such as van der Waals and electrostatic forces become major factors which greatly change the assembly sequence and path plans. We developed the mathematics required to determine the goal regions for pick up, holding, and release of a micro-sphere being handled by a rectangular tool. Finally, we implemented and tested the ability to assemble an array of LIGA parts attached to two 3 inch diameter wafers. In this way, hundreds of parts can be assembled in parallel rather than assembling each part individually.

  15. Solving Assembly Sequence Planning using Angle Modulated Simulated Kalman Filter

    Science.gov (United States)

    Mustapa, Ainizar; Yusof, Zulkifli Md.; Adam, Asrul; Muhammad, Badaruddin; Ibrahim, Zuwairie

    2018-03-01

    This paper presents an implementation of Simulated Kalman Filter (SKF) algorithm for optimizing an Assembly Sequence Planning (ASP) problem. The SKF search strategy contains three simple steps; predict-measure-estimate. The main objective of the ASP is to determine the sequence of component installation to shorten assembly time or save assembly costs. Initially, permutation sequence is generated to represent each agent. Each agent is then subjected to a precedence matrix constraint to produce feasible assembly sequence. Next, the Angle Modulated SKF (AMSKF) is proposed for solving ASP problem. The main idea of the angle modulated approach in solving combinatorial optimization problem is to use a function, g(x), to create a continuous signal. The performance of the proposed AMSKF is compared against previous works in solving ASP by applying BGSA, BPSO, and MSPSO. Using a case study of ASP, the results show that AMSKF outperformed all the algorithms in obtaining the best solution.

  16. Supramolecular ribbons from amphiphilic trisamides self-assembly.

    Science.gov (United States)

    García, Fátima; Buendía, Julia; Sánchez, Luis

    2011-08-05

    Two amphiphilic C(3)-symmetric OPE-based trisamides have been synthesized and their self-assembling features investigated in solution and on surface. Variable-temperature UV-vis experiments demonstrate the cooperative supramolecular polymerization of these trisamides that self-assemble by the operation of triple C═O···H-N H-bonding arrays between the amide functional groups and π-π stacking between the aromatic units. The helical organization of the aggregates has been demonstrated by circular dichroism at a concentration as low as 1 × 10(-4) M in acetonitrile. In the reported trisamides, the large hydrophobic aromatic core acts as a solvophobic module impeding the interaction between the polar TEG chains and the amide H-bonds. This strategy makes unnecessary the separation of the amide functional groups to the polar tri(ethylene glycol) chains by paraffinic fragments. Achiral trisamide 1 self-assembles into flat ribbon-like structures that experience an amplification of chirality by the addition of a small amount of chiral 2 that generates twisted stripes.

  17. The effect of thermal and vapor annealing treatments on the self-assembly of TiO2 /PS-b-PMMA nanocomposites generated via the sol-gel process

    International Nuclear Information System (INIS)

    Gutierrez, J; Tercjak, A; Garcia, I; Mondragon, I

    2009-01-01

    Polystyrene-block-poly(methyl methacrylate) (SMMA) block copolymer has been used as a structure-directing agent for generating TiO 2 /SMMA nanocomposites via the sol-gel process using a hydrophobic surfactant. The aim of the work has been focused on the preparation of well-defined nanostructured composites based on the self-assembling capability of the block copolymer using two different annealing methods: thermal- and solvent-induced microphase separation. The addition of different amounts of nanoparticles caused strong variations in the self-assembled morphology of the TiO 2 /SMMA nanocomposites with respect to the block copolymer, as observed by atomic force microscopy (AFM). To verify the confinement of the nanoparticles in the PMMA block 3D AFM images and corresponding AFM profiles have also been reported. UV light irradiation of the nanocomposite films provoked the removal of the organic matrix and consequently led to an array of TiO 2 nanoparticles on the substrate surface.

  18. Collagen I self-assembly: revealing the developing structures that generate turbidity.

    Science.gov (United States)

    Zhu, Jieling; Kaufman, Laura J

    2014-04-15

    Type I collagen gels are routinely used in biophysical studies and bioengineering applications. The structural and mechanical properties of these fibrillar matrices depend on the conditions under which collagen fibrillogenesis proceeds, and developing a fuller understanding of this process will enhance control over gel properties. Turbidity measurements have long been the method of choice for monitoring developing gels, whereas imaging methods are regularly used to visualize fully developed gels. In this study, turbidity and confocal reflectance microscopy (CRM) were simultaneously employed to track collagen fibrillogenesis and reconcile the information reported by the two techniques, with confocal fluorescence microscopy (CFM) used to supplement information about early events in fibrillogenesis. Time-lapse images of 0.5 mg/ml, 1.0 mg/ml, and 2.0 mg/ml acid-solubilized collagen I gels forming at 27°C, 32°C, and 37°C were collected. It was found that in situ turbidity measured in a scanning transmittance configuration was interchangeable with traditional turbidity measurements using a spectrophotometer. CRM and CFM were employed to reveal the structures responsible for the turbidity that develops during collagen self-assembly. Information from CRM and transmittance images was collapsed into straightforward single variables; total intensity in CRM images tracked turbidity development closely for all collagen gels investigated, and the two techniques were similarly sensitive to fibril number and dimension. Complementary CRM, CFM, and in situ turbidity measurements revealed that fibril and network formation occurred before substantial turbidity was present, and the majority of increasing turbidity during collagen self-assembly was due to increasing fibril thickness. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  19. On the influence of surface patterning on tissue self-assembly and mechanics.

    Science.gov (United States)

    Coppola, Valerio; Ventre, Maurizio; Natale, Carlo F; Rescigno, Francesca; Netti, Paolo A

    2018-04-28

    Extracellular matrix assembly and composition influence the biological and mechanical functions of tissues. Developing strategies to control the spatial arrangement of cells and matrix is of central importance for tissue engineering-related approaches relying on self-assembling and scaffoldless processes. Literature reports demonstrated that signals patterned on material surfaces are able to control cell positioning and matrix orientation. However, the mechanisms underlying the interactions between material signals and the structure of the de novo synthesized matrix are far from being thoroughly understood. In this work, we investigated the ordering effect provided by nanoscale topographic patterns on the assembly of tissue sheets grown in vitro. We stimulated MC3T3-E1 preosteoblasts to produce and assemble a collagen-rich matrix on substrates displaying patterns with long- or short-range order. Then, we investigated microstructural features and mechanical properties of the tissue in uniaxial tension. Our results demonstrate that patterned material surfaces are able to control the initial organization of cells in close contact to the surface; then cell-generated contractile forces profoundly remodel tissue structure towards mechanically stable spatial patterns. Such a remodelling effect acts both locally, as it affects cell and nuclear shape and globally, by affecting the gross mechanical response of the tissue. Such an aspect of dynamic interplay between cells and the surrounding matrix must be taken into account when designing material platform for the in vitro generation of tissue with specific microstructural assemblies. Copyright © 2018 John Wiley & Sons, Ltd.

  20. Compact assembly generates plastic foam, inflates flotation bag

    Science.gov (United States)

    1965-01-01

    Device for generating plastic foam consists of an elastomeric bag and two containers with liquid resin and a liquid catalyst. When the walls of the containers are ruptured the liquids come into contact producing foam which inflates the elastomeric bag.

  1. Burnup verification measurements on spent fuel assemblies at Arkansas Nuclear One

    International Nuclear Information System (INIS)

    Ewing, R.I.

    1995-01-01

    Burnup verification measurements have been performed using the Fork system at Arkansas Nuclear One, Units 1 and 2, operated by Energy Operations, Inc. Passive neutron and gamma-ray measurements on individual spent fuel assemblies were correlated with the reactor records for burnup, cooling time, and initial enrichment. The correlation generates an internal calibration for the system in the form of a power law determined by a least squares fit to the neutron data. The values of the exponent in the power laws were 3.83 and 4.35 for Units 1 and 2, respectively. The average deviation of the reactor burnup records from the calibration determined from the measurements is a measure of the random error in the burnup records. The observed average deviations were 2.7% and 3.5% for assemblies at Units 1 and 2, respectively, indicating a high degree of consistency in the reactor records. Two non-standard assemblies containing neutron sources were studied at Unit 2. No anomalous measurements were observed among the standard assemblies at either Unit. The effectiveness of the Fork system for verification of reactor records is due to the sensitivity of the neutron yield to burnup, the self-calibration generated by a series of measurements, the redundancy provided by three independent detection systems, and the operational simplicity and flexibility of the design

  2. Preliminary evaluation of pin power distribution for fuel assemblies of SMART by MCNP

    International Nuclear Information System (INIS)

    Kim, Kyo Youn

    1998-08-01

    Monte Carlo transport code MCNP can describe an object sophisticately by use of three-dimensional modelling and can adopt a continuous energy cross-section library. Therefore MCNP has been widely utilized in the field of radiation physics to estimate fluxes and dose rates for nuclear facilities and to review results from conventional methods such a as discrete ordinates method and point kernel method. The Monte Carlo method has recently been introduced to estimated the neutron multiplication factor and pin power distribution in the fuel assembly of a reactor core. The operating thermal power of SMART core is 330 MWt and there are 57 fuel assemblies in the core. In this study it was assumed that the core has 4 types of fuel assemblies. In this study, MCNP4a was used to perform to estimate criticality and normalized pin power distribution in a fuel assembly of SMART core. The results from MCNP4a calculations are able to be used review those from nuclear design/analysis code. It is very complicated to pick up interested data from MCNP output list and to normalize pin power distribution in a fuel assembly because MCNP is not only a nuclear design/analysis code. In this study a program FAPIN was developed to generated a generate a normalized pin power distribution from the MCNP output list. (author). 11 refs

  3. Desain Beam Shaping Assembly (BSA berbasis D-D Neutron Generator 2,45 MeV untuk Uji Fasilitas BNCT

    Directory of Open Access Journals (Sweden)

    Desman P. Gulo

    2015-12-01

    Full Text Available Boron Neutron Capture Therapy (BNCT is one of the cancer treatments that are being developed in nowadays. In order to support BNCT treatment for cancer that exists in underneath skin like breast cancer, the facility needs a generator that is able to produce epithermal neutron. One of the generator that is able to produce neutron is D-D neutron generator with 2.45 MeV energy. Based on the calculation of this paper, we found that the total production of neutron per second (neutron yield from Neutron Generator (NG by PSTA-BATAN Yogyakarta is 2.55×1011 n/s. The energy and flux that we found is in the range of quick neutron. Thus, it needs to be moderated to the level of epithermal neutron which is located in the interval energy of 1 eV to 10 KeV with 109 n/cm2s flux. This number is the recommendation standard from IAEA. Beam Shaping Assembly (BSA is needed in order to moderate the quick neutron to the level of epithermal neutron. One part of BSA that has the responsibility in moderating the quick neutron to epithermal neutron is the moderator. The substance of moderator used in this paper is MgF2 and A1F3. The thickness of moderator has been set in in such a way by using MCNPX software in order to fulfill the standard of IAEA. As the result of optimizing BSA moderator, the data obtain epithermal flux with the total number of 4.64×108 n/cm2/s for both of moderators with the thickness of moderator up to 15 cm. At the end of this research, the number of epithermal flux does not follow the standard of IAEA. This is because the flux neutron that is being produced by NG is relatively small. In conclusion, the NG from PSTA-BATAN Yogyakarta is not ready to be used for the BNCT treatment facility for the underneath skin cancer like breast cancer.

  4. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine

    Directory of Open Access Journals (Sweden)

    Wenming Xiao

    2016-04-01

    Full Text Available Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging “third generation sequencing” technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host

  5. Stoichiometric Assembly of the Cellulosome Generates Maximum Synergy for the Degradation of Crystalline Cellulose, as Revealed by In Vitro Reconstitution of the Clostridium thermocellum Cellulosome.

    Science.gov (United States)

    Hirano, Katsuaki; Nihei, Satoshi; Hasegawa, Hiroki; Haruki, Mitsuru; Hirano, Nobutaka

    2015-07-01

    The cellulosome is a supramolecular multienzyme complex formed by species-specific interactions between the cohesin modules of scaffoldin proteins and the dockerin modules of a wide variety of polysaccharide-degrading enzymes. Cellulosomal enzymes bound to the scaffoldin protein act synergistically to degrade crystalline cellulose. However, there have been few attempts to reconstitute intact cellulosomes due to the difficulty of heterologously expressing full-length scaffoldin proteins. We describe the synthesis of a full-length scaffoldin protein containing nine cohesin modules, CipA; its deletion derivative containing two cohesin modules, ΔCipA; and three major cellulosomal cellulases, Cel48S, Cel8A, and Cel9K, of the Clostridium thermocellum cellulosome. The proteins were synthesized using a wheat germ cell-free protein synthesis system, and the purified proteins were used to reconstitute cellulosomes. Analysis of the cellulosome assembly using size exclusion chromatography suggested that the dockerin module of the enzymes stoichiometrically bound to the cohesin modules of the scaffoldin protein. The activity profile of the reconstituted cellulosomes indicated that cellulosomes assembled at a CipA/enzyme molar ratio of 1/9 (cohesin/dockerin = 1/1) and showed maximum synergy (4-fold synergy) for the degradation of crystalline substrate and ∼2.4-fold-higher synergy for its degradation than minicellulosomes assembled at a ΔCipA/enzyme molar ratio of 1/2 (cohesin/dockerin = 1/1). These results suggest that the binding of more enzyme molecules on a single scaffoldin protein results in higher synergy for the degradation of crystalline cellulose and that the stoichiometric assembly of the cellulosome, without excess or insufficient enzyme, is crucial for generating maximum synergy for the degradation of crystalline cellulose. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  6. Assessment of Gamma Radiation Resistance of Spores Isolated from the Spacecraft Assembly Facility During MSL Assembly

    Science.gov (United States)

    Chopra, Arsh; Ramirez, Gustavo A.; Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

    2011-01-01

    Spore forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate extreme environmental conditions such as radiation, desiccation, and high temperatures. Since the Viking era (early 1970's), spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. There is a growing concern that desiccation and extreme radiation resistant spore forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequently proliferate on another solar body. Such forward contamination would certainly jeopardize future life detection or sample return technologies. It is important to recognize that different classes of organisms are critical while calculating the probability of contamination, and methods must be devised to estimate their abundances. Microorganisms can be categorized based on radiation sensitivity as Type A, B, C, and D. Type C represents spores resistant to radiation (10% or greater survival above 0.8 Mrad gamma radiation). To address these questions we have purified 96 spore formers, isolated during planetary protection efforts of Mars Science Laboratory assembly for gamma radiation resistance. The spores purified and stored will be used to generate data that can be used further to model and predict the probability of forward contamination.

  7. A Dynamic Combinatorial Approach for Identifying Side Groups that Stabilize DNA-Templated Supramolecular Self-Assemblies

    Directory of Open Access Journals (Sweden)

    Delphine Paolantoni

    2015-02-01

    Full Text Available DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.

  8. A static analysis tool set for assembler code verification

    International Nuclear Information System (INIS)

    Dhodapkar, S.D.; Bhattacharjee, A.K.; Sen, Gopa

    1991-01-01

    Software Verification and Validation (V and V) is an important step in assuring reliability and quality of the software. The verification of program source code forms an important part of the overall V and V activity. The static analysis tools described here are useful in verification of assembler code. The tool set consists of static analysers for Intel 8086 and Motorola 68000 assembly language programs. The analysers examine the program source code and generate information about control flow within the program modules, unreachable code, well-formation of modules, call dependency between modules etc. The analysis of loops detects unstructured loops and syntactically infinite loops. Software metrics relating to size and structural complexity are also computed. This report describes the salient features of the design, implementation and the user interface of the tool set. The outputs generated by the analyser are explained using examples taken from some projects analysed by this tool set. (author). 7 refs., 17 figs

  9. De novo transcriptome assembly of Sorghum bicolor variety Taejin

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2016-06-01

    Full Text Available Sorghum (Sorghum bicolor, also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

  10. How do eggs pan out?

    Science.gov (United States)

    Clark, N

    1998-07-01

    Once upon a time, eggs were considered a "breakfast of champions." Just about every active, hard-working person enjoyed them fried, scrambled, poached, or even raw in eggnog and protein drinks. Then, Americans became cholesterol-conscious and began to substitute bagels, cereal, and other high-carbohydrate, low-cholesterol breakfast foods.

  11. Sadhana | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    Home; Journals; Sadhana. R SIVARAJ. Articles written in Sadhana. Volume 41 Issue 8 August 2016 pp 825-836. BAGEL:A non-ignorable missing value estimation method for mixed attribute datasets · R DEVI PRIYA S KUPPUSWAMI R SIVARAJ · More Details Abstract Fulltext PDF. Surveys are mainly conducted to obtain ...

  12. Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

    Directory of Open Access Journals (Sweden)

    Andreas I Andreou

    Full Text Available Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

  13. Modular steam generator for use in nuclear power plants

    International Nuclear Information System (INIS)

    Cella, A.

    1979-01-01

    An improved steam generator for a PWR is described. A turbine generator is driven by the steam output of the steam generator to provide electrical power. The improvement provides vertically assemblable modules which are removably mounted together in sealing relationship. The modules comprising a base module, a tube bundle module removably mountable on the base module in sealing relationship, and an uppermost dryer module removably mountable on the tube bundle module in sealing relationship. Ready access to and removal of the tube bundle module in situ from the nuclear power plant steam generator is facilitated. The dryer module contains moisture separator for drying the generated steam. The base module, upon which the associated weight of the vertically assembled dryer module and tube bundle module are supported, contains the inlet and outlet for the heat exchange fluid. The tube bundle module contains the tube bundle through which the heat exchange fluid flows as well as an inlet for feedwater. The tube sheet serves as a closure flange for the tube bundle module, with the associated weight of the vertically assembled dryer module and tube bundle module on the tube sheet closure flange effectuating the sealing relationship between the base module and the tube bundle module for facilitating closure

  14. Sequential bottom-up assembly of mechanically stabilized synthetic cells by microfluidics

    Science.gov (United States)

    Weiss, Marian; Frohnmayer, Johannes Patrick; Benk, Lucia Theresa; Haller, Barbara; Janiesch, Jan-Willi; Heitkamp, Thomas; Börsch, Michael; Lira, Rafael B.; Dimova, Rumiana; Lipowsky, Reinhard; Bodenschatz, Eberhard; Baret, Jean-Christophe; Vidakovic-Koch, Tanja; Sundmacher, Kai; Platzman, Ilia; Spatz, Joachim P.

    2018-01-01

    Compartments for the spatially and temporally controlled assembly of biological processes are essential towards cellular life. Synthetic mimics of cellular compartments based on lipid-based protocells lack the mechanical and chemical stability to allow their manipulation into a complex and fully functional synthetic cell. Here, we present a high-throughput microfluidic method to generate stable, defined sized liposomes termed `droplet-stabilized giant unilamellar vesicles (dsGUVs)’. The enhanced stability of dsGUVs enables the sequential loading of these compartments with biomolecules, namely purified transmembrane and cytoskeleton proteins by microfluidic pico-injection technology. This constitutes an experimental demonstration of a successful bottom-up assembly of a compartment with contents that would not self-assemble to full functionality when simply mixed together. Following assembly, the stabilizing oil phase and droplet shells are removed to release functional self-supporting protocells to an aqueous phase, enabling them to interact with physiologically relevant matrices.

  15. Coulomb force directed single and binary assembly of nanoparticles from aqueous dispersions by AFM nanoxerography.

    Science.gov (United States)

    Palleau, Etienne; Sangeetha, Neralagatta M; Viau, Guillaume; Marty, Jean-Daniel; Ressier, Laurence

    2011-05-24

    We present a simple protocol to obtain versatile assemblies of nanoparticles from aqueous dispersions onto charge patterns written by atomic force microscopy, on a 100 nm thin film of polymethylmethacrylate spin-coated on silicon wafers. This protocol of nanoxerography uses a two-stage development involving incubation of the desired aqueous colloidal dispersion on charge patterns and subsequent immersion in an adequate water-soluble alcohol. The whole process takes only a few minutes. Numerical simulations of the evolution of the electric field generated by charge patterns in various solvents are done to resolve the mechanism by which nanoparticle assembly occurs. The generic nature of this protocol is demonstrated by constructing various assemblies of charged organic/inorganic/metallic (latex, silica, gold) nanoparticles of different sizes (3 to 100 nm) and surface functionalities from aqueous dispersions onto charge patterns of complex geometries. We also demonstrate that it is possible to construct a binary assembly of nanoparticles on a pattern made of positive and negative charges generated in a single charge writing step, by sequential developments in two aqueous dispersions of oppositely charged particles. This protocol literally extends the spectra of eligible colloids that can be assembled by nanoxerography and paves the way for building complex assemblies of nanoparticles on predefined areas of surfaces, which could be useful for the elaboration of nanoparticle-based functional devices.

  16. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

    Directory of Open Access Journals (Sweden)

    Materne Michael

    2011-05-01

    Full Text Available Abstract Background Lentil (Lens culinaris Medik. is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs. De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  17. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

    Science.gov (United States)

    Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

    2017-01-25

    Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

  18. Contemporary and prospective fuel cycles for WWER-440 based on new assemblies with higher uranium capacity and higher average fuel enrichment

    International Nuclear Information System (INIS)

    Gagarinskiy, A.A.; Saprykin, V.V.

    2009-01-01

    RRC 'Kurchatov Institute' has performed an extensive cycle of calculations intended to validate the opportunities of improving different fuel cycles for WWER-440 reactors. Works were performed to upgrade and improve WWER-440 fuel cycles on the basis of second-generation fuel assemblies allowing core thermal power to be uprated to 107 108 % of its nominal value (1375 MW), while maintaining the same fuel operation lifetime. Currently intensive work is underway to develop fuel cycles based on second-generation assemblies with higher fuel capacity and average fuel enrichment per assembly increased up to 4.87 % of U-235. Fuel capacity of second-generation assemblies was increased by means of eliminated central apertures of fuel pellets, and pellet diameter extended due to reduced fuel cladding thickness. This paper intends to summarize the results of works performed in the field of WWER-440 fuel cycle modernization, and to present yet unemployed opportunities and prospects of further improvement of WWER-440 neutronic and operating parameters by means of additional optimization of fuel assembly designs and fuel element arrangements applied. (Authors)

  19. PWR and BWR spent fuel assembly gamma spectra measurements

    Energy Technology Data Exchange (ETDEWEB)

    Vaccaro, S. [European Commission, DG Energy, Directorate EURATOM Safeguards Luxembourg (Luxembourg); Tobin, S.J.; Favalli, A. [Los Alamos National Laboratory, Los Alamos, NM (United States); Grogan, B. [Oak Ridge National Laboratory, Oak Ridge (United States); Jansson, P. [Uppsala University, Uppsala (Sweden); Liljenfeldt, H. [Oak Ridge National Laboratory, Oak Ridge (United States); Mozin, V. [Lawrence Livermore National Laboratory, Livermore, CA (United States); Hu, J. [Oak Ridge National Laboratory, Oak Ridge (United States); Schwalbach, P. [European Commission, DG Energy, Directorate EURATOM Safeguards Luxembourg (Luxembourg); Sjöland, A. [Swedish Nuclear Fuel and Waste Management Company (SKB) (Sweden); Trellue, H.; Vo, D. [Los Alamos National Laboratory, Los Alamos, NM (United States)

    2016-10-11

    A project to research the application of nondestructive assay (NDA) to spent fuel assemblies is underway. The research team comprises the European Atomic Energy Community (EURATOM), embodied by the European Commission, DG Energy, Directorate EURATOM Safeguards; the Swedish Nuclear Fuel and Waste Management Company (SKB); two universities; and several United States national laboratories. The Next Generation of Safeguards Initiative–Spent Fuel project team is working to achieve the following technical goals more easily and efficiently than in the past using nondestructive assay measurements of spent fuel assemblies: (1) verify the initial enrichment, burnup, and cooling time of facility declaration; (2) detect the diversion or replacement of pins, (3) estimate the plutonium mass, (4) estimate the decay heat, and (5) determine the reactivity of spent fuel assemblies. This study focuses on spectrally resolved gamma-ray measurements performed on a diverse set of 50 assemblies [25 pressurized water reactor (PWR) assemblies and 25 boiling water reactor (BWR) assemblies]; these same 50 assemblies will be measured with neutron-based NDA instruments and a full-length calorimeter. Given that encapsulation/repository and dry storage safeguards are the primarily intended applications, the analysis focused on the dominant gamma-ray lines of {sup 137}Cs, {sup 154}Eu, and {sup 134}Cs because these isotopes will be the primary gamma-ray emitters during the time frames of interest to these applications. This study addresses the impact on the measured passive gamma-ray signals due to the following factors: burnup, initial enrichment, cooling time, assembly type (eight different PWR and six different BWR fuel designs), presence of gadolinium rods, and anomalies in operating history. To compare the measured results with theory, a limited number of ORIGEN-ARP simulations were performed.

  20. Analysis of Advanced Fuel Assemblies and Core Designs for the Current and Next Generations of LWRs

    International Nuclear Information System (INIS)

    Ragusa, Jean; Vierow, Karen

    2011-01-01

    The objective of the project is to design and analyze advanced fuel assemblies for use in current and future light water reactors and to assess their ability to reduce the inventory of transuranic elements, while preserving operational safety. The reprocessing of spent nuclear fuel can delay or avoid the need for a second geological repository in the US. Current light water reactor fuel assembly designs under investigation could reduce the plutonium inventory of reprocessed fuel. Nevertheless, these designs are not effective in stabilizing or reducing the inventory of minor actinides. In the course of this project, we developed and analyzed advanced fuel assembly designs with improved thermal transmutation capability regarding transuranic elements and especially minor actinides. These designs will be intended for use in thermal spectrum (e.g., current and future fleet of light water reactors in the US). We investigated various fuel types, namely high burn-up advanced mixed oxides and inert matrix fuels, in various geometrical designs that are compliant with the core internals of current and future light water reactors. Neutronic/thermal hydraulic effects were included. Transmutation efficiency and safety parameters were used to rank and down-select the various designs.

  1. Analysis of Advanced Fuel Assemblies and Core Designs for the Current and Next Generations of LWRs

    Energy Technology Data Exchange (ETDEWEB)

    Ragusa, Jean; Vierow, Karen

    2011-09-01

    The objective of the project is to design and analyze advanced fuel assemblies for use in current and future light water reactors and to assess their ability to reduce the inventory of transuranic elements, while preserving operational safety. The reprocessing of spent nuclear fuel can delay or avoid the need for a second geological repository in the US. Current light water reactor fuel assembly designs under investigation could reduce the plutonium inventory of reprocessed fuel. Nevertheless, these designs are not effective in stabilizing or reducing the inventory of minor actinides. In the course of this project, we developed and analyzed advanced fuel assembly designs with improved thermal transmutation capability regarding transuranic elements and especially minor actinides. These designs will be intended for use in thermal spectrum (e.g., current and future fleet of light water reactors in the US). We investigated various fuel types, namely high burn-up advanced mixed oxides and inert matrix fuels, in various geometrical designs that are compliant with the core internals of current and future light water reactors. Neutronic/thermal hydraulic effects were included. Transmutation efficiency and safety parameters were used to rank and down-select the various designs.

  2. Integrating Test-Form Formatting into Automated Test Assembly

    Science.gov (United States)

    Diao, Qi; van der Linden, Wim J.

    2013-01-01

    Automated test assembly uses the methodology of mixed integer programming to select an optimal set of items from an item bank. Automated test-form generation uses the same methodology to optimally order the items and format the test form. From an optimization point of view, production of fully formatted test forms directly from the item pool using…

  3. Physics study of D-D/D-T neutron driven experimental subcritical assembly

    International Nuclear Information System (INIS)

    Sinha, Amar

    2015-01-01

    An experimental program to design and study external source driven subcritical assembly has been initiated at BARC. This program is aimed at understanding neutronic characteristics of accelerator driven system at low power level. In this series, a zero-power, sub-critical assembly driven by a D-D/D-T neutron generator has been developed. This system is modular in design and it is first in the series of subcritical assemblies being designed. The subcritical core consists of natural uranium fuel with high density polyethylene as moderator and beryllium oxide as reflector. The subcritical core is coupled to Purnima Neutron Generator. Preliminary experiments have been carried out for spatial flux measurement and reactivity estimation using pulsed neutron source (PNS) techniques. Further experiments are being planned to measure the reactivity and other kinetic parameters using noise methods. This facility would also be used for carrying out studies on effect of source importance and measurement of source multiplication factor k s and external neutron source efficiency φ* in great details. Some experiments with D-D and D-T neutrons have been presented. (author)

  4. Premitotic assembly of human CENPs -T and -W switches centromeric chromatin to a mitotic state.

    Directory of Open Access Journals (Sweden)

    Lisa Prendergast

    2011-06-01

    Full Text Available Centromeres are differentiated chromatin domains, present once per chromosome, that direct segregation of the genome in mitosis and meiosis by specifying assembly of the kinetochore. They are distinct genetic loci in that their identity in most organisms is determined not by the DNA sequences they are associated with, but through specific chromatin composition and context. The core nucleosomal protein CENP-A/cenH3 plays a primary role in centromere determination in all species and directs assembly of a large complex of associated proteins in vertebrates. While CENP-A itself is stably transmitted from one generation to the next, the nature of the template for centromere replication and its relationship to kinetochore function are as yet poorly understood. Here, we investigate the assembly and inheritance of a histone fold complex of the centromere, the CENP-T/W complex, which is integrated with centromeric chromatin in association with canonical histone H3 nucleosomes. We have investigated the cell cycle regulation, timing of assembly, generational persistence, and requirement for function of CENPs -T and -W in the cell cycle in human cells. The CENP-T/W complex assembles through a dynamic exchange mechanism in late S-phase and G2, is required for mitosis in each cell cycle and does not persist across cell generations, properties reciprocal to those measured for CENP-A. We propose that the CENP-A and H3-CENP-T/W nucleosome components of the centromere are specialized for centromeric and kinetochore activities, respectively. Segregation of the assembly mechanisms for the two allows the cell to switch between chromatin configurations that reciprocally support the replication of the centromere and its conversion to a mitotic state on postreplicative chromatin.

  5. Evaluation of residual radioactivity and dose rate of a target assembly in an IBA cyclotron

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Seon Yong; Kim, Young Ju; Lee, Seung Wook [School of Mechanical Engineering, Pusan National University (Korea, Republic of)

    2016-12-15

    When a cyclotron produces 18F-, accelerated protons interact with metal parts of the cyclotron machine and induces radioactivity. Especially, the target window and chamber of the target assembly are the main parts where long-lived radionuclides are generated as they are incident by direct beams. It is of great importance to identify radionuclides induced in the target assembly for the safe operation and maintenance of a cyclotron facility. In this study, we analyzed major radionuclides generated in the target assembly by an operation of the Cyclotron 18/9 machine and measured dose rates after the operation to establish the radiation safety guideline for operators and maintenance personnel of the machine. Gamma spectroscopy with HPGe was performed on samples from the target chamber and Havar foil target window to identify the radionuclides generated during the operation for production of 18F-- isotope and their specific activity. Also, the dose rates from the target were measured as a function of time after an operation. These data will help improve radiological safety of operating the cyclotron facilities.

  6. Radiation shield ring assembly and method of disassembling components of a nuclear steam generator using such assembly

    International Nuclear Information System (INIS)

    Meuschke, R.E.; Wolfe, D.L.

    1982-01-01

    This invention relates to an apparatus and a method for cutting, within a shielding confinement, the irradiated components of a nuclear steam generator to reduce such components to a size to permit their subsequent removal from the containment structure of the generator

  7. ITEP Subcritical Neutron Generator driven by charged particle accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Shvedov, O.V.; Chuvilo, I.V.; Vasiliev, V.V. [Institute of Theoretical and Experimental Physics, Moscow (Russian Federation)] [and others

    1995-10-01

    A research facility prototype including a combination of a linear accelerator, a neutron generating target, a nuclear safety ensuring and means of its attainment for Subcritical Neutron Generator are considered. The scheme of the multiplying is shown. The assembly will be mounted in the body of the partly dismantled ITEP HWR. Requirements for subcritical assembly are worked out and their feasibility within the framework of the heavy-water blanket is shown. The facility`s application as a full-scale model of more powerful installations of this kind and for fundamental experimental research has been investigated.

  8. Self-assembly of self-assembled molecular triangles

    Indian Academy of Sciences (India)

    While the solution state structure of 1 can be best described as a trinuclear complex, in the solidstate well-fashioned intermolecular - and CH- interactions are observed. Thus, in the solid-state further self-assembly of already self-assembled molecular triangle is witnessed. The triangular panels are arranged in a linear ...

  9. De Novo Genome and Transcriptome Assembly of the Canadian Beaver (Castor canadensis

    Directory of Open Access Journals (Sweden)

    Si Lok

    2017-02-01

    Full Text Available The Canadian beaver (Castor canadensis is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 × long reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by short reads (80 × and checked for accuracy by congruency against an independent short read assembly. We scaffolded the assembly using the exon–gene models derived from 9805 full-length open reading frames (FL-ORFs constructed from the beaver leukocyte and muscle transcriptomes. The final assembly comprised 22,515 contigs with an N50 of 278,680 bp and an N50-scaffold of 317,558 bp. Maximum contig and scaffold lengths were 3.3 and 4.2 Mb, respectively, with a combined scaffold length representing 92% of the estimated genome size. The completeness and accuracy of the scaffold assembly was demonstrated by the precise exon placement for 91.1% of the 9805 assembled FL-ORFs and 83.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs gene set used to assess the quality of genome assemblies. Well-represented were genes involved in dentition and enamel deposition, defining characteristics of rodents with which the beaver is well-endowed. The study provides insights for genome assembly and an important genomics resource for Castoridae and rodent evolutionary biology.

  10. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds.

    Science.gov (United States)

    Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D; Nyquist, Sarah K; Hoeger, Marie; Durand, Neva C; Shamim, Muhammad S; Machol, Ido; Lander, Eric S; Aiden, Aviva Presser; Aiden, Erez Lieberman

    2017-04-07

    The Zika outbreak, spread by the Aedes aegypti mosquito, highlights the need to create high-quality assemblies of large genomes in a rapid and cost-effective way. Here we combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds. We validate this method by assembling a human genome, de novo, from short reads alone (67× coverage). We then combine our method with draft sequences to create genome assemblies of the mosquito disease vectors Ae aegypti and Culex quinquefasciatus , each consisting of three scaffolds corresponding to the three chromosomes in each species. These assemblies indicate that almost all genomic rearrangements among these species occur within, rather than between, chromosome arms. The genome assembly procedure we describe is fast, inexpensive, and accurate, and can be applied to many species. Copyright © 2017, American Association for the Advancement of Science.

  11. Microfluidic Droplet-Facilitated Hierarchical Assembly for Dual Cargo Loading and Synergistic Delivery.

    Science.gov (United States)

    Yu, Ziyi; Zheng, Yu; Parker, Richard M; Lan, Yang; Wu, Yuchao; Coulston, Roger J; Zhang, Jing; Scherman, Oren A; Abell, Chris

    2016-04-06

    Bottom-up hierarchical assembly has emerged as an elaborate and energy-efficient strategy for the fabrication of smart materials. Herein, we present a hierarchical assembly process, whereby linear amphiphilic block copolymers are self-assembled into micelles, which in turn are accommodated at the interface of microfluidic droplets via cucurbit[8]uril-mediated host-guest chemistry to form supramolecular microcapsules. The monodisperse microcapsules can be used for simultaneous carriage of both organic (Nile Red) and aqueous-soluble (fluorescein isothiocyanate-dextran) cargo. Furthermore, the well-defined compartmentalized structure benefits from the dynamic nature of the supramolecular interaction and offers synergistic delivery of cargos with triggered release or through photocontrolled porosity. This demonstration of premeditated hierarchical assembly, where interactions from the molecular to microscale are designed, illustrates the power of this route toward accessing the next generation of functional materials and encapsulation strategies.

  12. Noncanonical self-assembly of multifunctional DNA nanoflowers for biomedical applications.

    Science.gov (United States)

    Zhu, Guizhi; Hu, Rong; Zhao, Zilong; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

    2013-11-06

    DNA nanotechnology has been extensively explored to assemble various functional nanostructures for versatile applications. Mediated by Watson-Crick base-pairing, these DNA nanostructures have been conventionally assembled through hybridization of many short DNA building blocks. Here we report the noncanonical self-assembly of multifunctional DNA nanostructures, termed as nanoflowers (NFs), and the versatile biomedical applications. These NFs were assembled from long DNA building blocks generated via rolling circle replication (RCR) of a designer template. NF assembly was driven by liquid crystallization and dense packaging of building blocks, without relying on Watson-Crick base-pairing between DNA strands, thereby avoiding the otherwise conventional complicated DNA sequence design. NF sizes were readily tunable in a wide range, by simply adjusting such parameters as assembly time and template sequences. NFs were exceptionally resistant to nuclease degradation, denaturation, or dissociation at extremely low concentration, presumably resulting from the dense DNA packaging in NFs. The exceptional biostability is critical for biomedical applications. By rational design, NFs can be readily incorporated with myriad functional moieties. All these properties make NFs promising for versatile applications. As a proof-of-principle demonstration, in this study, NFs were integrated with aptamers, bioimaging agents, and drug loading sites, and the resultant multifunctional NFs were demonstrated for selective cancer cell recognition, bioimaging, and targeted anticancer drug delivery.

  13. Three invariant Hi-C interaction patterns: Applications to genome assembly.

    Science.gov (United States)

    Oddes, Sivan; Zelig, Aviv; Kaplan, Noam

    2018-06-01

    Assembly of reference-quality genomes from next-generation sequencing data is a key challenge in genomics. Recently, we and others have shown that Hi-C data can be used to address several outstanding challenges in the field of genome assembly. This principle has since been developed in academia and industry, and has been used in the assembly of several major genomes. In this paper, we explore the central principles underlying Hi-C-based assembly approaches, by quantitatively defining and characterizing three invariant Hi-C interaction patterns on which these approaches can build: Intrachromosomal interaction enrichment, distance-dependent interaction decay and local interaction smoothness. Specifically, we evaluate to what degree each invariant pattern holds on a single locus level in different species, cell types and Hi-C map resolutions. We find that these patterns are generally consistent across species and cell types but are affected by sequencing depth, and that matrix balancing improves consistency of loci with all three invariant patterns. Finally, we overview current Hi-C-based assembly approaches in light of these invariant patterns and demonstrate how local interaction smoothness can be used to easily detect scaffolding errors in extremely sparse Hi-C maps. We suggest that simultaneously considering all three invariant patterns may lead to better Hi-C-based genome assembly methods. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Optimization of beam shaping assembly based on D-T neutron generator and dose evaluation for BNCT

    Science.gov (United States)

    Naeem, Hamza; Chen, Chaobin; Zheng, Huaqing; Song, Jing

    2017-04-01

    The feasibility of developing an epithermal neutron beam for a boron neutron capture therapy (BNCT) facility based on a high intensity D-T fusion neutron generator (HINEG) and using the Monte Carlo code SuperMC (Super Monte Carlo simulation program for nuclear and radiation process) is proposed in this study. The Monte Carlo code SuperMC is used to determine and optimize the final configuration of the beam shaping assembly (BSA). The optimal BSA design in a cylindrical geometry which consists of a natural uranium sphere (14 cm) as a neutron multiplier, AlF3 and TiF3 as moderators (20 cm each), Cd (1 mm) as a thermal neutron filter, Bi (5 cm) as a gamma shield, and Pb as a reflector and collimator to guide neutrons towards the exit window. The epithermal neutron beam flux of the proposed model is 5.73 × 109 n/cm2s, and other dosimetric parameters for the BNCT reported by IAEA-TECDOC-1223 have been verified. The phantom dose analysis shows that the designed BSA is accurate, efficient and suitable for BNCT applications. Thus, the Monte Carlo code SuperMC is concluded to be capable of simulating the BSA and the dose calculation for BNCT, and high epithermal flux can be achieved using proposed BSA.

  15. A conceptual design of assembly strategy and dedicated tools for assembly of 40o sector

    International Nuclear Information System (INIS)

    Park, H.K.; Nam, K.O.; Kim, D.J.; Ahn, H.J.; Lee, J.H.; Im, K.; Shaw, R.

    2010-01-01

    The International Thermanuclear Experimental Reactor (ITER) tokamak device is composed of 9 vacuum vessel (VV)/toroidal field coils (TFCs)/vacuum vessel thermal shields (VVTS) 40 o sectors. Each VV/TFCs/VVTS 40 o sector is made up of one 40 o VV, two 20 o TFCs and associated VVTS segments. The 40 o sectors are sub-assembled at assembly hall respectively and then nine 40 o sectors sub-assembled at assembly hall are finally assembled at tokamak in-pit hall. The assembly strategy and tools for the 40 o sector sub-assembly and final assembly should be developed to satisfy the basic assembly requirements of the ITER tokamak device. Accordingly, the purpose-built assembly tools should be designed and manufactured considering assembly plan, available space, cost, safety, easy operation, efficient maintenance, and so on. The 40 o sector assembly tools are classified into 2 groups. One group is the sub-assembly tools including upending tool, lifting tool, sub-assembly tool, VV supports and bracing tools used at assembly hall and the other group is the in-pit assembly tools including lifting tool, central column, radial beams and their supports. This paper describes the current status of the assembly strategy and major tools for the VV/TFCs/VVTS 40 o sector assembly at in-pit hall and assembly hall. The conceptual design of the major assembly tools and assembly process at assembly hall and tokamak in-pit hall are presented also.

  16. De novo assembly of leaf transcriptome in the medicinal plant Andrographis paniculata

    Directory of Open Access Journals (Sweden)

    Neeraja Cherukupalli

    2016-08-01

    Full Text Available Andrographis paniculata is an important medicinal plant containing various bioactive terpenoids and flavonoids. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeqTM 2000 platform followed by the de novo transcriptome assembly. A total of 189.22 million high quality paired reads were generated and 1,70,724 transcripts were predicted in the primary assembly. Secondary assembly generated a transcriptome size of ~88 Mb with 83,800 clustered transcripts. Based on the similarity searches against plant nonredundant protein database, gene ontology and eukaryotic orthologous groups, 49,363 transcripts were annotated constituting upto 58.91% of the identified unigenes. Annotation of transcripts − using kyoto encyclopedia of genes and genomes database − revealed 5,606 transcripts plausibly involved in 140 pathways including biosynthesis of terpenoids and other secondary metabolites. Transcription factor analysis showed 6,767 unique transcripts belonging to 97 different transcription factor families. A total number of 124 CYP450 transcripts belonging to seven divergent clans have been identified. Transcriptome revealed 146 different transcripts coding for enzymes involved in the biosynthesis of terpenoids of which 35 contained terpene synthase motifs. This study also revealed 32,341 simple sequence repeats (SSRs in 23,168 transcripts. Assembled sequences of transcriptome of A.paniculata generated in this study are made available, for the first time, in the TSA database, which provides useful information for functional and comparative genomic analyses besides identification of key enzymes involved in the various pathways of secondary metabolism.

  17. De novo Assembly of Leaf Transcriptome in the Medicinal Plant Andrographis paniculata

    Science.gov (United States)

    Cherukupalli, Neeraja; Divate, Mayur; Mittapelli, Suresh R.; Khareedu, Venkateswara R.; Vudem, Dashavantha R.

    2016-01-01

    Andrographis paniculata is an important medicinal plant containing various bioactive terpenoids and flavonoids. Despite its importance in herbal medicine, no ready-to-use transcript sequence information of this plant is made available in the public data base, this study mainly deals with the sequencing of RNA from A. paniculata leaf using Illumina HiSeq™ 2000 platform followed by the de novo transcriptome assembly. A total of 189.22 million high quality paired reads were generated and 1,70,724 transcripts were predicted in the primary assembly. Secondary assembly generated a transcriptome size of ~88 Mb with 83,800 clustered transcripts. Based on the similarity searches against plant non-redundant protein database, gene ontology, and eukaryotic orthologous groups, 49,363 transcripts were annotated constituting upto 58.91% of the identified unigenes. Annotation of transcripts—using kyoto encyclopedia of genes and genomes database—revealed 5606 transcripts plausibly involved in 140 pathways including biosynthesis of terpenoids and other secondary metabolites. Transcription factor analysis showed 6767 unique transcripts belonging to 97 different transcription factor families. A total number of 124 CYP450 transcripts belonging to seven divergent clans have been identified. Transcriptome revealed 146 different transcripts coding for enzymes involved in the biosynthesis of terpenoids of which 35 contained terpene synthase motifs. This study also revealed 32,341 simple sequence repeats (SSRs) in 23,168 transcripts. Assembled sequences of transcriptome of A. paniculata generated in this study are made available, for the first time, in the TSA database, which provides useful information for functional and comparative genomic analysis besides identification of key enzymes involved in the various pathways of secondary metabolism. PMID:27582746

  18. Assembly and diploid architecture of an individual human genome via single-molecule technologies.

    Science.gov (United States)

    Pendleton, Matthew; Sebra, Robert; Pang, Andy Wing Chun; Ummat, Ajay; Franzen, Oscar; Rausch, Tobias; Stütz, Adrian M; Stedman, William; Anantharaman, Thomas; Hastie, Alex; Dai, Heng; Fritz, Markus Hsi-Yang; Cao, Han; Cohain, Ariella; Deikus, Gintaras; Durrett, Russell E; Blanchard, Scott C; Altman, Roger; Chin, Chen-Shan; Guo, Yan; Paxinos, Ellen E; Korbel, Jan O; Darnell, Robert B; McCombie, W Richard; Kwok, Pui-Yan; Mason, Christopher E; Schadt, Eric E; Bashir, Ali

    2015-08-01

    We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.

  19. Scaffold Free Bio-orthogonal Assembly of 3-Dimensional Cardiac Tissue via Cell Surface Engineering

    Science.gov (United States)

    Rogozhnikov, Dmitry; O'Brien, Paul J.; Elahipanah, Sina; Yousaf, Muhammad N.

    2016-12-01

    There has been tremendous interest in constructing in vitro cardiac tissue for a range of fundamental studies of cardiac development and disease and as a commercial system to evaluate therapeutic drug discovery prioritization and toxicity. Although there has been progress towards studying 2-dimensional cardiac function in vitro, there remain challenging obstacles to generate rapid and efficient scaffold-free 3-dimensional multiple cell type co-culture cardiac tissue models. Herein, we develop a programmed rapid self-assembly strategy to induce specific and stable cell-cell contacts among multiple cell types found in heart tissue to generate 3D tissues through cell-surface engineering based on liposome delivery and fusion to display bio-orthogonal functional groups from cell membranes. We generate, for the first time, a scaffold free and stable self assembled 3 cell line co-culture 3D cardiac tissue model by assembling cardiomyocytes, endothelial cells and cardiac fibroblast cells via a rapid inter-cell click ligation process. We compare and analyze the function of the 3D cardiac tissue chips with 2D co-culture monolayers by assessing cardiac specific markers, electromechanical cell coupling, beating rates and evaluating drug toxicity.

  20. Research on multi - channel interactive virtual assembly system for power equipment under the “VR+” era

    Science.gov (United States)

    Ren, Yilong; Duan, Xitong; Wu, Lei; He, Jin; Xu, Wu

    2017-06-01

    With the development of the “VR+” era, the traditional virtual assembly system of power equipment has been unable to satisfy our growing needs. In this paper, based on the analysis of the traditional virtual assembly system of electric power equipment and the application of VR technology in the virtual assembly system of electric power equipment in our country, this paper puts forward the scheme of establishing the virtual assembly system of power equipment: At first, we should obtain the information of power equipment, then we should using OpenGL and multi texture technology to build 3D solid graphics library. After the completion of three-dimensional modeling, we can use the dynamic link library DLL package three-dimensional solid graphics generation program to realize the modularization of power equipment model library and power equipment model library generated hidden algorithm. After the establishment of 3D power equipment model database, we set up the virtual assembly system of 3D power equipment to separate the assembly operation of the power equipment from the space. At the same time, aiming at the deficiency of the traditional gesture recognition algorithm, we propose a gesture recognition algorithm based on improved PSO algorithm for BP neural network data glove. Finally, the virtual assembly system of power equipment can really achieve multi-channel interaction function.

  1. Localization of adenovirus morphogenesis players, together with visualization of assembly intermediates and failed products, favor a model where assembly and packaging occur concurrently at the periphery of the replication center.

    Directory of Open Access Journals (Sweden)

    Gabriela N Condezo

    2017-04-01

    Full Text Available Adenovirus (AdV morphogenesis is a complex process, many aspects of which remain unclear. In particular, it is not settled where in the nucleus assembly and packaging occur, and whether these processes occur in a sequential or a concerted manner. Here we use immunofluorescence and immunoelectron microscopy (immunoEM to trace packaging factors and structural proteins at late times post infection by either wildtype virus or a delayed packaging mutant. We show that representatives of all assembly factors are present in the previously recognized peripheral replicative zone, which therefore is the AdV assembly factory. Assembly intermediates and abortive products observed in this region favor a concurrent assembly and packaging model comprising two pathways, one for capsid proteins and another one for core components. Only when both pathways are coupled by correct interaction between packaging proteins and the genome is the viral particle produced. Decoupling generates accumulation of empty capsids and unpackaged cores.

  2. Fuel injection assembly for use in turbine engines and method of assembling same

    Science.gov (United States)

    Berry, Jonathan Dwight; Johnson, Thomas Edward; York, William David; Uhm, Jong Ho

    2015-12-15

    A fuel injection assembly for use in a turbine engine is provided. The fuel injection assembly includes an end cover, an endcap assembly, a fluid supply chamber, and a plurality of tube assemblies positioned at the endcap assembly. Each of the tube assemblies includes housing having a fuel plenum and a cooling fluid plenum. The cooling fluid plenum is positioned downstream from the fuel plenum and separated from the fuel plenum by an intermediate wall. The plurality of tube assemblies also include a plurality of tubes that extends through the housing. Each of the plurality of tubes is coupled in flow communication with the fluid supply chamber and a combustion chamber positioned downstream from the tube assembly. The plurality of tube assemblies further includes an aft plate at a downstream end of the cooling fluid plenum. The plate includes at least one aperture.

  3. Flow induced vibrations in gas tube assembly of centrifuge

    International Nuclear Information System (INIS)

    Alam, M.; Atta, M.A.; Mirza, J.A.; Khan, A.Q.

    1986-01-01

    A centrifuge essentially consists of a rotor rotating at very high speed. Gas tube assembly, located at the center of the rotor, is used to introduce feed gas into the rotor and remove product and waste streams from it. The gas tube assembly is thus a static component, the product and waste scoops of which are lying in the high pressure region of a fluid rotating at very high speed. This can cause flow induced vibrations in the gas tube assembly. Such vibrations affect not only the mechanical stability of the gas tube assembly but may also reduce the separative power of the centrifuge. In a cascade, if some of the centrifuges have gas tube vibration, then cascade performance will be affected. A theoretical analysis of the effect of waste tube vibrations on product and waste flow rates and pressures in the centrifuge is presented. A simple stage consisting of two centrifuges, in which one has tube vibration, is considered for this purpose. The results are compared with experiment. It is shown that waste tube vibration generates oscillations in waste and product flow rates that are observable outside the centrifuge. (author)

  4. Orientation-controlled parallel assembly at the air–water interface

    International Nuclear Information System (INIS)

    Park, Kwang Soon; Hoo, Ji Hao; Baskaran, Rajashree; Böhringer, Karl F

    2012-01-01

    This paper presents an experimental and theoretical study with statistical analysis of a high-yield, orientation-specific fluidic self-assembly process on a preprogrammed template. We demonstrate self-assembly of thin (less than few hundred microns in thickness) parts, which is vital for many applications in miniaturized platforms but problematic for today's pick-and-place robots. The assembly proceeds row-by-row as the substrate is pulled up through an air–water interface. Experiments and analysis are presented with an emphasis on the combined effect of controlled surface waves and magnetic force. For various gap values between a magnet and Ni-patterned parts, magnetic force distributions are generated using Monte Carlo simulation and employed to predict assembly yield. An analysis of these distributions shows that a gradual decline in yield following the probability density function can be expected with degrading conditions. The experimentally determined critical magnetic force is in good agreement with a derived value from a model of competing forces acting on a part. A general set of design guidelines is also presented from the developed model and experimental data. (paper)

  5. On numerical simulation of fuel assembly bow in pressurized water reactors

    Energy Technology Data Exchange (ETDEWEB)

    Horváth, Ákos, E-mail: akoshorvath@t-online.hu [AREVA, AREVA NP GmbH, Paul-Gossen-Str. 100, 91052 Erlangen (Germany); Budapest University of Technology and Economics, Department of Aircraft and Ships, Stoczek Street 6, Building J, H-1111 Budapest (Hungary); Dressel, Bernd [AREVA, AREVA NP GmbH, Paul-Gossen-Str. 100, 91052 Erlangen (Germany)

    2013-12-15

    Highlights: • Simulation of fuel assembly bow by coupled CFD and finite element method. • Comparison of calculated and experimentally measured bow shapes. • Investigation of boundary condition effect on bow pattern of a fuel assembly row. • Highlighting importance of consideration of fluid–structure interaction. • Assessment of flow redistribution within the fuel assembly row model. - Abstract: Fuel assembly bow in pressurized water reactor cores is largely triggered by lateral hydraulic forces together with creep processes generated by neutron flux. A detailed understanding of the flow induced bow behaviour is, therefore, an important issue. The experimental feedbacks and laboratory tests on fuel assembly bow show that it is characterized to a high degree by fluid–structure interaction (FSI) effects, therefore, consideration of FSI is essential and indispensable in full comprehension of the bow mechanism. In the present study, coupled computational fluid dynamics (CFD) and finite element simulations are introduced, calculating fuel assembly deformation under different conditions as a quasi-stationary phenomenon. The aim has been, on the one hand, to develop such a simplified fuel assembly CFD model, which allows set up of fuel assembly rows without loosing its main hydraulic characteristic; on the other hand, to investigate the bow pattern of a given fuel assembly row under different boundary conditions. The former one has been achieved by comparing bow shapes obtained with different fuel assembly (spacer grid) modelling approaches and mesh resolutions with experimental data. In the second part of the paper a row model containing 7.5 fuel assemblies is introduced, investigating the effect of flow distribution at inlet and outlet boundary regions on fuel assembly bow behaviour. The post processing has been focused on the bow pattern, lateral hydraulic forces, and horizontal flow distribution. The results have revealed importance of consideration of

  6. Self-Organization and the Self-Assembling Process in Tissue Engineering

    Science.gov (United States)

    Eswaramoorthy, Rajalakshmanan; Hadidi, Pasha; Hu, Jerry C.

    2015-01-01

    In recent years, the tissue engineering paradigm has shifted to include a new and growing subfield of scaffoldless techniques which generate self-organizing and self-assembling tissues. This review aims to provide a cogent description of this relatively new research area, with special emphasis on applications toward clinical use and research models. Particular emphasis is placed on providing clear definitions of self-organization and the self-assembling process, as delineated from other scaffoldless techniques in tissue engineering and regenerative medicine. Significantly, during formation, self-organizing and self-assembling tissues display biological processes similar to those that occur in vivo. These help lead to the recapitulation of native tissue morphological structure and organization. Notably, functional properties of these tissues also approach native tissue values; some of these engineered tissues are already in clinical trials. This review aims to provide a cohesive summary of work in this field, and to highlight the potential of self-organization and the self-assembling process to provide cogent solutions to current intractable problems in tissue engineering. PMID:23701238

  7. Controlled assembly of multi-segment nanowires by histidine-tagged peptides

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Aijun A; Lee, Joun; Jenikova, Gabriela; Mulchandani, Ashok; Myung, Nosang V; Chen, Wilfred [Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521 (United States)

    2006-07-28

    A facile technique was demonstrated for the controlled assembly and alignment of multi-segment nanowires using bioengineered polypeptides. An elastin-like-polypeptide (ELP)-based biopolymer consisting of a hexahistine cluster at each end (His{sub 6}-ELP-His{sub 6}) was generated and purified by taking advantage of the reversible phase transition property of ELP. The affinity between the His{sub 6} domain of biopolymers and the nickel segment of multi-segment nickel/gold/nickel nanowires was exploited for the directed assembly of nanowires onto peptide-functionalized electrode surfaces. The presence of the ferromagnetic nickel segments on the nanowires allowed the control of directionality by an external magnetic field. Using this method, the directed assembly and positioning of multi-segment nanowires across two microfabricated nickel electrodes in a controlled manner was accomplished with the expected ohmic contact.

  8. Dynamic Self-Assembly of Homogenous Microcyclic Structures Controlled by a Silver-Coated Nanopore.

    Science.gov (United States)

    Gao, Rui; Lin, Yao; Ying, Yi-Lun; Liu, Xiao-Yuan; Shi, Xin; Hu, Yong-Xu; Long, Yi-Tao; Tian, He

    2017-07-01

    The self-assembly of nanoparticles is a challenging process for organizing precise structures with complicated and ingenious structures. In the past decades, a simple, high-efficiency, and reproducible self-assembly method from nanoscale to microscale has been pursued because of the promising and extensive application prospects in bioanalysis, catalysis, photonics, and energy storage. However, microscale self-assembly still faces big challenges including improving the stability and homogeneity as well as pursuing new assembly methods and templates for the uniform self-assembly. To address these obstacles, here, a novel silver-coated nanopore is developed which serves as a template for electrochemically generating microcyclic structures of gold nanoparticles at micrometers with highly homogenous size and remarkable reproducibility. Nanopore-induced microcyclic structures are further applied to visualize the diffusion profile of ionic flux. Based on this novel strategy, a nanopore could potentially facilitate the delivery of assembled structures for many practical applications including drug delivery, cellular detection, catalysis, and plasmonic sensing. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Assembly, alignment and test of the Transiting Exoplanet Survey Satellite (TESS) optical assemblies

    Science.gov (United States)

    Balonek, Gregory; Brown, Joshua J.; Andre, James E.; Chesbrough, Christian D.; Chrisp, Michael P.; Dalpiaz, Michael; Lennon, Joseph; Richards, B. C.; Clark, Kristin E.

    2017-08-01

    The Transiting Exoplanet Survey Satellite (TESS) will carry four visible waveband, seven-element, refractive F/1.4 lenses, each with a 34 degree diagonal field of view. This paper describes the methods used for the assembly, alignment and test of the four flight optical assemblies. Prior to commencing the build of the four flight optical assemblies, a Risk Reduction Unit (RRU) was successfully assembled and tested [1]. The lessons learned from the RRU were applied to the build of the flight assemblies. The main modifications to the flight assemblies include the inking of the third lens element stray light mitigation, tighter alignment tolerances, and diamond turning for critical mechanical surfaces. Each of the optical assemblies was tested interferometrically and measured with a low coherence distance measuring interferometer (DMI) to predict the optimal shim thickness between the lens assembly and detector before -75°C environmental testing. In addition to individual test data, environmental test results from prior assemblies allow for the exploration of marginal performance differences between each of the optical assemblies.

  10. Assembly tool design

    International Nuclear Information System (INIS)

    Kanamori, Naokazu; Nakahira, Masataka; Ohkawa, Yoshinao; Tada, Eisuke; Seki, Masahiro

    1996-06-01

    The reactor core of the International Thermonuclear Experimental Reactor (ITER) is assembled with a number of large and asymmetric components within a tight tolerance in order to assure the structural integrity for various loads and to provide the tritium confinement. In addition, the assembly procedure should be compatible with remote operation since the core structures will be activated by 14-MeV neutrons once it starts operation and thus personal access will be prohibited. Accordingly, the assembly procedure and tool design are quite essential and should be designed from the beginning to facilitate remote operation. According to the ITER Design Task Agreement, the Japan Atomic Energy Research Institute (JAERI) has performed design study to develop the assembly procedures and associated tool design for the ITER tokamak assembly. This report describes outlines of the assembly tools and the remaining issues obtained in this design study. (author)

  11. Development of the control assembly pattern and dynamic analysis of the Generation IV large gas-cooled fast reactor (GFR)

    Energy Technology Data Exchange (ETDEWEB)

    Girardin, G.

    2009-07-15

    During the past ten years, different independent factors, such as the rapidly increasing worldwide demand in energy, societal concerns about greenhouse gas emissions, and the high and volatile prices for fossil fuels, have contributed to the renewed interest in nuclear technology. In this context, the Generation IV International Forum (GIF) launched the initiative to collaborate on the research and development efforts needed for the next generation of nuclear reactors. A particular goal set for Generation IV systems is closure of the nuclear fuel cycle; they are expected to offer a better utilization of natural resources, as also a minimization of long-lived radioactive wastes. Among the systems selected by the GIF, the Gas-cooled Fast Reactor (GFR) is a highly innovative system with advanced fuel geometry and materials. The principal aim of the present research is to develop and qualify the control assembly (CA) pattern and corresponding CA implementation scheme for the 2400 MWth reference GFR design. The work has been carried out in three successive phases: (1) validation of the neutronics tools, (2) the CA pattern development and related static analysis, and (3) dynamic core behaviour studies for hypothetical CA driven transients. The deterministic code system ERANOS and its associated nuclear data libraries for fast reactors were developed and validated for sodium-cooled reactors. In order to validate ERANOS for GFR applications, a systematic reanalysis of the GFR-relevant integral data generated at PSI during the GCFR-PROTEUS experimental program of the 1970’s was undertaken. The reference PROTEUS test lattice has been analyzed with ERANOS-2.0 and its associated, adjusted nuclear data library ERALIB1. Benchmark calculations were performed with the Monte Carlo code MCNPX, allowing one to both check the deterministic results and to analyze the sensitivity to different modern data libraries. For the main reaction rate ratios, the new analysis of the GCFR

  12. Development of the control assembly pattern and dynamic analysis of the Generation IV large gas-cooled fast reactor (GFR)

    International Nuclear Information System (INIS)

    Girardin, G.

    2009-07-01

    During the past ten years, different independent factors, such as the rapidly increasing worldwide demand in energy, societal concerns about greenhouse gas emissions, and the high and volatile prices for fossil fuels, have contributed to the renewed interest in nuclear technology. In this context, the Generation IV International Forum (GIF) launched the initiative to collaborate on the research and development efforts needed for the next generation of nuclear reactors. A particular goal set for Generation IV systems is closure of the nuclear fuel cycle; they are expected to offer a better utilization of natural resources, as also a minimization of long-lived radioactive wastes. Among the systems selected by the GIF, the Gas-cooled Fast Reactor (GFR) is a highly innovative system with advanced fuel geometry and materials. The principal aim of the present research is to develop and qualify the control assembly (CA) pattern and corresponding CA implementation scheme for the 2400 MWth reference GFR design. The work has been carried out in three successive phases: (1) validation of the neutronics tools, (2) the CA pattern development and related static analysis, and (3) dynamic core behaviour studies for hypothetical CA driven transients. The deterministic code system ERANOS and its associated nuclear data libraries for fast reactors were developed and validated for sodium-cooled reactors. In order to validate ERANOS for GFR applications, a systematic reanalysis of the GFR-relevant integral data generated at PSI during the GCFR-PROTEUS experimental program of the 1970’s was undertaken. The reference PROTEUS test lattice has been analyzed with ERANOS-2.0 and its associated, adjusted nuclear data library ERALIB1. Benchmark calculations were performed with the Monte Carlo code MCNPX, allowing one to both check the deterministic results and to analyze the sensitivity to different modern data libraries. For the main reaction rate ratios, the new analysis of the GCFR

  13. Analysis of the assembling phase of lattice slabs

    Directory of Open Access Journals (Sweden)

    A. L. Sartorti

    Full Text Available Lattice slabs are usual in Brazil. They are formed by precast joists with latticed bars on a base of concrete, and a cover of concrete placed at the jobsite. The assembly of the joists and the filling elements is simple and do not require manpower with great skill, presenting low cost-benefit ratio. However, it is precisely in assembling phase that arise questions related to the scaffold support distance. A mistake in the proper positioning can lead to two undesirable situations. In one of them, a small space between the support lines increases the cost of scaffold, and in other an excessive space can generate exaggerated displacements, and even the collapse of the slab in the stage of concreting. The objective of this work is to analyze the bearing capacity of lattice joists in assembling phase, looking for information that is useful in defining the scaffold support distance. Several joists were tested to define the failure modes and their load bearing capacities. The results allowed to determine equations for calculating the appropriate distance between the support lines of the joists.

  14. Electrostatic Assembly of Nanomaterials for Hybrid Electrodes and Supercapacitors

    Science.gov (United States)

    Hammond, Paula

    2015-03-01

    Electrostatic assembly methods have been used to generate a range of new materials systems of interest for electrochemical energy and storage applications. Over the past several years, it has been demonstrated that carbon nanotubes, metals, metal oxides, polymeric nanomaterials, and biotemplated materials systems can be incorporated into ultrathin films to generate supercapacitors and battery electrodes that illustrate significant energy density and power. The unique ability to control the incorporation of such a broad range of materials at the nanometer length scale allows tailoring of the final properties of these unique composite systems, as well as the capability of creating complex micron-scale to nanoporous morphologies based on the scale of the nanomaterial that is absorbed within the structure, or the conditions of self-assembly. Recently we have expanded these capabilities to achieve new electrodes that are templated atop electrospun polmer fiber scaffolds, in which the polymer can be selectively removed to achieve highly porous materials. Spray-layer-by-layer and filtration methods of functionalized multiwall carbon nanotubes and polyaniline nanofibers enable the generation of electrode systems with unusually high surface. Incorporation of psuedocapacitive nanoparticles can enhance capacitive properties, and other catalytic or metallic nanoparticles can be implemented to enhance electrochemical or catalytic function.

  15. Drive piston assembly for a valve actuator assembly

    Science.gov (United States)

    Sun, Zongxuan

    2010-02-23

    A drive piston assembly is provided that is operable to selectively open a poppet valve. The drive piston assembly includes a cartridge defining a generally stepped bore. A drive piston is movable within the generally stepped bore and a boost sleeve is coaxially disposed with respect to the drive piston. A main fluid chamber is at least partially defined by the generally stepped bore, drive piston, and boost sleeve. First and second feedback chambers are at least partially defined by the drive piston and each are disposed at opposite ends of the drive piston. At least one of the drive piston and the boost sleeve is sufficiently configured to move within the generally stepped bore in response to fluid pressure within the main fluid chamber to selectively open the poppet valve. A valve actuator assembly and engine are also provided incorporating the disclosed drive piston assembly.

  16. Quantum-Chemical Insights into the Self-Assembly of Carbon-Based Supramolecular Complexes

    Directory of Open Access Journals (Sweden)

    Joaquín Calbo

    2018-01-01

    Full Text Available Understanding how molecular systems self-assemble to form well-organized superstructures governed by noncovalent interactions is essential in the field of supramolecular chemistry. In the nanoscience context, the self-assembly of different carbon-based nanoforms (fullerenes, carbon nanotubes and graphene with, in general, electron-donor molecular systems, has received increasing attention as a means of generating potential candidates for technological applications. In these carbon-based systems, a deep characterization of the supramolecular organization is crucial to establish an intimate relation between supramolecular structure and functionality. Detailed structural information on the self-assembly of these carbon-based nanoforms is however not always accessible from experimental techniques. In this regard, quantum chemistry has demonstrated to be key to gain a deep insight into the supramolecular organization of molecular systems of high interest. In this review, we intend to highlight the fundamental role that quantum-chemical calculations can play to understand the supramolecular self-assembly of carbon-based nanoforms through a limited selection of supramolecular assemblies involving fullerene, fullerene fragments, nanotubes and graphene with several electron-rich π-conjugated systems.

  17. Wind turbine/generator set having a stator cooling system located between stator frame and active coils

    Science.gov (United States)

    Bevington, Christopher M.; Bywaters, Garrett L.; Coleman, Clint C.; Costin, Daniel P.; Danforth, William L.; Lynch, Jonathan A.; Rolland, Robert H.

    2012-11-13

    A wind turbine comprising an electrical generator that includes a rotor assembly. A wind rotor that includes a wind rotor hub is directly coupled to the rotor assembly via a simplified connection. The wind rotor and generator rotor assembly are rotatably mounted on a central spindle via a bearing assembly. The wind rotor hub includes an opening having a diameter larger than the outside diameter of the central spindle adjacent the bearing assembly so as to allow access to the bearing assembly from a cavity inside the wind rotor hub. The spindle is attached to a turret supported by a tower. Each of the spindle, turret and tower has an interior cavity that permits personnel to traverse therethrough to the cavity of the wind rotor hub. The wind turbine further includes a frictional braking system for slowing, stopping or keeping stopped the rotation of the wind rotor and rotor assembly.

  18. The Sentinel-4 UVN focal plane assemblies

    Science.gov (United States)

    Hinger, Jürgen; Hohn, Rüdiger; Gebhardt, Eyk; Reichardt, Jörg

    2017-09-01

    The Sentinel-4 UVN Instrument is a dispersive imaging spectrometer covering the UV-VIS and the NIR wavelength. It is developed and built under an ESA contract by an industrial consortium led by Airbus Defence and Space. It will be accommodated on board of the MTG-S (Meteosat Third Generation - Sounder) satellite that will be placed in a geostationary orbit over Europe sampling data for generating two-dimensional maps of a number of atmospheric trace gases. The incoming light is dispersed by reflective gratings and detected by the two (UVVIS and NIR) CCDs mounted inside the focal plane assemblies. Both CCD detectors acquire spectral channels and spatial sampling in two orthogonal directions and will be operated at about 215 K mainly to minimize random telegraph signal effects and to reduce dark current. Stringent detector temperature as well as alignment stability requirements of less than +/-0.1 K per day respectively of less than 2 micrometers/2 arcseconds from ground to orbit are driving the FPA thermo-mechanical design. A specific FPA design feature is the redundant LED-calibration system for bad pixel detection as well as pixel gain and linearity monitoring. This paper reports on the design and qualification of the Focal Plane Assemblies with emphasis on thermo-mechanical as well as alignment stability verification.

  19. Test data generation for LRU cache-memory testing

    OpenAIRE

    Evgeni, Kornikhin

    2009-01-01

    System functional testing of microprocessors deals with many assembly programs of given behavior. The paper proposes new constraint-based algorithm of initial cache-memory contents generation for given behavior of assembly program (with cache misses and hits). Although algorithm works for any types of cache-memory, the paper describes algorithm in detail for basis types of cache-memory only: fully associative cache and direct mapped cache.

  20. Self-assembled nanostructures

    CERN Document Server

    Zhang, Jin Z; Liu, Jun; Chen, Shaowei; Liu, Gang-yu

    2003-01-01

    Nanostructures refer to materials that have relevant dimensions on the nanometer length scales and reside in the mesoscopic regime between isolated atoms and molecules in bulk matter. These materials have unique physical properties that are distinctly different from bulk materials. Self-Assembled Nanostructures provides systematic coverage of basic nanomaterials science including materials assembly and synthesis, characterization, and application. Suitable for both beginners and experts, it balances the chemistry aspects of nanomaterials with physical principles. It also highlights nanomaterial-based architectures including assembled or self-assembled systems. Filled with in-depth discussion of important applications of nano-architectures as well as potential applications ranging from physical to chemical and biological systems, Self-Assembled Nanostructures is the essential reference or text for scientists involved with nanostructures.

  1. Passive gamma analysis of the boiling-water-reactor assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Vo, D., E-mail: ducvo@lanl.gov [Los Alamos National Laboratory, Los Alamos, NM (United States); Favalli, A. [Los Alamos National Laboratory, Los Alamos, NM (United States); Grogan, B. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); Jansson, P. [Uppsala University, Uppsala (Sweden); Liljenfeldt, H. [Oak Ridge National Laboratory, Oak Ridge, TN (United States); Mozin, V. [Lawrence Livermore National Laboratory, Livermore, CA (United States); Schwalbach, P. [European Atomic Energy Community (EURATOM), Luxemburg (Luxembourg); Sjöland, A. [Swedish Nuclear Fuel and Waste Management Company, Stockholm (Sweden); Tobin, S.; Trellue, H. [Los Alamos National Laboratory, Los Alamos, NM (United States); Vaccaro, S. [European Atomic Energy Community (EURATOM), Luxemburg (Luxembourg)

    2016-09-11

    This research focused on the analysis of a set of stationary passive gamma measurements taken on the spent nuclear fuel assemblies from a boiling water reactor (BWR) using pulse height analysis data acquisition. The measurements were performed on 25 different BWR assemblies in 2014 at Sweden's Central Interim Storage Facility for Spent Nuclear Fuel (Clab). This study was performed as part of the Next Generation of Safeguards Initiative–Spent Fuel project to research the application of nondestructive assay (NDA) to spent fuel assemblies. The NGSI–SF team is working to achieve the following technical goals more easily and efficiently than in the past using nondestructive assay (NDA) measurements of spent fuel assemblies: (1) verify the initial enrichment, burnup, and cooling time of facility declaration; (2) detect the diversion or replacement of pins, (3) estimate the plutonium mass, (4) estimate the decay heat, and (5) determine the reactivity of spent fuel assemblies. The final objective of this project is to quantify the capability of several integrated NDA instruments to meet the aforementioned goals using the combined signatures of neutrons, gamma rays, and heat. This report presents a selection of the measured data and summarizes an analysis of the results. Specifically, trends in the count rates measured for spectral lines from the following isotopes were analyzed as a function of the declared burnup and cooling time: {sup 137}Cs, {sup 154}Eu, {sup 134}Cs, and to a lesser extent, {sup 106}Ru and {sup 144}Ce. From these measured count rates, predictive algorithms were developed to enable the estimation of the burnup and cooling time. Furthermore, these algorithms were benchmarked on a set of assemblies not included in the standard assemblies set used by this research team.

  2. The self-assembling process and applications in tissue engineering

    Science.gov (United States)

    Lee, Jennifer K.; Link, Jarrett M.; Hu, Jerry C. Y.; Athanasiou, Kyriacos A.

    2018-01-01

    Tissue engineering strives to create neotissues capable of restoring function. Scaffold-free technologies have emerged that can recapitulate native tissue function without the use of an exogenous scaffold. This chapter will survey, in particular, the self-assembling and self-organization processes as scaffold-free techniques. Characteristics and benefits of each process are described, and key examples of tissues created using these scaffold-free processes are examined to provide guidance for future tissue engineering developments. This chapter aims to explore the potential of self-assembly and self-organization scaffold-free approaches, detailing the recent progress in the in vitro tissue engineering of biomimetic tissues with these methods, toward generating functional tissue replacements. PMID:28348174

  3. Primary manway shielding and exhaust covers for a steam generator

    International Nuclear Information System (INIS)

    Wallace, W.R.; Immel, A.K.; Boro, I.; Lester, W.E. II.

    1990-01-01

    This paper discusses a radiation emission shielding cover in combination with a steam generator of a nuclear reactor for covering at least a portion of a manway of the steam generator for protecting an operator from radiation emission. It comprises a plate; a mounting assembly including a mounting flange for securing the mounting assembly adjacent the manway of the steam generator and a mounting bracket; a slide means mounted on the mounting bracket adjacent the manway; and guide means mounted on the plate for receiving the slide means such that the plate can be moved from an open position adjacent the manway to a closed position over at least a portion of the manway

  4. Opto-mechanical design of the MTG FCI spectral separation assembly

    Science.gov (United States)

    Riguet, François; Brousse, Emmanuel; Carel, Jean-Louis; Cottenye, Justine; Harmann, David; Joncour, Marc; Makhlouf, Houssine; Mouricaud, Daniel; Oussalah, Meihdi; Rodolfo, Jacques

    2015-09-01

    The Spectral Separation Assembly is a key component of the Flexible Combined Imager, an instrument that will be on-board Meteosat Third Generation. It splits the input beam coming from the telescope into five spectral groups, for a total of 16 channels, from 0.4 to 13.3 μm. It comprises a set of four dichroics separators followed by four collimating optics for the infrared spectral groups, which feed the cold imaging optics. The visible spectral group is directly imaged on a detector. This paper presents the optical design of the assembly, the mechanical mounting of the optical components, and the coatings developed for the dichroics, mirrors and lenses.

  5. Newnes electronics assembly handbook

    CERN Document Server

    Brindley, Keith

    2013-01-01

    Newnes Electronics Assembly Handbook: Techniques, Standards and Quality Assurance focuses on the aspects of electronic assembling. The handbook first looks at the printed circuit board (PCB). Base materials, basic mechanical properties, cleaning of assemblies, design, and PCB manufacturing processes are then explained. The text also discusses surface mounted assemblies and packaging of electromechanical assemblies, as well as the soldering process. Requirements for the soldering process; solderability and protective coatings; cleaning of PCBs; and mass solder/component reflow soldering are des

  6. Molecular self-assembly approaches for supramolecular electronic and organic electronic devices

    Science.gov (United States)

    Yip, Hin-Lap

    Molecular self-assembly represents an efficient bottom-up strategy to generate structurally well-defined aggregates of semiconducting pi-conjugated materials. The capability of tuning the chemical structures, intermolecular interactions and nanostructures through molecular engineering and novel materials processing renders it possible to tailor a large number of unprecedented properties such as charge transport, energy transfer and light harvesting. This approach does not only benefit traditional electronic devices based on bulk materials, but also generate a new research area so called "supramolecular electronics" in which electronic devices are built up with individual supramolecular nanostructures with size in the sub-hundred nanometers range. My work combined molecular self-assembly together with several novel materials processing techniques to control the nucleation and growth of organic semiconducting nanostructures from different type of pi-conjugated materials. By tailoring the interactions between the molecules using hydrogen bonds and pi-pi stacking, semiconducting nanoplatelets and nanowires with tunable sizes can be fabricated in solution. These supramolecular nanostructures were further patterned and aligned on solid substrates through printing and chemical templating methods. The capability to control the different hierarchies of organization on surface provides an important platform to study their structural-induced electronic properties. In addition to using molecular self-assembly to create different organic nanostructures, functional self-assembled monolayer (SAM) formed by spontaneous chemisorption on surfaces was used to tune the interfacial property in organic solar cells. Devices showed dramatically improved performance when appropriate SAMs were applied to optimize the contact property for efficiency charge collection.

  7. Performance of multihundred-watt fueled-sphere assemblies in the safety verification test

    International Nuclear Information System (INIS)

    Cramer, E.M.

    1975-09-01

    Seven fueled-sphere assemblies equivalent to those proposed for use in multihundred-watt thermoelectric generators were subjected to conditions that simulated the sequential environments produced by an orbital abort and earth impact. The procedures were similar to those in the Safety Sequential Test, and the assemblies differed only in minor dimensional and power level changes. All assemblies met the specifications for flight quality units. Visual examination indicated that all the iridium shells had lost their containment capability; however, rupturing of two shells was not confirmed. Five were obviously ruptured, and the fuel in three was exposed. All iridium fractures were essentially intergranular. A large grain size may have promoted this type of failure. Half of the vent assemblies failed to pass helium at ambient temperature after the test. Failure was because of nonmetallic materials in the vent frits. Release of plutonia per unit area of cracks in a containment shell ruptured by simulated earth impact was determined

  8. Information-optimal genome assembly via sparse read-overlap graphs.

    Science.gov (United States)

    Shomorony, Ilan; Kim, Samuel H; Courtade, Thomas A; Tse, David N C

    2016-09-01

    In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence? Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50. Available at github.com/samhykim/nsg courtade@eecs.berkeley.edu or dntse@stanford.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  9. A Framework for the Development of Automatic DFA Method to Minimize the Number of Components and Assembly Reorientations

    Science.gov (United States)

    Alfadhlani; Samadhi, T. M. A. Ari; Ma’ruf, Anas; Setiasyah Toha, Isa

    2018-03-01

    Assembly is a part of manufacturing processes that must be considered at the product design stage. Design for Assembly (DFA) is a method to evaluate product design in order to make it simpler, easier and quicker to assemble, so that assembly cost is reduced. This article discusses a framework for developing a computer-based DFA method. The method is expected to aid product designer to extract data, evaluate assembly process, and provide recommendation for the product design improvement. These three things are desirable to be performed without interactive process or user intervention, so product design evaluation process could be done automatically. Input for the proposed framework is a 3D solid engineering drawing. Product design evaluation is performed by: minimizing the number of components; generating assembly sequence alternatives; selecting the best assembly sequence based on the minimum number of assembly reorientations; and providing suggestion for design improvement.

  10. Self-assembly of diphenylalanine backbone homologues and their combination with functionalized carbon nanotubes.

    Science.gov (United States)

    Dinesh, Bhimareddy; Squillaci, Marco A; Ménard-Moyon, Cécilia; Samorì, Paolo; Bianco, Alberto

    2015-10-14

    The integration of carbon nanotubes (CNTs) into organized nanostructures is of great interest for applications in materials science and biomedicine. In this work we studied the self-assembly of β and γ homologues of diphenylalanine peptides under different solvent and pH conditions. We aimed to investigate the role of peptide backbone in tuning the formation of different types of nanostructures alone or in combination with carbon nanotubes. In spite of having the same side chain, β and γ peptides formed distinctively different nanofibers, a clear indication of the role played by the backbone homologation on the self-assembly. The variation of the pH allowed to transform the nanofibers into spherical structures. Moreover, the co-assembly of β and γ peptides with carbon nanotubes covalently functionalized with the same peptide generated unique dendritic assemblies. This comparative study on self-assembly using diphenylalanine backbone homologues and of the co-assembly with CNT covalent conjugates is the first example exploring the capacity of β and γ peptides to adopt precise nanostructures, particularly in combination with carbon nanotubes. The dendritic organization obtained by mixing carbon nanotubes and peptides might find interesting applications in tissue engineering and neuronal interfacing.

  11. Thermohydraulic analysis of BWR and PWR spent fuel assemblies contained within square canisters

    International Nuclear Information System (INIS)

    Wiles, L.E.; McCann, R.A.

    1981-09-01

    This report presents the results of several thermohydraulic simulations of spent fuel assembly/canister configurations performed in support of a program investigating the feasibility of storing spent nuclear fuel assemblies in canisters that would be stored in an air environment. Eleven thermohydraulic simulations were performed. Five simulations were performed using a single BWR fuel assembly/canister design. The various cases were defined by changing the canister spacing and the heat generation rate of the fuel assembly. For each simulation a steady-state thermohydraulic solution was achieved for the region inside the canister. Similarly, six simulations were performed for a single PWR fuel assembly/canister design. The square fuel rod arrays were contained in square canisters which would permit closer packing of the canisters in a storage facility. However, closer packing of the canisters would result in higher fuel temperatures which would possibly have an adverse impact on fuel integrity. Thus, the most important aspect of the analysis was to define the peak fuel assembly temperatures for each case. These results are presented along with various temperature profiles, heat flux distributions, and air velocity profiles within the canister. 48 figures, 4 tables

  12. Fuel Assembly Damping Summary

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kanghee; Kang, Heungseok; Oh, Dongseok; Yoon, Kyungho; Kim, Hyungkyu; Kim, Jaeyong [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-10-15

    This paper summary the fuel assembly damping data in air/in still water/under flow, released from foreign fuel vendors, compared our data with the published data. Some technical issues in fuel assembly damping measurement testing are also briefly discussed. Understanding of each fuel assembly damping mechanisms according to the surrounding medium and flow velocity can support the fuel design improvement in fuel assembly dynamics and structural integrity aspect. Because the upgraded requirements of the newly-developed advanced reactor system will demands to minimize fuel design margin in integrity evaluation, reduction in conservatism of fuel assembly damping can contribute to alleviate the fuel design margin for sure. Damping is an energy dissipation mechanism in a vibrating mechanical structure and prevents a resonant structure from having infinite vibration amplitudes. The sources of fuel assembly damping are various from support friction to flow contribution, and it can be increased by the viscosity or drag of surrounding fluid medium or the average velocity of water flowing. Fuel licensing requires fuel design evaluation in transient or accidental condition. Dynamic response analysis of fuel assembly is to show fuel integrity and requires information on assembly-wise damping in dry condition and under wet or water flowing condition. However, damping measurement test for the full-scale fuel assembly prototype is not easy to carry out because of the scale (fuel prototype, test facility), unsteadiness of test data (scattering, random sampling and processing), instrumentation under water flowing (water-proof response measurement), and noise. LWR fuel technology division in KAERI is preparing the infra structure for damping measurement test of full-scale fuel assembly, to support fuel industries and related research activities. Here is a preliminary summary of fuel assembly damping, published in the literature. Some technical issues in fuel assembly damping

  13. Table-top deterministic and collective colloidal assembly using videoprojector lithography

    International Nuclear Information System (INIS)

    Cordeiro, J.; Zelsmann, M.; Honegger, T.; Picard, E.; Hadji, E.; Peyrade, D.

    2015-01-01

    Graphical abstract: - Highlights: • Micrometric resolution substrates are made at low cost using a videoprojector. • Fabricated patterns could be used as substrates for capillary force assembly. • Arrays of organized particles are made using a table-top capillary assembly tool. • This process offers a new bridge between the colloidal domain and the chip world. - Abstract: In the field of micro- and nanotechnology, most lithography and fabrication tools coming from the microelectronic industry are expensive, time-consuming and may need some masks that have to be subcontracted. Such approach is not suitable for other fields that require rapid prototyping such as chemistry, life science or energy and may hinder research creativity. In this work, we present two table-top equipments dedicated to the fabrication of deterministic colloidal particles assemblies onto micro-structured substrates. We show that, with a limited modification of the optics of a standard videoprojector, it is possible to quickly obtain substrates with thousands of micrometric features. Then, we combine these substrates with thermodynamic colloidal assembly and generate arrays of particles without defects. This work opens the way to a simple and table-top fabrication of devices based on colloidal particles

  14. Mind the gap; seven reasons to close fragmented genome assemblies.

    Science.gov (United States)

    Thomma, Bart P H J; Seidl, Michael F; Shi-Kunne, Xiaoqian; Cook, David E; Bolton, Melvin D; van Kan, Jan A L; Faino, Luigi

    2016-05-01

    Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Table-top deterministic and collective colloidal assembly using videoprojector lithography

    Energy Technology Data Exchange (ETDEWEB)

    Cordeiro, J. [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France); Zelsmann, M., E-mail: marc.zelsmann@cea.fr [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France); Honegger, T. [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France); Picard, E.; Hadji, E. [Univ Grenoble Alpes, F-38000 Grenoble (France); CEA, INAC-SP2M, F-38000 Grenoble (France); Peyrade, D. [Univ Grenoble Alpes, F-38000 Grenoble (France); CNRS, LTM, F-38000 Grenoble (France); CEA, LETI, MINATEC Campus, F-38000 Grenoble (France)

    2015-09-15

    Graphical abstract: - Highlights: • Micrometric resolution substrates are made at low cost using a videoprojector. • Fabricated patterns could be used as substrates for capillary force assembly. • Arrays of organized particles are made using a table-top capillary assembly tool. • This process offers a new bridge between the colloidal domain and the chip world. - Abstract: In the field of micro- and nanotechnology, most lithography and fabrication tools coming from the microelectronic industry are expensive, time-consuming and may need some masks that have to be subcontracted. Such approach is not suitable for other fields that require rapid prototyping such as chemistry, life science or energy and may hinder research creativity. In this work, we present two table-top equipments dedicated to the fabrication of deterministic colloidal particles assemblies onto micro-structured substrates. We show that, with a limited modification of the optics of a standard videoprojector, it is possible to quickly obtain substrates with thousands of micrometric features. Then, we combine these substrates with thermodynamic colloidal assembly and generate arrays of particles without defects. This work opens the way to a simple and table-top fabrication of devices based on colloidal particles.

  16. Tunable and rapid self-assembly of block copolymers using mixed solvent vapors.

    Science.gov (United States)

    Park, Woon Ik; Tong, Sheng; Liu, Yuzi; Jung, Il Woong; Roelofs, Andreas; Hong, Seungbum

    2014-12-21

    Pattern generation of well-controlled block copolymers (BCPs) with a high Flory-Huggins interaction parameter (χ) is important for applications in sub-20 nm nanolithography. We used mixed solvents of dimethylformamide (DMF) and toluene to control the morphology as well as the time to achieve the targeted morphology via self-assembly of BCPs. By precisely controlling the volume ratio of DMF and toluene, well-ordered line, honeycomb, circular hole, and lamellar nanostructures were obtained from a cylinder-forming poly(styrene-b-2-vinylpyridine) (PS-b-P2VP) BCP with high χ. Furthermore, a well-aligned 12 nm line pattern was successfully achieved in the guiding template within one minute using the mixed solvents. This practical method may also be applicable to self-assembly of other BCPs, providing more opportunities for the next-generation sub-10 nm lithography applications.

  17. Fuel assembly

    International Nuclear Information System (INIS)

    Abe, Hideaki; Sakai, Takao; Ishida, Tomio; Yokota, Norikatsu.

    1992-01-01

    The lower ends of a plurality of plate-like shape memory alloys are secured at the periphery of the upper inside of the handling head of a fuel assembly. As the shape memory alloy, a Cu-Zn alloy, a Ti-Pd alloy or a Fe-Ni alloy is used. When high temperature coolants flow out to the handling head, the shape memory alloy deforms by warping to the outer side more greatly toward the upper portion thereof with the temperature increase of the coolants. As the result, the shape of the flow channel of the coolants is changed so as to enlarge at the exit of the upper end of the fuel assembly. Then, the pressure loss of the coolants in the fuel assembly is decreased by the enlargement. Accordingly, the flow rate of the coolants in the fuel assembly is increased to lower the temperature of the coolants. Further, high temperature coolants and low temperature coolants are mixed sufficiently just above the fuel assembly. This can suppress the temperature fluctuation of the mixed coolants in the upper portion of the reactor core, thereby enabling to decrease a fatigue and failures of the structural components in the upper portion of the reactor core. (I.N.)

  18. Soldering in electronics assembly

    CERN Document Server

    Judd, Mike

    2013-01-01

    Soldering in Electronics Assembly discusses several concerns in soldering of electronic assemblies. The book is comprised of nine chapters that tackle different areas in electronic assembly soldering. Chapter 1 discusses the soldering process itself, while Chapter 2 covers the electronic assemblies. Chapter 3 talks about solders and Chapter 4 deals with flux. The text also tackles the CS and SC soldering process. The cleaning of soldered assemblies, solder quality, and standards and specifications are also discussed. The book will be of great use to professionals who deal with electronic assem

  19. Optimization of the beam shaping assembly in the D-D neutron generators-based BNCT using the response matrix method.

    Science.gov (United States)

    Kasesaz, Y; Khalafi, H; Rahmani, F

    2013-12-01

    Optimization of the Beam Shaping Assembly (BSA) has been performed using the MCNP4C Monte Carlo code to shape the 2.45 MeV neutrons that are produced in the D-D neutron generator. Optimal design of the BSA has been chosen by considering in-air figures of merit (FOM) which consists of 70 cm Fluental as a moderator, 30 cm Pb as a reflector, 2mm (6)Li as a thermal neutron filter and 2mm Pb as a gamma filter. The neutron beam can be evaluated by in-phantom parameters, from which therapeutic gain can be derived. Direct evaluation of both set of FOMs (in-air and in-phantom) is very time consuming. In this paper a Response Matrix (RM) method has been suggested to reduce the computing time. This method is based on considering the neutron spectrum at the beam exit and calculating contribution of various dose components in phantom to calculate the Response Matrix. Results show good agreement between direct calculation and the RM method. Copyright © 2013 Elsevier Ltd. All rights reserved.

  20. Multivalent protein assembly using monovalent self-assembling building blocks

    NARCIS (Netherlands)

    Petkau - Milroy, K.; Sonntag, M.H.; Colditz, A.; Brunsveld, L.

    2013-01-01

    Discotic molecules, which self-assemble in water into columnar supramolecular polymers, emerged as an alternative platform for the organization of proteins. Here, a monovalent discotic decorated with one single biotin was synthesized to study the self-assembling multivalency of this system in regard

  1. Bearing assemblies, apparatuses, and motor assemblies using the same

    Science.gov (United States)

    Sexton, Timothy N.; Cooley, Craig H.; Knuteson, Cody W.

    2015-12-29

    Various embodiments of the invention relate to bearing assemblies, apparatuses and motor assemblies that include geometric features configured to impart a selected amount of heat transfer and/or hydrodynamic film formation. In an embodiment, a bearing assembly may include a plurality of superhard bearing pads distributed circumferentially about an axis. At least some of the plurality of superhard bearing pads may include a plurality of sub-superhard bearing elements defining a bearing surface. At least some of the plurality of sub-superhard bearing elements may be spaced from one another by one or more voids to impart a selected amount of heat transfer and hydrodynamic film formation thereon during operation. The bearing assembly may also include a support ring that carries the plurality of superhard bearing pads. In addition, at least a portion of the sub-superhard bearing elements may extend beyond the support ring.

  2. Fuel assembly

    International Nuclear Information System (INIS)

    Gjertsen, R.K.; Bassler, E.A.; Huckestein, E.A.; Salton, R.B.; Tower, S.N.

    1988-01-01

    A fuel assembly adapted for use with a pressurized water nuclear reactor having capabilities for fluid moderator spectral shift control is described comprising: parallel arranged elongated nuclear fuel elements; means for providing for axial support of the fuel elements and for arranging the fuel elements in a spaced array; thimbles interspersed among the fuel elements adapted for insertion of a rod control cluster therewithin; means for structurally joining the fuel elements and the guide thimbles; fluid moderator control means for providing a volume of low neutron absorbing fluid within the fuel assembly and for removing a substantially equivalent volume of reactor coolant water therefrom, a first flow manifold at one end of the fuel assembly sealingly connected to a first end of the moderator control tubes whereby the first ends are commonly flow connected; and a second flow manifold, having an inlet passage and an outlet passage therein, sealingly connected to a second end of the moderator control tubes at a second end of the fuel assembly

  3. Self assembly of organic nanostructures and dielectrophoretic assembly of inorganic nanowires.

    Science.gov (United States)

    Dholakia, Geetha; Kuo, Steven; Allen, E. L.

    2007-03-01

    Self assembly techniques enable the organization of organic molecules into nanostructures. Currently engineering strategies for efficient assembly and routine integration of inorganic nanoscale objects into functional devices is very limited. AC Dielectrophoresis is an efficient technique to manipulate inorganic nanomaterials into higher dimensional structures. We used an alumina template based sol-gel synthesis method for the growth of various metal oxide nanowires with typical diameters of 100-150 nm, ranging in length from 3-10 μm. Here we report the dielectrophoretic assembly of TiO2 nanowires, an important material for photocatalysis and photovoltaics, onto interdigitated devices. Self assembly in organic nanostructures and its dependence on structure and stereochemistry of the molecule and dielectrophoretic field dependence in the assembly of inorganic nanowires will be compared and contrasted. Tunneling spectroscopy and DOS of these nanoscale systems will also be discussed.

  4. De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes

    Science.gov (United States)

    2012-01-01

    Background Molecular breeding of pepper (Capsicum spp.) can be accelerated by developing DNA markers associated with transcriptomes in breeding germplasm. Before the advent of next generation sequencing (NGS) technologies, the majority of sequencing data were generated by the Sanger sequencing method. By leveraging Sanger EST data, we have generated a wealth of genetic information for pepper including thousands of SNPs and Single Position Polymorphic (SPP) markers. To complement and enhance these resources, we applied NGS to three pepper genotypes: Maor, Early Jalapeño and Criollo de Morelos-334 (CM334) to identify SNPs and SSRs in the assembly of these three genotypes. Results Two pepper transcriptome assemblies were developed with different purposes. The first reference sequence, assembled by CAP3 software, comprises 31,196 contigs from >125,000 Sanger-EST sequences that were mainly derived from a Korean F1-hybrid line, Bukang. Overlapping probes were designed for 30,815 unigenes to construct a pepper Affymetrix GeneChip® microarray for whole genome analyses. In addition, custom Python scripts were used to identify 4,236 SNPs in contigs of the assembly. A total of 2,489 simple sequence repeats (SSRs) were identified from the assembly, and primers were designed for the SSRs. Annotation of contigs using Blast2GO software resulted in information for 60% of the unigenes in the assembly. The second transcriptome assembly was constructed from more than 200 million Illumina Genome Analyzer II reads (80–120 nt) using a combination of Velvet, CLC workbench and CAP3 software packages. BWA, SAMtools and in-house Perl scripts were used to identify SNPs among three pepper genotypes. The SNPs were filtered to be at least 50 bp from any intron-exon junctions as well as flanking SNPs. More than 22,000 high-quality putative SNPs were identified. Using the MISA software, 10,398 SSR markers were also identified within the Illumina transcriptome assembly and primers were

  5. Advances in the design and higher-order assembly of collagen mimetic peptides for regenerative medicine.

    Science.gov (United States)

    Strauss, Kevin; Chmielewski, Jean

    2017-08-01

    Regenerative medicine makes use of cell-supporting biomaterials to replace lost or damaged tissue. Collagen holds great potential in this regard caused by its biocompatibility and structural versatility. While natural collagen has shown promise for regenerative medicine, collagen mimetic peptides (CMPs) have emerged that allow far higher degrees of customization and ease of preparation. A wide range of two and three-dimensional assemblies have been generated from CMPs, many of which accommodate cellular adhesion and encapsulation, through careful sequence design and the exploitation of electrostatic and hydrophobic forces. But the methodology that has generated the greatest plethora of viable biomaterials is metal-promoted assembly of CMP triple helices-a rapid process that occurs under physiological conditions. Architectures generated in this manner promote cell growth, enable directed attachment of bioactive cargo, and produce living tissue. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Tabulation of Fundamental Assembly Heat and Radiation Source Files

    International Nuclear Information System (INIS)

    T. deBues; J.C. Ryman

    2006-01-01

    The purpose of this calculation is to tabulate a set of computer files for use as input to the WPLOAD thermal loading software. These files contain details regarding heat and radiation from pressurized water reactor (PWR) assemblies and boiling water reactor (BWR) assemblies. The scope of this calculation is limited to rearranging and reducing the existing file information into a more streamlined set of tables for use as input to WPLOAD. The electronic source term files used as input to this calculation were generated from the output files of the SAS2H/ORIGIN-S sequence of the SCALE Version 4.3 modular code system, as documented in References 2.1.1 and 2.1.2, and are included in Attachment II

  7. Fire resistant PV shingle assembly

    Science.gov (United States)

    Lenox, Carl J.

    2012-10-02

    A fire resistant PV shingle assembly includes a PV assembly, including PV body, a fire shield and a connection member connecting the fire shield below the PV body, and a support and inter-engagement assembly. The support and inter-engagement assembly is mounted to the PV assembly and comprises a vertical support element, supporting the PV assembly above a support surface, an upper interlock element, positioned towards the upper PV edge, and a lower interlock element, positioned towards the lower PV edge. The upper interlock element of one PV shingle assembly is inter-engageable with the lower interlock element of an adjacent PV shingle assembly. In some embodiments the PV shingle assembly may comprise a ventilation path below the PV body. The PV body may be slidably mounted to the connection member to facilitate removal of the PV body.

  8. A puzzle assembly strategy for fabrication of large engineered cartilage tissue constructs.

    Science.gov (United States)

    Nover, Adam B; Jones, Brian K; Yu, William T; Donovan, Daniel S; Podolnick, Jeremy D; Cook, James L; Ateshian, Gerard A; Hung, Clark T

    2016-03-21

    Engineering of large articular cartilage tissue constructs remains a challenge as tissue growth is limited by nutrient diffusion. Here, a novel strategy is investigated, generating large constructs through the assembly of individually cultured, interlocking, smaller puzzle-shaped subunits. These constructs can be engineered consistently with more desirable mechanical and biochemical properties than larger constructs (~4-fold greater Young׳s modulus). A failure testing technique was developed to evaluate the physiologic functionality of constructs, which were cultured as individual subunits for 28 days, then assembled and cultured for an additional 21-35 days. Assembled puzzle constructs withstood large deformations (40-50% compressive strain) prior to failure. Their ability to withstand physiologic loads may be enhanced by increases in subunit strength and assembled culture time. A nude mouse model was utilized to show biocompatibility and fusion of assembled puzzle pieces in vivo. Overall, the technique offers a novel, effective approach to scaling up engineered tissues and may be combined with other techniques and/or applied to the engineering of other tissues. Future studies will aim to optimize this system in an effort to engineer and integrate robust subunits to fill large defects. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Tailoring the self-assembly of linear alkyl chains for the design of advanced materials with technological applications.

    Science.gov (United States)

    Hoppe, Cristina E; Williams, Roberto J J

    2018-03-01

    The self-assembly of n-alkyl chains at the bulk or at the interface of different types of materials and substrates has been extensively studied in the past. The packing of alkyl chains is driven by Van der Waals interactions and can generate crystalline or disordered domains, at the bulk of the material, or self-assembled monolayers at an interface. This natural property of alkyl chains has been employed in recent years to develop a new generation of materials for technological applications. These studies are dispersed in a variety of journals. The purpose of this article was to discuss some selected examples where these advanced properties arise from a process involving the self-assembly of alkyl chains. We included a description of electronic devices and new-generation catalysts with properties derived from a controlled two-dimensional (2D) or three-dimensional (3D) self-assembly of alkyl chains at an interface. Then, we showed that controlling the crystallization of alkyl chains at the bulk can be used to generate a variety of advanced materials such as superhydrophobic coatings, shape memory hydrogels, hot-melt adhesives, thermally reversible light scattering (TRLS) films for intelligent windows and form-stable phase change materials (FS-PCMs) for the storage of thermal energy. Finally, we discussed two examples where advanced properties derive from the formation of disordered domains by physical association of alkyl chains. This was the case of photoluminescent nanocomposites and materials used for reversible optical storage. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Nuclear reactor fuel assembly

    International Nuclear Information System (INIS)

    Marmonier, Pierre; Mesnage, Bernard; Nervi, J.C.

    1975-01-01

    This invention refers to fuel assemblies for a liquid metal cooled fast neutron reactor. Each assembly is composed of a hollow vertical casing, of regular polygonal section, containing a bundle of clad pins filled with a fissile or fertile substance. The casing is open at its upper end and has a cylindrical foot at its lower end for positioning the assembly in a housing provided in the horizontal diagrid, on which the core assembly rests. A set of flat bars located on the external surface of the casing enables it to be correctly orientated in its housing among the other core assemblies [fr

  11. Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass

    Directory of Open Access Journals (Sweden)

    Kevin L. Childs

    2014-07-01

    Full Text Available Switchgrass is a North American perennial prairie species that has been used as a rangeland and forage crop and has recently been targeted as a potential biofuel feedstock species. Switchgrass, which occurs as tetraploid and octoploid forms, is classified into lowland or upland ecotypes that differ in growth phenotypes and adaptation to distinct habitats. Using RNA-sequencing (RNA-seq reads derived from crown, young shoot, and leaf tissues, we generated sequence data from seven switchgrass cultivars, three lowland and four upland, to enable comparative analyses between switchgrass cultivars and to identify single nucleotide polymorphisms (SNPs for use in breeding and genetic analysis. We also generated individual transcript assemblies for each of the cultivars. Transcript data indicate that subgenomes of octoploid switchgrass are not substantially different from subgenomes of tetraploids as expected for an autopolyploid origin of switchgrass octoploids. Using RNA-seq reads aligned to the switchgrass Release 0 AP13 reference genome, we identified 1,305,976 high-confidence SNPs. Of these SNPs, 438,464 were unique to lowland cultivars, but only 12,002 were found in all lowlands. Conversely, 723,678 SNPs were unique to upland cultivars, with only 34,665 observed in all uplands. Comparison of our high-confidence transcriptome-derived SNPs with SNPs previously identified in a genotyping-by-sequencing (GBS study of an association panel revealed limited overlap between the two methods, highlighting the utility of transcriptome-based SNP discovery in augmenting genome diversity polymorphism datasets. The transcript and SNP data described here provide a useful resource for switchgrass gene annotation and marker-based analyses of the switchgrass genome.

  12. A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.

    Science.gov (United States)

    Melicher, Dacotah; Torson, Alex S; Dworkin, Ian; Bowsher, Julia H

    2014-03-12

    The Sepsidae family of flies is a model for investigating how sexual selection shapes courtship and sexual dimorphism in a comparative framework. However, like many non-model systems, there are few molecular resources available. Large-scale sequencing and assembly have not been performed in any sepsid, and the lack of a closely related genome makes investigation of gene expression challenging. Our goal was to develop an automated pipeline for de novo transcriptome assembly, and to use that pipeline to assemble and analyze the transcriptome of the sepsid Themira biloba. Our bioinformatics pipeline uses cloud computing services to assemble and analyze the transcriptome with off-site data management, processing, and backup. It uses a multiple k-mer length approach combined with a second meta-assembly to extend transcripts and recover more bases of transcript sequences than standard single k-mer assembly. We used 454 sequencing to generate 1.48 million reads from cDNA generated from embryo, larva, and pupae of T. biloba and assembled a transcriptome consisting of 24,495 contigs. Annotation identified 16,705 transcripts, including those involved in embryogenesis and limb patterning. We assembled transcriptomes from an additional three non-model organisms to demonstrate that our pipeline assembled a higher-quality transcriptome than single k-mer approaches across multiple species. The pipeline we have developed for assembly and analysis increases contig length, recovers unique transcripts, and assembles more base pairs than other methods through the use of a meta-assembly. The T. biloba transcriptome is a critical resource for performing large-scale RNA-Seq investigations of gene expression patterns, and is the first transcriptome sequenced in this Dipteran family.

  13. Accomplishments in Field Period Assembly for NCSX. This is how we did it

    International Nuclear Information System (INIS)

    Viola, Michael; Edwards, J.; Brown, T.; Dudek, L.; Ellis, R.; Heitzenroeder, P.; Strykowsky, R.; Cole, Michael

    2009-01-01

    The National Compact Stellarator Experiment (NCSX) was a collaborative effort between ORNL and PPPL. PPPL provided the assembly techniques with guidance from ORNL to meet design criteria. The individual vacuum vessel segments, modular coils, trim coils, and toroidal field coils components were delivered to the Field Period Assembly (FPA) crew who then would complete the component assemblies and then assemble the final three field period assemblies, each consisting of two sets of three modular coils assembled over a 120o vacuum vessel segment with the trim coils and toroidal field coils providing the outer layer. The requirements for positioning the modular coils were found to be most demanding. The assembly tolerances required for accurate positioning of the field coil windings in order to generate sufficiently accurate magnetic fields strained state of the art techniques in metrology and alignment and required constant monitoring of assembly steps with laser trackers, measurement arms, and photogrammetry. The FPA activities were being performed concurrently while engineering challenges were being resolved. For example, it was determined that high friction electrically isolated shims were needed between the modular coil interface joints and low distortion welding was required in the nose region of those joints. This took months of analysis and development yet the assembly was not significantly impacted because other assembly tasks could be performed in parallel with ongoing assembly tasks as well as tasks such as advance tooling setup preparation for the eventual welding tasks. The crew technicians developed unique, accurate time saving techniques and tooling which provided significant cost and schedule savings. Project management displayed extraordinary foresight and every opportunity to gain advanced knowledge and develop techniques was taken advantage of. Despite many risk concerns, the cost and schedule performance index was maintained nearly 1.0 during the

  14. Heat evaluation examination of fuel assembly

    International Nuclear Information System (INIS)

    Suto, Shinya; Nakabayashi, Hiroki; Yao, Kaoru

    2007-03-01

    The cooling examination was executed by using the simulated fuel assembly to obtain the basic data of the most effective cooling system in the lazer disassembling process of the spent fuel assembly of prototype fast breeder reactor 'Monju'. As a result, the following have been understood. (1) Before the laser disassembling (there is not any duct tube cutting), it is possible to cool enough by the amount of the wind of 20m 3 /h or more flowing from the handling head side. (2) After the laser disassembling begins (duct tube is cut), 1kW or more of the heat generation cannot be cooled by ventilation from the handling head side. (3) Cooling by the flow across fuel pin is required during lazer disassembling. The basic data of the cooling system was obtained from these examination results. However, for cooling across fuel pin during the laser disassembling, it is necessary to examine shape of the side cooling nozzle, spraying angle, and flow velocity at the nozzle exit, etc. enough. (author)

  15. Self assembly of rectangular shapes on concentration programming and probabilistic tile assembly models.

    Science.gov (United States)

    Kundeti, Vamsi; Rajasekaran, Sanguthevar

    2012-06-01

    Efficient tile sets for self assembling rectilinear shapes is of critical importance in algorithmic self assembly. A lower bound on the tile complexity of any deterministic self assembly system for an n × n square is [Formula: see text] (inferred from the Kolmogrov complexity). Deterministic self assembly systems with an optimal tile complexity have been designed for squares and related shapes in the past. However designing [Formula: see text] unique tiles specific to a shape is still an intensive task in the laboratory. On the other hand copies of a tile can be made rapidly using PCR (polymerase chain reaction) experiments. This led to the study of self assembly on tile concentration programming models. We present two major results in this paper on the concentration programming model. First we show how to self assemble rectangles with a fixed aspect ratio ( α:β ), with high probability, using Θ( α + β ) tiles. This result is much stronger than the existing results by Kao et al. (Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008) and Doty (Randomized self-assembly for exact shapes. In: proceedings of the 50th annual IEEE symposium on foundations of computer science (FOCS), IEEE, Atlanta. pp 85-94, 2009)-which can only self assembly squares and rely on tiles which perform binary arithmetic. On the other hand, our result is based on a technique called staircase sampling . This technique eliminates the need for sub-tiles which perform binary arithmetic, reduces the constant in the asymptotic bound, and eliminates the need for approximate frames (Kao et al. Randomized self-assembly for approximate shapes, LNCS, vol 5125. Springer, Heidelberg, 2008). Our second result applies staircase sampling on the equimolar concentration programming model (The tile complexity of linear assemblies. In: proceedings of the 36th international colloquium automata, languages and programming: Part I on ICALP '09, Springer-Verlag, pp 235

  16. Assembling large, complex environmental metagenomes

    Energy Technology Data Exchange (ETDEWEB)

    Howe, A. C. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Jansson, J. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Malfatti, S. A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tringe, S. G. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Tiedje, J. M. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Plant Soil and Microbial Sciences; Brown, C. T. [Michigan State Univ., East Lansing, MI (United States). Microbiology and Molecular Genetics, Computer Science and Engineering

    2012-12-28

    The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more computationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.

  17. Substantiation of vibration strength of nuclear reactor and steam generator internals. Main problems

    International Nuclear Information System (INIS)

    Fyodorov, V.G.; Sinyavasky, V.F.

    1977-01-01

    The report details the scope and priority of studies necessary for substantiation of vibration strength of steam generator tube bundles and reactor fuel assemblies, and design modifications helping to reduce flow-induced vibration of the internals specified. Steam generator tube bundles are studied on the basis of a standard establishing vibration requirements at various stages of design, manufacture and operation of a steam generator at a nuclear power station. The main vibration characteristics of tubes obtained through model and full-scale tests are compared with calculation results. Results are provided concerning test-stand vibration tests of fuel elements and fuel assemblies. (author)

  18. Filtration of Carbon Particulate Emissions from a Plasma Pyrolysis Assembly

    Science.gov (United States)

    Agui, Juan H.; Green, Robert; Vijayakumar, R.; Berger, Gordon; Greenwood, Zach; Abney, Morgan; Peterson, Elspeth

    2016-01-01

    NASA is investigating plasma pyrolysis as a candidate technology that will enable the recovery of hydrogen from the methane produced by the ISS Sabatier Reactor. The Plasma Pyrolysis Assembly (PPA) is the current prototype of this technology which converts the methane product from the Carbon Dioxide Reduction Assembly (CRA) to acetylene and hydrogen with 90% or greater conversion efficiency. A small amount of solid carbon particulates are generated as a side product and must be filtered before the acetylene is removed and the hydrogen-rich gas stream is recycled back to the CRA. We discuss developmental work on several options for filtering out the carbon particulate emissions from the PPA exit gas stream. The filtration technologies and concepts investigated range from fibrous media to monolithic ceramic and sintered metal media. This paper describes the different developed filter prototypes and characterizes their performance from integrated testing at the Environmental Chamber (E-Chamber) at MSFC. In addition, characterization data on the generated carbon particulates, that help to define filter requirements, are also presented.

  19. Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

    Directory of Open Access Journals (Sweden)

    Duan Jialei

    2012-08-01

    Full Text Available Abstract Background Rapid advances in next-generation sequencing methods have provided new opportunities for transcriptome sequencing (RNA-Seq. The unprecedented sequencing depth provided by RNA-Seq makes it a powerful and cost-efficient method for transcriptome study, and it has been widely used in model organisms and non-model organisms to identify and quantify RNA. For non-model organisms lacking well-defined genomes, de novo assembly is typically required for downstream RNA-Seq analyses, including SNP discovery and identification of genes differentially expressed by phenotypes. Although RNA-Seq has been successfully used to sequence many non-model organisms, the results of de novo assembly from short reads can still be improved by using recent bioinformatic developments. Results In this study, we used 212.6 million pair-end reads, which accounted for 16.2 Gb, to assemble the hexaploid wheat transcriptome. Two state-of-the-art assemblers, Trinity and Trans-ABySS, which use the single and multiple k-mer methods, respectively, were used, and the whole de novo assembly process was divided into the following four steps: pre-assembly, merging different samples, removal of redundancy and scaffolding. We documented every detail of these steps and how these steps influenced assembly performance to gain insight into transcriptome assembly from short reads. After optimization, the assembled transcripts were comparable to Sanger-derived ESTs in terms of both continuity and accuracy. We also provided considerable new wheat transcript data to the community. Conclusions It is feasible to assemble the hexaploid wheat transcriptome from short reads. Special attention should be paid to dealing with multiple samples to balance the spectrum of expression levels and redundancy. To obtain an accurate overview of RNA profiling, removal of redundancy may be crucial in de novo assembly.

  20. A peptide extension dictates IgM assembly.

    Science.gov (United States)

    Pasalic, Dzana; Weber, Benedikt; Giannone, Chiara; Anelli, Tiziana; Müller, Roger; Fagioli, Claudio; Felkl, Manuel; John, Christine; Mossuto, Maria Francesca; Becker, Christian F W; Sitia, Roberto; Buchner, Johannes

    2017-10-10

    Professional secretory cells can produce large amounts of high-quality complex molecules, including IgM antibodies. Owing to their multivalency, polymeric IgM antibodies provide an efficient first-line of defense against pathogens. To decipher the mechanisms of IgM assembly, we investigated its biosynthesis in living cells and faithfully reconstituted the underlying processes in vitro. We find that a conserved peptide extension at the C-terminal end of the IgM heavy (Ig-μ) chains, termed the tailpiece, is necessary and sufficient to establish the correct geometry. Alanine scanning revealed that hydrophobic amino acids in the first half of the tailpiece contain essential information for generating the correct topology. Assembly is triggered by the formation of a disulfide bond linking two tailpieces. This induces conformational changes in the tailpiece and the adjacent domain, which drive further polymerization. Thus, the biogenesis of large and topologically challenging IgM complexes is dictated by a local conformational switch in a peptide extension.

  1. Buildup of radioxenon isotopes in MOX-assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Gniffke, Thomas; Kirchner, Gerald [Carl Friedrich von Weizsaecker-Centre for Science and Peace Research, Hamburg (Germany)

    2015-07-01

    Radioxenon is the main tracer for detection of nuclear tests conducted underground under the verification regime of the Comprehensive Nuclear Test Ban Treaty (CTBT). Since radioxenon is emitted by civilian sources too, like commercial nuclear reactors, source discrimination is still an important issue. Inventory calculations are necessary to predict which xenon isotopic ratios are built up in a reactor and how they differ from those generated by a nuclear explosion. The screening line actually used by the CTBT Organization for source discrimination is based on calculations for uranium fuel of various enrichments used in pressurized water reactors (PWRs). The usage of different fuel, especially mixed U/Pu oxide (MOX) assemblies with reprocessed plutonium, may alter the radioxenon signature of civilian reactors. In this talk, calculations of the radioxenon buildup in a MOX-assembly used in a commercial PWR are presented. Implications for the CTBT verification regimes are discussed and open questions are addressed.

  2. Nuclear fuel string assembly

    International Nuclear Information System (INIS)

    Ip, A.K.; Koyanagi, K.; Tarasuk, W.R.

    1976-01-01

    A method of fabricating rodded fuels suitable for use in pressure tube type reactors and in pressure vessel type reactors is described. Fuel rods are secured as an inner and an outer sub-assembly, each rod attached between mounting rings secured to the rod ends. The two sub-assemblies are telescoped together and positioned by spaced thimbles located between them to provide precise positioning while permittng differential axial movement between the sub-assemblies. Such sub-assemblies are particularly suited for mounting as bundle strings. The method provides particular advantages in the assembly of annular-section fuel pins, which includes booster fuel containing enriched fuel material. (LL)

  3. Fuel assembly reconstitution

    International Nuclear Information System (INIS)

    Morgado, Mario M.; Oliveira, Monica G.N.; Ferreira Junior, Decio B.M.; Santos, Barbara O. dos; Santos, Jorge E. dos

    2009-01-01

    Fuel failures have been happened in Nuclear Power Plants worldwide, without lost of integrity and safety, mainly for the public, environment and power plants workers. The most common causes of these events are corrosion (CRUD), fretting and pellet cladding interaction. These failures are identified by increasing the activity of fission products, verified by chemical analyses of reactor coolant. Through these analyses, during the fourth operation cycle of Angra 2 Nuclear Power Plant, was possible to observe fuel failure indication. This indication was confirmed in the end of the cycle during the unloading of reactor core through leakage tests of fuel assembly, using the equipment called 'In Mast Sipping' and 'Box Sipping'. After confirmed, the fuel assembly reconstitution was scheduled, and happened in April, 2007, where was identified the cause and the fuel rod failure, which was substitute by dummy rods (zircaloy). The cause was fretting by 'debris'. The actions to avoid and prevent fuel assemblies failures are important. The goals of this work are to describe the methodology of fuel assembly reconstitution using the FARE (Fuel Assembly Reconstitution Equipment) system, to describe the results of this task in economic and security factors of the company and show how the fuel assembly failures are identified during operation and during the outage. (author)

  4. De novo transcriptome assembly of Setatria italica variety Taejin

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2016-06-01

    Full Text Available Foxtail millet (Setaria italica belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.

  5. Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome.

    Science.gov (United States)

    Su, Tsung-Wei; Yang, Chao-Yu; Kao, Wen-Pin; Kuo, Bai-Jiun; Lin, Shan-Meng; Lin, Jung-Yaw; Lo, Yu-Chih; Lin, Su-Chang

    2017-03-07

    Death domain (DD)-fold assemblies play a crucial role in regulating the signaling to cell survival or death. Here we report the crystal structure of the caspase recruitment domain (CARD)-CARD disk of the human apoptosome. The structure surprisingly reveals that three 1:1 Apaf-1:procaspase-9 CARD protomers form a novel helical DD-fold assembly on the heptameric wheel-like platform of the apoptosome. The small-angle X-ray scattering and multi-angle light scattering data also support that three protomers could form an oligomeric complex similar to the crystal structure. Interestingly, the quasi-equivalent environment of CARDs could generate different quaternary CARD assemblies. We also found that the type II interaction is conserved in all DD-fold complexes, whereas the type I interaction is found only in the helical DD-fold assemblies. This study provides crucial insights into the caspase activation mechanism, which is tightly controlled by a sophisticated and highly evolved CARD assembly on the apoptosome, and also enables better understanding of the intricate DD-fold assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Automated optical assembly

    Science.gov (United States)

    Bala, John L.

    1995-08-01

    Automation and polymer science represent fundamental new technologies which can be directed toward realizing the goal of establishing a domestic, world-class, commercial optics business. Use of innovative optical designs using precision polymer optics will enable the US to play a vital role in the next generation of commercial optical products. The increased cost savings inherent in the utilization of optical-grade polymers outweighs almost every advantage of using glass for high volume situations. Optical designers must gain experience with combined refractive/diffractive designs and broaden their knowledge base regarding polymer technology beyond a cursory intellectual exercise. Implementation of a fully automated assembly system, combined with utilization of polymer optics, constitutes the type of integrated manufacturing process which will enable the US to successfully compete with the low-cost labor employed in the Far East, as well as to produce an equivalent product.

  7. ZOMG - I. How the cosmic web inhibits halo growth and generates assembly bias

    Science.gov (United States)

    Borzyszkowski, Mikolaj; Porciani, Cristiano; Romano-Díaz, Emilio; Garaldi, Enrico

    2017-07-01

    The clustering of dark matter haloes with fixed mass depends on their formation history, an effect known as assembly bias. We use zoom N-body simulations to investigate the origin of this phenomenon. For each halo at redshift z = 0, we determine the time in which the physical volume containing its final mass becomes stable. We consider five examples for which this happens at z ˜ 1.5 and two that do not stabilize by z = 0. The zoom simulations show that early-collapsing haloes do not grow in mass at z = 0 while late-forming ones show a net inflow. The reason is that 'accreting' haloes are located at the nodes of a network of thin filaments feeding them. Conversely, each 'stalled' halo lies within a prominent filament that is thicker than the halo size. Infalling material from the surroundings becomes part of the filament while matter within it recedes from the halo. We conclude that assembly bias originates from quenching halo growth due to tidal forces following the formation of non-linear structures in the cosmic web, as previously conjectured in the literature. Also the internal dynamics of the haloes change: the velocity anisotropy profile is biased towards radial (tangential) orbits in accreting (stalled) haloes. Our findings reveal the cause of the yet unexplained dependence of halo clustering on the anisotropy. Finally, we extend the excursion-set theory to account for these effects. A simple criterion based on the ellipticity of the linear tidal field combined with the spherical-collapse model provides excellent predictions for both classes of haloes.

  8. Reflector-moderated critical assemblies

    International Nuclear Information System (INIS)

    Paxton, H.C.; Jarvis, G.A.; Byers, C.C.

    1975-07-01

    Experiments with reflector-moderated critical assemblies were part of the Rover Program at the Los Alamos Scientific Laboratory (LASL). These assemblies were characterized by thick D 2 O or beryllium reflectors surrounding large cavities that contained highly enriched uranium at low average densities. Because interest in this type of system has been revived by LASL Plasma Cavity Assembly studies, more detailed descriptions of the early assemblies than had been available in the unclassified literature are provided. (U.S.)

  9. SWAP-Assembler 2: Optimization of De Novo Genome Assembler at Large Scale

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Jintao; Seo, Sangmin; Balaji, Pavan; Wei, Yanjie; Wang, Bingqiang; Feng, Shengzhong

    2016-08-16

    In this paper, we analyze and optimize the most time-consuming steps of the SWAP-Assembler, a parallel genome assembler, so that it can scale to a large number of cores for huge genomes with the size of sequencing data ranging from terabyes to petabytes. According to the performance analysis results, the most time-consuming steps are input parallelization, k-mer graph construction, and graph simplification (edge merging). For the input parallelization, the input data is divided into virtual fragments with nearly equal size, and the start position and end position of each fragment are automatically separated at the beginning of the reads. In k-mer graph construction, in order to improve the communication efficiency, the message size is kept constant between any two processes by proportionally increasing the number of nucleotides to the number of processes in the input parallelization step for each round. The memory usage is also decreased because only a small part of the input data is processed in each round. With graph simplification, the communication protocol reduces the number of communication loops from four to two loops and decreases the idle communication time. The optimized assembler is denoted as SWAP-Assembler 2 (SWAP2). In our experiments using a 1000 Genomes project dataset of 4 terabytes (the largest dataset ever used for assembling) on the supercomputer Mira, the results show that SWAP2 scales to 131,072 cores with an efficiency of 40%. We also compared our work with both the HipMER assembler and the SWAP-Assembler. On the Yanhuang dataset of 300 gigabytes, SWAP2 shows a 3X speedup and 4X better scalability compared with the HipMer assembler and is 45 times faster than the SWAP-Assembler. The SWAP2 software is available at https://sourceforge.net/projects/swapassembler.

  10. A Theoretical and Experimental Study of DNA Self-assembly

    Science.gov (United States)

    Chandran, Harish

    providing detailed designs for local molecular computations that involve spatially contiguous molecules arranged on addressable substrates via enzyme-free DNA hybridization reaction cascades. We use the Visual DSD simulation software in conjunction with localized reaction rates obtained from biophysical modeling to create chemical reaction networks of localized hybridization circuits that are then model checked using the PRISM model checking software. We develop a DNA detection system employing the triggered self-assembly of a novel DNA dendritic nanostructure. Detection begins when a specific, single-stranded target DNA strand triggers a hybridization chain reaction between two distinct DNA hairpins. Each hairpin opens and hybridizes up to two copies of the other, and hence each layer of the growing dendritic nanostructure can in principle accommodate an exponentially increasing number of cognate molecules, generating a nanostructure with high molecular weight. We build linear activatable assemblies employing a novel protection/deprotection strategy to strictly enforce the direction of tiling assembly growth to ensure the robustness of the assembly process. Our system consists of two tiles that can form a linear co-polymer. These tiles, which are initially protected such that they do not react with each other, can be activated to form linear co-polymers via the use of a strand displacing enzyme.

  11. Methods and apparatus for cooling wind turbine generators

    Science.gov (United States)

    Salamah, Samir A [Niskayuna, NY; Gadre, Aniruddha Dattatraya [Rexford, NY; Garg, Jivtesh [Schenectady, NY; Bagepalli, Bharat Sampathkumaran [Niskayuna, NY; Jansen, Patrick Lee [Alplaus, NY; Carl, Jr., Ralph James

    2008-10-28

    A wind turbine generator includes a stator having a core and a plurality of stator windings circumferentially spaced about a generator longitudinal axis. A rotor is rotatable about the generator longitudinal axis, and the rotor includes a plurality of magnetic elements coupled to the rotor and cooperating with the stator windings. The magnetic elements are configured to generate a magnetic field and the stator windings are configured to interact with the magnetic field to generate a voltage in the stator windings. A heat pipe assembly thermally engaging one of the stator and the rotor to dissipate heat generated in the stator or rotor.

  12. Life extension and replacement management for RAPS type steam generators

    International Nuclear Information System (INIS)

    Arya, R.C.; Rastogi, A.K.

    1996-01-01

    The steam generating equipment in first four units of Indian PHWRs Rajasthan Atomic Power Station (RAPS) 1-2 and Madras Atomic Power Station (MAPS) 1-2 are hairpin type and comprise of eight boiler assemblies. Each assembly consists of identical, single pass, inverted and vertical hairpin heat exchangers (10 for RAPS and 11 for MAPS) containing 195 monel-400 U tubes of 12.7 mm dia x 1.242 mm thick. The hot heavy water flows through these tubes and imparts heat to feed, light demineralized water entering the shell at the bottom of preheat leg. The heat is generated on the outer surface of the tubes. Details of studies carried out for life extension and replacement management for RAPS type steam generators are given. 1 fig., 5 tabs

  13. Predicting Chiral Nanostructures, Lattices and Superlattices in Complex Multicomponent Nanoparticle Self-Assembly

    KAUST Repository

    Hur, Kahyun

    2012-06-13

    "Bottom up" type nanoparticle (NP) self-assembly is expected to provide facile routes to nanostructured materials for various, for example, energy related, applications. Despite progress in simulations and theories, structure prediction of self-assembled materials beyond simple model systems remains challenging. Here we utilize a field theory approach for predicting nanostructure of complex and multicomponent hybrid systems with multiple types of short- and long-range interactions. We propose design criteria for controlling a range of NP based nanomaterial structures. In good agreement with recent experiments, the theory predicts that ABC triblock terpolymer directed assemblies with ligand-stabilized NPs can lead to chiral NP network structures. Furthermore, we predict that long-range Coulomb interactions between NPs leading to simple NP lattices, when applied to NP/block copolymer (BCP) assemblies, induce NP superlattice formation within the phase separated BCP nanostructure, a strategy not yet realized experimentally. We expect such superlattices to be of increasing interest to communities involved in research on, for example, energy generation and storage, metamaterials, as well as microelectronics and information storage. © 2012 American Chemical Society.

  14. Diagnostic testing and repair of Hollingsworth Generating Station`s Unit One

    Energy Technology Data Exchange (ETDEWEB)

    Atkins, R.; Epple, W.; Stevenson, D. [Great Lakes Power Ltd., Sault Ste. Marie, ON (Canada); Brotherton, L.; Crahan, M.; Ghate, A.

    1995-12-31

    A case history of the diagnosis and corrections implemented to resolve vibration problems in a 22,222 kVA hydroelectric generator was presented. The problem prevented the utility from operating the unit throughout the range of its nameplate rating and caused periodic failures of the generator`s guide and thrust bearing. Tests identified that the rim assembly was fastened onto the spider in a manner that resulted in tilting of the rim with respect to the axis of rotation, consequently, there was an unbalanced generator static air gap. A unique repair was implemented to fully restore the rim assembly to its proper position. Problems associated with carrying out such major in-situ repairs in a remote environment and within a scheduled maintenance outage were discussed. Economic benefits and costs associated with the repair were also discussed.

  15. Improving startup performance with carbon mesh anodes in separator electrode assembly microbial fuel cells

    KAUST Repository

    Zhang, Fang; Xia, Xue; Luo, Yong; Sun, Dan; Call, Douglas F.; Logan, Bruce E.

    2013-01-01

    In a separator electrode assembly microbial fuel cell, oxygen crossover from the cathode inhibits current generation by exoelectrogenic bacteria, resulting in poor reactor startup and performance. To determine the best approach for improving startup

  16. Polymer Directed Protein Assemblies

    NARCIS (Netherlands)

    van Rijn, Patrick

    2013-01-01

    Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e. g., virus particles. Viruses are a multi-protein assembly of which the morphology is

  17. Systems engineering studies of on-orbit assembly operation

    Science.gov (United States)

    Morgenthaler, George W.

    1991-01-01

    While the practice of construction has a long history, the underlying theory of construction is relatively young. Very little has been documented as to techniques of logistic support, construction planning, construction scheduling, construction testing, and inspection. The lack of 'systems approaches' to construction processes is certainly one of the most serious roadblocks to the construction of space structures. System engineering research efforts at CSC are aimed at developing concepts and tools which contribute to a systems theory of space construction. The research is also aimed at providing means for trade-offs of design parameters for other research areas in CSC. Systems engineering activity at CSC has divided space construction into the areas of orbital assembly, lunar base construction, interplanetary transport vehicle construction, and Mars base construction. A brief summary of recent results is given. Several models for 'launch-on-time' were developed. Launch-on-time is a critical concept to the assembly of such Earth-orbiting structures as the Space Station Freedom, and to planetary orbiters such as the Mars transfer vehicle. CSC has developed a launch vehicle selection model which uses linear programming to find optimal combinations of launch vehicles of various sizes (Atlas, Titan, Shuttles, HLLV's) to support SEI missions. Recently, the Center developed a cost trade-off model for studying on orbit assembly logistics. With this model it was determined that the most effective size of the HLLV would be in the range of 120 to 200 metric tons to LEO, which is consistent with the choices of General Stafford's Synthesis Group Report. A second-generation Dynamic Construction Activities Model ('DYCAM') process model has been under development, based on our past results in interruptability and our initial DYCAM model. This second-generation model is built on the paradigm of knowledge-based expert systems. It is aimed at providing answers to two questions: (1

  18. Core/coil assembly for use in superconducting magnets and method for assembling the same

    Science.gov (United States)

    Kassner, David A.

    1979-01-01

    A core/coil assembly for use in a superconducting magnet of the focusing or bending type used in syncronous particle accelerators comprising a coil assembly contained within an axial bore of the stacked, washer type, carbon steel laminations which comprise the magnet core assembly, and forming an interference fit with said laminations at the operating temperature of said magnet. Also a method for making such core/coil assemblies comprising the steps of cooling the coil assembly to cryogenic temperatures and drawing it rapidly upwards into the bore of said stacked laminations.

  19. High-speed assembly language (80386/80387) programming for laser spectra scan control and data acquisition providing improved resolution water vapor spectroscopy

    Science.gov (United States)

    Allen, Robert J.

    1988-01-01

    An assembly language program using the Intel 80386 CPU and 80387 math co-processor chips was written to increase the speed of data gathering and processing, and provide control of a scanning CW ring dye laser system. This laser system is used in high resolution (better than 0.001 cm-1) water vapor spectroscopy experiments. Laser beam power is sensed at the input and output of white cells and the output of a Fabry-Perot. The assembly language subroutine is called from Basic, acquires the data and performs various calculations at rates greater than 150 faster than could be performed by the higher level language. The width of output control pulses generated in assembly language are 3 to 4 microsecs as compared to 2 to 3.7 millisecs for those generated in Basic (about 500 to 1000 times faster). Included are a block diagram and brief description of the spectroscopy experiment, a flow diagram of the Basic and assembly language programs, listing of the programs, scope photographs of the computer generated 5-volt pulses used for control and timing analysis, and representative water spectrum curves obtained using these programs.

  20. Telescoping cylindrical piezoelectric fiber composite actuator assemblies

    Science.gov (United States)

    Allison, Sidney G. (Inventor); Shams, Qamar A. (Inventor); Fox, Robert L. (Inventor); Fox, legal representative, Christopher L. (Inventor); Fox Chattin, legal representative, Melanie L. (Inventor)

    2010-01-01

    A telescoping actuator assembly includes a plurality of cylindrical actuators in a concentric arrangement. Each cylindrical actuator is at least one piezoelectric fiber composite actuator having a plurality of piezoelectric fibers extending parallel to one another and to the concentric arrangement's longitudinal axis. Each cylindrical actuator is coupled to concentrically-adjacent ones of the cylindrical actuators such that the plurality of cylindrical actuators can experience telescopic movement. An electrical energy source coupled to the cylindrical actuators applies actuation energy thereto to generate the telescopic movement.

  1. FOLDNA, a Web Server for Self-Assembled DNA Nanostructure Autoscaffolds and Autostaples

    Directory of Open Access Journals (Sweden)

    Chensheng Zhou

    2012-01-01

    Full Text Available DNA self-assembly is a nanotechnology that folds DNA into desired shapes. Self-assembled DNA nanostructures, also known as origami, are increasingly valuable in nanomaterial and biosensing applications. Two ways to use DNA nanostructures in medicine are to form nanoarrays, and to work as vehicles in drug delivery. The DNA nanostructures perform well as a biomaterial in these areas because they have spatially addressable and size controllable properties. However, manually designing complementary DNA sequences for self-assembly is a technically demanding and time consuming task, which makes it advantageous for computers to do this job instead. We have developed a web server, FOLDNA, which can automatically design 2D self-assembled DNA nanostructures according to custom pictures and scaffold sequences provided by the users. It is the first web server to provide an entirely automatic design of self-assembled DNA nanostructure, and it takes merely a second to generate comprehensive information for molecular experiments including: scaffold DNA pathways, staple DNA directions, and staple DNA sequences. This program could save as much as several hours in the designing step for each DNA nanostructure. We randomly selected some shapes and corresponding outputs from our server and validated its performance in molecular experiments.

  2. Wave propagation visualization in an experimental model for a control rod drive mechanism assembly

    International Nuclear Information System (INIS)

    Lee, Jung-Ryul; Jeong, Hyomi; Kong, Churl-Won

    2011-01-01

    Highlights: → We fabricate a full-scale mock-up of the control rod drive mechanism (CRDM) assembly in the upper reactor head of the nuclear power plant. → An ultrasonic propagation imaging method using a scanning laser ultrasonic generator is proposed to visualize and simulate ultrasonic wave propagation around the CRDM assembly. → The ultrasonic source location and frequency are simulated by changing the sensor location and the band pass-filtering zone. → The ultrasonic propagation patterns before and after cracks in the weld and nozzle of the CRDM assembly are analyzed. - Abstract: Nondestructive inspection techniques such as ultrasonic testing, eddy current testing, and visual testing are being developed to detect primary water stress corrosion cracks in control rod drive mechanism (CRDM) assemblies of nuclear power plants. A unit CRDM assembly consists of a reactor upper head including cladding, a penetration nozzle, and J-groove dissimilar metal welds with buttering. In this study, we fabricated a full-scale CRDM assembly mock-up. An ultrasonic propagation imaging (UPI) method using a scanning laser ultrasonic generator is proposed to visualize and simulate ultrasonic wave propagation around the thick and complex CRDM assembly. First, the proposed laser UPI system was validated for a simple aluminium plate by comparing the ultrasonic wave propagation movie (UWPM) obtained using the system with numerical simulation results reported in the literature. Lamb wave mode identification and damage detectability, depending on the ultrasonic frequency, were also included in the UWPM analysis. A CRDM assembly mock-up was fabricated in full-size and its vertical cross section was scanned using the laser UPI system to investigate the propagation characteristics of the longitudinal and Rayleigh waves in the complex structure. The ultrasonic source location and frequency were easily simulated by changing the sensor location and the band pass filtering zone

  3. Rotor assembly and method for automatically processing liquids

    Science.gov (United States)

    Burtis, C.A.; Johnson, W.F.; Walker, W.A.

    1992-12-22

    A rotor assembly is described for performing a relatively large number of processing steps upon a sample, such as a whole blood sample, and a diluent, such as water. It includes a rotor body for rotation about an axis and includes a network of chambers within which various processing steps are performed upon the sample and diluent and passageways through which the sample and diluent are transferred. A transfer mechanism is movable through the rotor body by the influence of a magnetic field generated adjacent the transfer mechanism and movable along the rotor body, and the assembly utilizes centrifugal force, a transfer of momentum and capillary action to perform any of a number of processing steps such as separation, aliquoting, transference, washing, reagent addition and mixing of the sample and diluent within the rotor body. The rotor body is particularly suitable for automatic immunoassay analyses. 34 figs.

  4. Narrowing the diversification of supramolecular assemblies by preorganization.

    Science.gov (United States)

    Wang, Zhongyan; Liang, Chunhui; Shang, Yuna; He, Shuangshuang; Wang, Ling; Yang, Zhimou

    2018-03-13

    We designed and synthesized three phosphorylated peptides as precursors of the same peptide Nap-YYY. We found that different precursors led to different materials with almost identical chemical compositions at the final stages. Only Nap-YpYY could form very uniform nanofibers in a stable supramolecular hydrogel by enzyme-instructed self-assembly (EISA) at the physiological temperature (37 °C). In contrast, de-phosphorylation of the other two precursors (Nap-pYYY and Nap-YYpY) resulted in diverse nanostructures in metastable hydrogels with precipitates. The formation of uniform nanomaterials in the stable hydrogels was due to the preorganization property of the precursor Nap-YpYY, which facilitated rapid folding and accelerated the kinetics of hydrogelation of the resulting peptide Nap-YYY generated by the EISA process. Our study demonstrated the importance of the precursor for the self-assembly of nanomaterials and provided a useful strategy to manipulate them.

  5. Structure and assembly of a paramyxovirus matrix protein.

    Science.gov (United States)

    Battisti, Anthony J; Meng, Geng; Winkler, Dennis C; McGinnes, Lori W; Plevka, Pavel; Steven, Alasdair C; Morrison, Trudy G; Rossmann, Michael G

    2012-08-28

    Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.

  6. Nuclear fuel assemblies and fuel pins usable in such assemblies

    International Nuclear Information System (INIS)

    Jolly, R.

    1982-01-01

    A novel end cap for a nuclear fuel assembly is described in detail. It consists of a trisection arrangement which is received within a cell of a cellular grid. The cell contains abutment means with which the trisection comes into abutment. The grid also contains an abutment means for preventing the trisections from being inserted into the cell in an incorrect orientation. The present design allows fuel pins to be securely held in a hold-down grid of a sub-assembly. The design also allows easier dis-assembly of the swollen and embrittled fuel pins prior to reprocessing. (U.K.)

  7. Expert System analysis of non-fuel assembly hardware and spent fuel disassembly hardware: Its generation and recommended disposal

    International Nuclear Information System (INIS)

    Williamson, D.A.

    1991-01-01

    Almost all of the effort being expended on radioactive waste disposal in the United States is being focused on the disposal of spent Nuclear Fuel, with little consideration for other areas that will have to be disposed of in the same facilities. one area of radioactive waste that has not been addressed adequately because it is considered a secondary part of the waste issue is the disposal of the various Non-Fuel Bearing Components of the reactor core. These hardware components fall somewhat arbitrarily into two categories: Non-Fuel Assembly (NFA) hardware and Spent Fuel Disassembly (SFD) hardware. This work provides a detailed examination of the generation and disposal of NFA hardware and SFD hardware by the nuclear utilities of the United States as it relates to the Civilian Radioactive Waste Management Program. All available sources of data on NFA and SFD hardware are analyzed with particular emphasis given to the Characteristics Data Base developed by Oak Ridge National Laboratory and the characterization work performed by Pacific Northwest Laboratories and Rochester Gas ampersand Electric. An Expert System developed as a portion of this work is used to assist in the prediction of quantities of NFA hardware and SFD hardware that will be generated by the United States' utilities. Finally, the hardware waste management practices of the United Kingdom, France, Germany, Sweden, and Japan are studied for possible application to the disposal of domestic hardware wastes. As a result of this work, a general classification scheme for NFA and SFD hardware was developed. Only NFA and SFD hardware constructed of zircaloy and experiencing a burnup of less than 70,000 MWD/MTIHM and PWR control rods constructed of stainless steel are considered Low-Level Waste. All other hardware is classified as Greater-ThanClass-C waste

  8. Controlled dielectrophoretic nanowire self-assembly using atomic layer deposition and suspended microfabricated electrodes

    International Nuclear Information System (INIS)

    Baca, Alicia I; Brown, Joseph J; Bright, Victor M; Bertness, Kris A

    2012-01-01

    Effects of design and materials on the dielectrophoretic self-assembly of individual gallium nitride nanowires (GaN NWs) onto microfabricated electrodes have been experimentally investigated. The use of TiO 2 surface coating generated by atomic layer deposition (ALD) improves dielectrophoretic assembly yield of individual GaN nanowires on microfabricated structures by as much as 67%. With a titanium dioxide coating, individual nanowires were placed across suspended electrode pairs in 46% of tests (147 out of 320 total), versus 28% of tests (88 out of 320 total tests) that used uncoated GaN NWs. An additional result from these tests was that suspending the electrodes 2.75 μm above the substrate corresponded with up to 15.8% improvement in overall assembly yield over that of electrodes fabricated directly on the substrate. (paper)

  9. Self-assembly of coiled coil peptides into nanoparticles vs 2-d plates: effects of assembly pathway

    Science.gov (United States)

    Kim, Kyunghee; Pochan, Darrin

    Molecular solution assembly, or self-assembly, is a process by which ordered nanostructures or patterns are formed by non-covalent interactions during assembly. Biomimicry, the use of bioinspired molecules or biologically relevant materials, is an important area of self-assembly research with peptides serving a critical role as molecular tools. The morphology of peptide assemblies can be controlled by adjusting solution conditions such as the concentration of peptides, the temperature, and pH. Herein, spherical nanostructures, which have potential for creating an encapsulation system, are formed by self-assembly when coiled coil peptides are combined in solution. These peptides are homotrimeric and heterodimeric coiled-coil bundles and the homotrimer is connected with each of heterodimer through their external surfaces via disulfide bonds. The resultant covalent constructs could co-assemble into complementary trimeric hubs, respectively. The two peptide constructs are directly mixed and assembled in solution in order to produce either spherical particles or 2-d plates depending on the solution conditions and kinetic pathway of assembly. In particular, structural changes of the self-assembled peptides are explored by control of the thermal history of the assembly solution.

  10. Desain Sistem Pendeteksi untuk Citra Base Sub-assembly dengan Algoritma Backpropagation

    Directory of Open Access Journals (Sweden)

    Kasdianto Kasdianto

    2017-04-01

    Full Text Available Object identification technique using machine vision has been implemented in industrial of electronic manufacturers for years. This technique is commonly used for reject detection (for disqualified product based on existing standard or defect detection. This research aims to build a reject detector of sub-assembly condition which is differed by two conditions that are missing screw and wrong position screw using neural network backpropagation. The image taken using camera will be converted into grayscale before it is processed in backpropagation methods to generate a weight value. The experiment result shows that the network architecture with two layers has the most excellent accuracy level. Using learning rate of 0.5, target error 0.015%, and the number of node 1 of 100 and node 2 of 50, the successive rate for sub-assembly detection in right condition reached 99.02% while no error occurs in detecting the wrong condition of Sub-assembly (missing screw and wrong position screw.

  11. Analysis Of Transcriptomes In A Porcine Tissue Collection Using RNA-Seq And Genome Assembly 10

    DEFF Research Database (Denmark)

    Hornshøj, Henrik; Thomsen, Bo; Hedegaard, Jakob

    2011-01-01

    The release of Sus scrofa genome assembly 10 supports improvement of the pig genome annotation and in depth transcriptome analyses using next-generation sequencing technologies. In this study we analyze RNA-seq reads from a tissue collection, including 10 separate tissues from Duroc boars and 10...... short read alignment software we mapped the reads to the genome assembly 10. We extracted contig sequences of gene transcripts using the Cufflinks software. Based on this information we identified expressed genes that are present in the genome assembly. The portion of these genes being previously known...... was roughly estimated by sequence comparison to known genes. Similarly, we searched for genes that are expressed in the tissues but not present in the genome assembly by aligning the non-genome-mapped reads to known gene transcripts. For the genes predicted to have alternative transcript variants by Cufflinks...

  12. Rapid centriole assembly in Naegleria reveals conserved roles for both de novo and mentored assembly.

    Science.gov (United States)

    Fritz-Laylin, Lillian K; Levy, Yaron Y; Levitan, Edward; Chen, Sean; Cande, W Zacheus; Lai, Elaine Y; Fulton, Chandler

    2016-03-01

    Centrioles are eukaryotic organelles whose number and position are critical for cilia formation and mitosis. Many cell types assemble new centrioles next to existing ones ("templated" or mentored assembly). Under certain conditions, centrioles also form without pre-existing centrioles (de novo). The synchronous differentiation of Naegleria amoebae to flagellates represents a unique opportunity to study centriole assembly, as nearly 100% of the population transitions from having no centrioles to having two within minutes. Here, we find that Naegleria forms its first centriole de novo, immediately followed by mentored assembly of the second. We also find both de novo and mentored assembly distributed among all major eukaryote lineages. We therefore propose that both modes are ancestral and have been conserved because they serve complementary roles, with de novo assembly as the default when no pre-existing centriole is available, and mentored assembly allowing precise regulation of number, timing, and location of centriole assembly. © 2016 Wiley Periodicals, Inc.

  13. Self-Assembly of Infinite Structures

    Directory of Open Access Journals (Sweden)

    Scott M. Summers

    2009-06-01

    Full Text Available We review some recent results related to the self-assembly of infinite structures in the Tile Assembly Model. These results include impossibility results, as well as novel tile assembly systems in which shapes and patterns that represent various notions of computation self-assemble. Several open questions are also presented and motivated.

  14. One-step polypyrrole coating of self-assembled silver nanoprisms for enhanced stability and Raman scattering

    Science.gov (United States)

    Jeong, Dong-Won; Jeong, Sugyeong; Jang, Du-Jeon

    2017-07-01

    Self-assemblies of silver nanoprisms (AgPRs) having enhanced structural stability and optical properties have been facilely coated with polypyrrole (PPy) via the in situ polymerization of pyrrole monomers that also act as an assembling agent. The assemblies of AgPRs, whose edge lengths and thicknesses are typically 78 and 4 nm, respectively, have been surrounded by a PPy coating of 6 nm. AgPRs are assembled in a side-to-side orientation, and the degree of assembly has been controlled by varying the concentration of trisodium citrate dihydrate, which attaches selectively to the {111} facets of AgPRs. The morphology deformation time of PPy-coated AgPRs in 0.6 mM H2O2(aq) is seven times longer than that of PPy-free AgPRs, suggesting that PPy coating prevents the sharp tips of AgPRs from being truncated by oxidizing agents. The SERS effect of highly self-assembled and PPy-coated AgPRs becomes as high as 6.3 due to numerous hot spots generated between nanoprisms. Overall, our fabricated AgPRs assemblies with PPy coating have not only improved structural stability but also enhanced optical properties, extending the practical use of noble-metal nanoprisms for various optical applications.

  15. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    Anthony, A.J.

    1980-01-01

    A bimetallic spacer means is cooperatively associated with a nuclear fuel assembly and operative to resist the occurrence of in-reactor bowing of the nuclear fuel assembly. The bimetallic spacer means in one embodiment of the invention includes a space grid formed, at least principally, of zircaloy to the external surface of which are attached a plurality of stainless steel strips. In another embodiment the strips are attached to fuel pins. In each of the embodiments, the stainless steel strips during power production expand outwardly to a greater extent than do the members to which the stainless steel strips are attached, thereby forming stiff springs which abut against like bimetallic spacer means with which the other nuclear fuel assemblies are provided in a given nuclear reactor core to thus prevent the occurrence of in-reactor bowing of the nuclear fuel assemblies. (author)

  16. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    Betten, P.R.

    1976-01-01

    Under the invention the fuel assembly is particularly suitable for liquid metal cooled fast neutron breeder reactors. Hence, according to the invention a fuel assembly cladding includes inward corrugations with respect to the remainder of the cladding according to a recurring pattern determined by the pitch of the metal wire helically wound round the fuel rods of the assembly. The parts of the cladding pressed inwards correspond to the areas in which the wire encircling the peripheral fuel rods is generally located apart from the cladding, thereby reducing the play between the cladding and the peripheral fuel rods situated in these areas. The reduction in the play in turn improves the coolant flow in the internal secondary channels of the fuel assembly to the detriment of the flow in the peripheral secondary channels and thereby establishes a better coolant fluid temperature profile [fr

  17. DOWNHOLE POWER GENERATION AND WIRELESS COMMUNICATIONS FOR INTELLIGENT COMPLETIONS APPLICATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Paul Tubel

    2004-02-01

    The development work during this quarter was focused in the assembly of the downhole power generator hardware and its electronics module. The quarter was also spent in the development of the surface system electronics and software to extract the acoustic data transmitted from downhole to the surface from the noise generated by hydrocarbon flow in wells and to amplify very small acoustic signals to increase the distance between the downhole tool and the surface receiver. The tasks accomplished during this report period were: (1) Assembly of the downhole power generator mandrel for generation of electrical power due to flow in the wellbore. (2) Test the piezoelectric wafers to assure that they are performing properly prior to integrating them to the mechanical power generator mandrel. (3) Coat the power generator wafers to prevent water from shorting the power generator wafers. (4) Test of the power generator using a water tower and an electric pump to create a water flow loop. (5) Test the power harvesting electronics module. (6) Upgrade the signal condition and amplification from downhole into the surface system. (7) Upgrade the surface processing system capability to process data faster. (8) Create a new filtering technique to extract the signal from noise after the data from downhole is received at the surface system.

  18. Method and apparatus for assembling a permanent magnet pole assembly

    Science.gov (United States)

    Carl, Jr., Ralph James; Bagepalli, Bharat Sampathkumaran [Niskayuna, NY; Jansen, Patrick Lee [Scotia, NY; Dawson, Richard Nils [Voorheesville, NY; Qu, Ronghai [Clifton Park, NY; Avanesov, Mikhail Avramovich [Moscow, RU

    2009-08-11

    A pole assembly for a rotor, the pole assembly includes a permanent magnet pole including at least one permanent magnet block, a plurality of laminations including a pole cap mechanically coupled to the pole, and a plurality of laminations including a base plate mechanically coupled to the pole.

  19. TPX assembly plan

    International Nuclear Information System (INIS)

    Knutson, D.

    1993-01-01

    The TPX machine will be assembled in the TFTR Test Cell at the Plasma Physics Laboratory, utilizing the existing TFTR machine foundation. Preparation of the area for assembly will begin after completion of the decontamination and decommissioning phase on TFTR and certification that the radiation levels remaining, if any, are consistent with the types of operations planned. Assembly operations begin with the arrival of the first components, and conclude, approximately 24 months later, with the successful completion of the integrated systems tests and the achievement of a first plasma

  20. Fuel assemblies with inert matrices as reloads of cycle 11 of the Unit 1 of the LVNC

    International Nuclear Information System (INIS)

    Lucatero, M.A.; Hernandez M, N.; Hernandez L, H.

    2005-01-01

    In this work the results that were obtained of the analysis of three different reloads of the cycle 11 with fuel assemblies containing a mixture of UO 2 and plutonium grade armament in an inert matrix. The proposed assemble, consists of an arrangement 10x10 with 42 bars fuels of PuO 2 -CeO 2 , 34 fuel bars with UO 2 and 16 fuel bars with UO 2 -Gd 2O 3. The proposed assemble is equivalent to an it reloadable assemble of the cycle 11. The fuel bars of uranium and gadolinium, are of the same type of those that are used in the reloadable assemble of uranium. The design and generation of the nuclear databases of the fuel cell with mixed fuel, it was carried out with the HELIUMS code. The simulation of operation of the cycle 11, it was carried out with the CM-PRESTO code. The results show that with one reload of 72 assemblies of UO 2 and 32 assemblies with mixed fuel has a cycle length of smaller in 10.5 days to the cycle length with the complete reload of assemblies of UO 2 and a length smaller cycle in 34 days with the complete reload of 104 assemblies with mixed fuel. (Author)

  1. Design and optimization of a beam shaping assembly for BNCT based on D-T neutron generator and dose evaluation using a simulated head phantom.

    Science.gov (United States)

    Rasouli, Fatemeh S; Masoudi, S Farhad

    2012-12-01

    A feasibility study was conducted to design a beam shaping assembly for BNCT based on D-T neutron generator. The optimization of this configuration has been realized in different steps. This proposed system consists of metallic uranium as neutron multiplier, TiF(3) and Al(2)O(3) as moderators, Pb as reflector, Ni as shield and Li-Poly as collimator to guide neutrons toward the patient position. The in-air parameters recommended by IAEA were assessed for this proposed configuration without using any filters which enables us to have a high epithermal neutron flux at the beam port. Also a simulated Snyder head phantom was used to evaluate dose profiles due to the irradiation of designed beam. The dose evaluation results and depth-dose curves show that the neutron beam designed in this work is effective for deep-seated brain tumor treatments even with D-T neutron generator with a neutron yield of 2.4×10(12) n/s. The Monte Carlo Code MCNP-4C is used in order to perform these calculations. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Digital test assembly of truck parts with the IMMA-tool--an illustrative case.

    Science.gov (United States)

    Hanson, L; Högberg, D; Söderholm, M

    2012-01-01

    Several digital human modelling (DHM) tools have been developed for simulation and visualisation of human postures and motions. In 2010 the DHM tool IMMA (Intelligently Moving Manikins) was introduced as a DHM tool that uses advanced path planning techniques to generate collision free and biomechanically acceptable motions for digital human models (as well as parts) in complex assembly situations. The aim of the paper is to illustrate how the IPS/IMMA tool is used at Scania CV AB in a digital test assembly process, and to compare the tool with other DHM tools on the market. The illustrated case of using the IMMA tool, here combined with the path planner tool IPS, indicates that the tool is promising. The major strengths of the tool are its user friendly interface, the motion generation algorithms, the batch simulation of manikins and the ergonomics assessment methods that consider time.

  3. Mesoporous generation-inspired ultrahigh capacitive deionization performance by sono-assembled activated carbon/inter-connected graphene network architecture

    International Nuclear Information System (INIS)

    Song, Haiou; Wu, Yifan; Zhang, Shupeng; Li, Wentao; Wang, Baijun; Wang, Changming; Gao, Juanjuan; Li, Aimin

    2016-01-01

    Highlights: • 3D AC/inter-connected graphene network architecture has been constructed for CDI application. • Generated mesoporous structures can inspire ultrahigh capacitive deionization performance. • Usage of the smaller amounts (5 wt%) of functionalized graphene reduce the secondary pollution. • Inter-connected graphene network as the conductive bridge can decrease the aggregation of AC. • The environmental and economical composite electrode is suitable for practical CDI application. - Abstract: Capacitive deionization (CDI) is an emerging technology that supplies deionized water to resolve the fresh water shortage. CDI electrodes are mainly made up of carbon materials, of which the deionization performance is closely related to their physical properties and structures. Hence, a rational design of electrode material structure is essentially significant. Functionalized graphene (fG) in particular has recently been regarded as characteristic CDI electrode material. However, preparation of fG based on graphene oxide usually results in serious secondary pollution due to usage of highly poisonous chemicals, and thus still cannot meet the demand of practical application. It is feasible that environmentally-friendly activated carbon (AC) and small amounts of fGs can be combined rationally, and used as CDI electrodes. Here, sono-assembled AC/m-phenylenediamine (mPEA) or p-phenylenediaminefG inter-connected network architecture has been constructed for the first time successfully. The specific capacitances of the AC/fG composites were found to be significantly higher than that of the AC electrode owing to mesoporous generation. Also, among all the samples, the AC composite with 5 wt % mPEA-fG exhibited an ultrahigh electrosorption capacity of 12.58 mg/g (or 0.22 mmol/g) in NaCl solution. These observations indicate that fG can serve as an efficient conductive bridge to decrease the aggregation of AC particles, and improve the electron transfer with the

  4. Characterization of self-assembled virus-like particles of dromedary camel hepatitis e virus generated by recombinant baculoviruses.

    Science.gov (United States)

    Zhou, Xianfeng; Kataoka, Michiyo; Liu, Zheng; Takeda, Naokazu; Wakita, Takaji; Li, Tian-Cheng

    2015-12-02

    Dromedary camel hepatitis E virus (DcHEV), a novel hepatitis E virus, has been identified in dromedary camels in Dubai, United Arab Emirates. The antigenicity, pathogenicity and epidemiology of this virus have been unclear. Here we first used a recombinant baculovirus expression system to express the 13 and 111 N-terminus amino-acid-truncated DcHEV ORF2 protein in insect Tn5 cells, and we obtained two types of virus-like particles (VLPs) with densities of 1.300 g/cm(3) and 1.285 g/cm(3), respectively. The small VLPs (Dc4sVLPs) were estimated to be 24 nm in diameter, and were assembled by a protein with the molecular mass 53 kDa. The large VLPs (Dc3nVLPs and Dc4nVLPs) were 35 nm in diameter, and were assembled by a 64-kDa protein. An antigenic analysis demonstrated that DcHEV was cross-reactive with G1, G3-G6, ferret and rat HEVs, and DcHEV showed a stronger cross-reactivity to G1 G3-G6 HEV than it did to rat and ferret HEV. In addition, the antibody against DcHEV-LPs neutralized G1 and G3 HEV in a cell culture system, suggesting that the serotypes of these HEVs are identical. We also found that the amino acid residue Met-358 affects the small DcHEV-LPs assembly. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop.

    Science.gov (United States)

    Hatakeyama, Masaomi; Aluri, Sirisha; Balachadran, Mathi Thumilan; Sivarajan, Sajeevan Radha; Patrignani, Andrea; Grüter, Simon; Poveda, Lucy; Shimizu-Inatsugi, Rie; Baeten, John; Francoijs, Kees-Jan; Nataraja, Karaba N; Reddy, Yellodu A Nanja; Phadnis, Shamprasad; Ravikumar, Ramapura L; Schlapbach, Ralph; Sreeman, Sheshshayee M; Shimizu, Kentaro K

    2017-09-05

    Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available. One of the major problems encountered in the genome assembly of this species was its polyploidy, which hampers genome assembly compared with a diploid genome. To overcome this problem, we sequenced its genome using diverse technologies with sufficient coverage and assembled it via a novel multiple hybrid assembly workflow that combines next-generation with single-molecule sequencing, followed by whole-genome optical mapping using the Bionano Irys® system. The total number of scaffolds was 1,897 with an N50 length >2.6 Mb and detection of 96% of the universal single-copy orthologs. The majority of the homeologs were assembled separately. This indicates that the proposed workflow is applicable to the assembly of other allotetraploid genomes. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  6. Assembly Modulated by Particle Position and Shape: A New Concept in Self-Assembly

    DEFF Research Database (Denmark)

    Tavacoli, Joe W; Heuvingh, Julien; Du Roure, Olivia

    2017-01-01

    In this communication we outline how the bespoke arrangements and design of micron-sized superparamagnetic shapes provide levers to modulate their assembly under homogeneous magnetic fields. We label this new approach, 'assembly modulated by particle position and shape' (APPS). Specifically, using...... rectangular lattices of superparamagnetic micron-sized cuboids, we construct distinct microstructures by adjusting lattice pitch and angle of array with respect to a magnetic field. Broadly, we find two modes of assembly: (1) immediate 2D jamming of the cuboids as they rotate to align with the applied field...... (rotation-induced jamming) and (2) aggregation via translation after their full alignment (dipole-dipole assembly). The boundary between these two assembly pathways is independent on field strength being solely a function of the cuboid's dimensions, lattice pitch, and array angle with respect to field...

  7. Inter-assembly gap deviations in VVER-1000: Accounting for effects on engineering margin factors

    Energy Technology Data Exchange (ETDEWEB)

    Shishkov, Lev; Gorodkov, Sergey; Mikailov, Eldar; Sukhino-Khomenko, Evgenia [Nuclear Research Centre ' ' Kurchatov Institute' ' , Moscow (Russian Federation)

    2015-09-15

    Jacketless fuel assemblies change their form in the course of operation. Often they bow lengthwise. Primarily, these fuel assembly (FA) bows threaten to reduce the control rods' fall rate, but at the same time they change (e.g. increase) the amount of moderator in inter-assembly gaps, thus producing additional power surges. Gap sizes vary randomly and their impact is accounted for with the help of engineering margin factors. For VVER-1000, this account of engineering margin factors increases the fuel component of electricity generation cost by 3 - 5 %, and a half of this increase is due to inter- assembly gap variations. This paper discusses the technique used to account for the impact produced by these gaps on fuel rod power; gives numerical values of sensitivity factors for power variations vs. gap sizes depending on the computational model assumed; and discusses the interference of gap effects and the account of power and coolant temperature feedbacks.

  8. The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

    Directory of Open Access Journals (Sweden)

    J. W. Clouse

    2016-03-01

    Full Text Available Amaranth ( L. is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32, and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and and their putative progenitor ( were resequenced. A single nucleotide polymorphism (SNP phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L. and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

  9. Dynamic behaviour of diagnostic assemblies

    International Nuclear Information System (INIS)

    Pecinka, L.

    1980-01-01

    The methodology is shown of calculating the frequency spectrum of a diagnostic assembly. The oscillations of the assembly as a whole, of a fuel rod bundle, the assembly jacket and of the individual rods in the bundle were considered. The manufacture is suggested of a model assembly which would be used for testing forced vibrations using an experimental water loop. (M.S.)

  10. Flashback resistant pre-mixer assembly

    Science.gov (United States)

    Laster, Walter R [Oviedo, FL; Gambacorta, Domenico [Oviedo, FL

    2012-02-14

    A pre-mixer assembly associated with a fuel supply system for mixing of air and fuel upstream from a main combustion zone in a gas turbine engine. The pre-mixer assembly includes a swirler assembly disposed about a fuel injector of the fuel supply system and a pre-mixer transition member. The swirler assembly includes a forward end defining an air inlet and an opposed aft end. The pre-mixer transition member has a forward end affixed to the aft end of the swirler assembly and an opposed aft end defining an outlet of the pre-mixer assembly. The aft end of the pre-mixer transition member is spaced from a base plate such that a gap is formed between the aft end of the pre-mixer transition member and the base plate for permitting a flow of purge air therethrough to increase a velocity of the air/fuel mixture exiting the pre-mixer assembly.

  11. Nuclear reactor fuel assembly

    International Nuclear Information System (INIS)

    Sasaki, Y.; Tashima, J.

    1975-01-01

    A description is given of nuclear reactor fuel assemblies arranged in the form of a lattice wherein there is attached to the interface of one of two adjacent fuel assemblies a plate spring having a concave portion curved toward said interface and to the interface of the other fuel assembly a plate spring having a convex portion curved away from said interface

  12. Design of the ITER Tokamak Assembly Tools

    International Nuclear Information System (INIS)

    Park, Hyunki; Her, Namil; Kim, Byungchul; Im, Kihak; Jung, Kijung; Lee, Jaehyuk; Im, Kisuk

    2006-01-01

    ITER (International Thermonuclear Experimental Reactor) Procurement allocation among the seven Parties, EU, JA, CN, IN , KO, RF and US had been decided in Dec. 2005. ITER Tokamak assembly tools is one of the nine components allocated to Korea for the construction of the ITER. Assembly tools except measurement and common tools are supplied to assemble the ITER Tokamak and classified into 9 groups according to components to be assembled. Among the 9 groups of assembly tools, large-sized Sector Sub-assembly Tools and Sector Assembly Tools are used at the first stage of ITER Tokamak construction and need to be designed faster than seven other assembly tools. ITER IT (International Team) proposed Korea to accomplish ITA (ITER Transitional Arrangements) Task on detailed design, manufacturing feasibility and contract specification of specific, large sized tools such as Upending Tool, Lifting Tool, Sector Sub-assembly Tool and Sector Assembly Tool in Oct. 2004. Based on the concept design by ITER IT, Korea carried out ITA Task on detailed design of large-sized and specific Sector Sub-assembly and Sector Assembly Tools until Mar. 2006. The Sector Sub-assembly Tools mainly consist of the Upending, Lifting, Vacuum Vessel Support and Bracing, and Sector Sub-assembly Tool, among which the design of three tools are herein. The Sector Assembly Tools mainly consist of the Toroidal Field (TF) Gravity Support Assembly, Sector In-pit Assembly, TF Coil Assembly, Vacuum Vessel (VV) Welding and Vacuum Vessel Thermal Shield (TS) Assembly Tool, among which the design of Sector In-pit Assembly Tool is described herein

  13. Judgement on the data for fuel assembly outlet temperatures of WWER fuel assemblies in power reactors based on measurements with experimental fuel assemblies

    International Nuclear Information System (INIS)

    Krause, F.

    1986-01-01

    In the period from 1980 to 1985, in the Rheinsberg nuclear power plant experimental fuel assemblies were used on lattices at the periphery of the core. These particular fuel assemblies dispose of an extensive in-core instrumentation with different sensors. Besides this, they are fit out with a device to systematically thottle the coolant flow. The large power gradient present at the core position of the experimental fuel assembly causes a temperature profile along the fuel assemblies which is well provable at the measuring points of the outlet temperature. Along the direction of flow this temperature profile in the coolant degrades only slowly. This effect is to be taken into account when measuring the fuel assembly outlet temperature of WWER fuel assemblies. Besides this, the results of the measurements hinted both at a γ-heating of the temperature measuring points and at tolerances in the calculation of the micro power density distribution. (author)

  14. Fuel assemblies

    International Nuclear Information System (INIS)

    Nagano, Mamoru; Yoshioka, Ritsuo

    1983-01-01

    Purpose: To effectively utilize nuclear fuels by increasing the reactivity of a fuel assembly and reduce the concentration at the central region thereof upon completion of the burning. Constitution: A fuel assembly is bisected into a central region and a peripheral region by disposing an inner channel box within a channel box. The flow rate of coolants passing through the central region is made greater than that in the peripheral region. The concentration of uranium 235 of the fuel rods in the central region is made higher. In such a structure, since the moderating effect in the central region is improved, the reactivity of the fuel assembly is increased and the uranium concentration in the central region upon completion of the burning can be reduced, fuel economy and effective utilization of uranium can be attained. (Kamimura, M.)

  15. Fuel assembly

    International Nuclear Information System (INIS)

    Nakatsuka, Masafumi; Matsuzuka, Ryuji.

    1976-01-01

    Object: To provide a fuel assembly which can decrease pressure loss of coolant to uniform temperature. Structure: A sectional area of a flow passage in the vicinity of an inner peripheral surface of a wrapper tube is limited over the entire length to prevent the temperature of a fuel element in the outermost peripheral portion from being excessively decreased to thereby flatten temperature distribution. To this end, a plurality of pincture-frame-like sheet metals constituting a spacer for supporting a fuel assembly, which has a plurality of fuel elements planted lengthwise and in given spaced relation within the wrapper tube, is disposed in longitudinal grooves and in stacked fashion to form a substantially honeycomb-like space in cross section. The fuel elements are inserted and supported in the space to form a fuel assembly. (Kamimura, M.)

  16. Welding facilities for NPP assembling

    International Nuclear Information System (INIS)

    Rojtenberg, S.S.

    1987-01-01

    Recommendations concerning the choice of equipment for welding in pre-assembling work shops, in the enlarging assembling shops and at the assembling site, are given. Advanced production automatic welders and semiautomatic machines, applied during the NPP equipment assembling as well as automatic machines specially produced for welding the main reactor components and pipelines are described. Automatic and semiautomatic machine and manual welding post supply sources are considered

  17. De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome

    Science.gov (United States)

    Schulze, Thomas T.; Ali, Jonathan M.; Bartlett, Maggie L.; McFarland, Madalyn M.; Clement, Emalie J.; Won, Harim I.; Sanford, Austin G.; Monzingo, Elyssa B.; Martens, Matthew C.; Hemsley, Ryan M.; Kumar, Sidharta; Gouin, Nicolas; Kolok, Alan S.; Davis, Paul H.

    2016-01-01

    Trichomycterus areolatus is an endemic species of pencil catfish that inhabits the riffles and rapids of many freshwater ecosystems of Chile. Despite its unique adaptation to Chile's high gradient watersheds and therefore potential application in the investigation of ecosystem integrity and environmental contamination, relatively little is known regarding the molecular biology of this environmental sentinel. Here, we detail the assembly of the Trichomycterus areolatus transcriptome, a molecular resource for the study of this organism and its molecular response to the environment. RNA-Seq reads were obtained by next-generation sequencing with an Illumina® platform and processed using PRINSEQ. The transcriptome assembly was performed using TRINITY assembler. Transcriptome validation was performed by functional characterization with KOG, KEGG, and GO analyses. Additionally, differential expression analysis highlights sex-specific expression patterns, and a list of endocrine and oxidative stress related transcripts are included. PMID:27672404

  18. Light-activated control of protein channel assembly mediated by membrane mechanics

    Science.gov (United States)

    Miller, David M.; Findlay, Heather E.; Ces, Oscar; Templer, Richard H.; Booth, Paula J.

    2016-12-01

    Photochemical processes provide versatile triggers of chemical reactions. Here, we use a photoactivated lipid switch to modulate the folding and assembly of a protein channel within a model biological membrane. In contrast to the information rich field of water-soluble protein folding, there is only a limited understanding of the assembly of proteins that are integral to biological membranes. It is however possible to exploit the foreboding hydrophobic lipid environment and control membrane protein folding via lipid bilayer mechanics. Mechanical properties such as lipid chain lateral pressure influence the insertion and folding of proteins in membranes, with different stages of folding having contrasting sensitivities to the bilayer properties. Studies to date have relied on altering bilayer properties through lipid compositional changes made at equilibrium, and thus can only be made before or after folding. We show that light-activation of photoisomerisable di-(5-[[4-(4-butylphenyl)azo]phenoxy]pentyl)phosphate (4-Azo-5P) lipids influences the folding and assembly of the pentameric bacterial mechanosensitive channel MscL. The use of a photochemical reaction enables the bilayer properties to be altered during folding, which is unprecedented. This mechanical manipulation during folding, allows for optimisation of different stages of the component insertion, folding and assembly steps within the same lipid system. The photochemical approach offers the potential to control channel assembly when generating synthetic devices that exploit the mechanosensitive protein as a nanovalve.

  19. Plasmon-enhanced photocurrent generation from self-assembled monolayers of phthalocyanine by using gold nanoparticle films.

    Science.gov (United States)

    Sugawa, Kosuke; Akiyama, Tsuyoshi; Kawazumi, Hirofumi; Yamada, Sunao

    2009-04-09

    The effect of localized electric fields on the photocurrent responses of phthalocyanine that was self-assembled on a gold nanoparticle film was investigated by comparing the conventional and the total internal reflection (TIR) experimental systems. In the case of photocurrent measurements, self-assembled monolayers (SAMs) of a thiol derivative of palladium phthalocyanine (PdPc) were prepared on the surface of gold-nanoparticle film that was fixed on the surface of indium-tin-oxide (ITO) substrate via a polyion (PdPc/AuP/polyion/ITO) or on the ITO surface (PdPc/ITO). Photocurrent action spectra from the two samples were compared by using the conventional spectrometer, and were found that PdPc/AuP/polyion/ITO gave considerably larger photocurrent signals than PdPc/ITO under the identical concentration of PdPc. In the case of the TIR experiments for the PdPc/AuP/polyion/ITO and the PdPc/AuP/Glass systems, incident-angle profiles of photocurrent and emission signals were correlated with each other, and they were different from that of the PdPc/ITO system. Accordingly, it was demonstrated that the photocurrent signals were certainly enhanced by the localized electric fields of the gold-nanoparticle film.

  20. Composite turbine bucket assembly

    Science.gov (United States)

    Liotta, Gary Charles; Garcia-Crespo, Andres

    2014-05-20

    A composite turbine blade assembly includes a ceramic blade including an airfoil portion, a shank portion and an attachment portion; and a transition assembly adapted to attach the ceramic blade to a turbine disk or rotor, the transition assembly including first and second transition components clamped together, trapping said ceramic airfoil therebetween. Interior surfaces of the first and second transition portions are formed to mate with the shank portion and the attachment portion of the ceramic blade, and exterior surfaces of said first and second transition components are formed to include an attachment feature enabling the transition assembly to be attached to the turbine rotor or disk.

  1. Neutron transport assembly calculation with non-zero net current boundary condition

    International Nuclear Information System (INIS)

    Jo, Chang Keun

    1993-02-01

    Fuel assembly calculation for the homogenized group constants is one of the most important parts in the reactor core analysis. The homogenized group constants of one a quarter assembly are usually generated for the nodal calculation of the reactor core. In the current nodal calculation, one or a quarter of the fuel assembly corresponds to a unit node. The homogenized group constant calculation for a fuel assembly proceeds through cell spectrum calculations, group condensation and cell homogenization calculations, two dimensional fuel assembly calculation, and then depletion calculations of fuel rods. To obtain the assembly wise homogenized group constants, the two dimensional transport calculation is usually performed. Most codes for the assembly wise homogenized group constants employ a zero net current boundary condition. CASMO-3 is such a code that is in wide use. The zero net current boundary condition is plausible and valid in an infinite reactor composed of the same kind of assemblies. However, the reactor is finite and the core is constructed by different kinds of assemblies. Hence, the assumption of the zero net current boundary condition is not valid in the actual reactor. The objective of this study is to develop a homogenization methodology that can treat any actual boundary condition, i.e. non-zero net current boundary condition. In order to treat the non-zero net current boundary condition, we modify CASMO-3. For the two-dimensional treatment in CASMO-3, a multigroup integral transport routine based on the method of transmission probability is used. The code performs assembly calculation with zero net current boundary condition. CASMO-3 is modified to consider the inhomogeneous source at the assembly boundary surface due to the non-zero net current. The modified version of CASMO-3 is called CASMO-3M. CASMO-3M is applied to several benchmark problems. In order to obtain the inhomogeneous source, the global calculation is performed. The local calculation

  2. TOOL ASSEMBLY WITH BI-DIRECTIONAL BEARING

    Science.gov (United States)

    Longhurst, G.E.

    1961-07-11

    A two-direction motion bearing which is incorporated in a refueling nuclear fuel element trsnsfer tool assembly is described. A plurality of bi- directional bearing assembliesare fixed equi-distantly about the circumference of the transfer tool assembly to provide the tool assembly with a bearing surface- for both axial and rotational motion. Each bi-directional bearing assembly contains a plurality of circumferentially bulged rollers mounted in a unique arrangement which will provide a bearing surface for rotational movement of the tool assembly within a bore. The bi-direc tional bearing assembly itself is capable of rational motion and thus provides for longitudinal movement of the tool assembly.

  3. BAGEL2 : mining for bacteriocins in genomic data

    NARCIS (Netherlands)

    de Jong, Anne; van Heel, Auke J.; Kok, Jan; Kuipers, Oscar P.

    Mining bacterial genomes for bacteriocins is a challenging task due to the substantial structure and sequence diversity, and generally small sizes, of these antimicrobial peptides. Major progress in the research of antimicrobial peptides and the ever-increasing quantities of genomic data, varying

  4. Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research.

    Science.gov (United States)

    Xu, Jiajia; Li, Yuanyuan; Ma, Xiuling; Ding, Jianfeng; Wang, Kai; Wang, Sisi; Tian, Ye; Zhang, Hui; Zhu, Xin-Guang

    2013-09-01

    Setaria viridis is an emerging model species for genetic studies of C4 photosynthesis. Many basic molecular resources need to be developed to support for this species. In this paper, we performed a comprehensive transcriptome analysis from multiple developmental stages and tissues of S. viridis using next-generation sequencing technologies. Sequencing of the transcriptome from multiple tissues across three developmental stages (seed germination, vegetative growth, and reproduction) yielded a total of 71 million single end 100 bp long reads. Reference-based assembly using Setaria italica genome as a reference generated 42,754 transcripts. De novo assembly generated 60,751 transcripts. In addition, 9,576 and 7,056 potential simple sequence repeats (SSRs) covering S. viridis genome were identified when using the reference based assembled transcripts and the de novo assembled transcripts, respectively. This identified transcripts and SSR provided by this study can be used for both reverse and forward genetic studies based on S. viridis.

  5. Fuel assembly spacer

    International Nuclear Information System (INIS)

    Shirakawa, Ken-etsu.

    1988-01-01

    Purpose: To reduce the pressure loss of coolants by fuel assembly spacers. Constitution: Spacers for supporting a fuel assembly are attached by means of a plurality of wires to an outer frame. The outer frame is made of shape memory alloy such that the wires are caused to slacken at normal temperature and the slacking of the wires is eliminated in excess of the transition temperature. Since the wires slacken at the normal temperature, fuel rods can be inserted easily. After the insertion of the fuel rods, when the entire portion or the outer frame is heated by water or gas at a predetermined temperature, the outer frame resumes its previously memorized shape to tighten the wires and, accordingly, the fuel rods can be supported firmly. In this way, since the fuel rods are inserted in the slacken state of the wires and, after the assembling, the outer frame resumes its memorized shape, the assembling work can be conducted efficiently. (Kamimura, M.)

  6. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2011-01-01

    Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation et and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly ma...

  7. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2011-01-01

    Tuesday 12 April at 14.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 20 April 2010 Presentation and approval of the Activity Report 2010 Presentation and approval of the Financial Report 2010 Presentation and approval of the Auditors Report 2010 Programme for 2011 Presentation and approval of the draft budget and subscription rate 2012 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may r...

  8. Ordinary General Assembly

    CERN Multimedia

    Staff Association

    2010-01-01

    Tuesday 20 April at 10.00 Council Chamber, Bldg 503 In conformity with the Statutes of the Staff Association, an ordinary General Assembly is organized once a year (article IV.2.1). Agenda   Adoption of the Agenda Approval of the Draft Minutes of the Ordinary General Assembly of 12 May 2009 Presentation and approval of the Activity Report 2009 Presentation and approval of the Financial Report 2009 Presentation and approval of the Auditors Report 2009 Programme for 2010 Presentation et and approval of the draft budget and subscription rate 2010 Election of the Election Committee Election of the Board of Auditors Miscellaneous We remind members of article IV.3.4 in the Statutes of the Association which reads: “After having dealt with all the items on the agenda, the members may, with the consent of the Assembly, have other matters discussed, but decisions may be taken only on the items listed on the agenda. Nevertheless, the Assembly may require t...

  9. Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

    Science.gov (United States)

    Senol Cali, Damla; Kim, Jeremie S; Ghose, Saugata; Alkan, Can; Mutlu, Onur

    2018-04-02

    Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating accurate genome assemblies. The tools used for nanopore sequence analysis are of critical importance, as they should overcome the high error rates of the technology. Our goal in this work is to comprehensively analyze current publicly available tools for nanopore sequence analysis to understand their advantages, disadvantages and performance bottlenecks. It is important to understand where the current tools do not perform well to develop better tools. To this end, we (1) analyze the multiple steps and the associated tools in the genome assembly pipeline using nanopore sequence data, and (2) provide guidelines for determining the appropriate tools for each step. Based on our analyses, we make four key observations: (1) the choice of the tool for basecalling plays a critical role in overcoming the high error rates of nanopore sequencing technology. (2) Read-to-read overlap finding tools, GraphMap and Minimap, perform similarly in terms of accuracy. However, Minimap has a lower memory usage, and it is faster than GraphMap. (3) There is a trade-off between accuracy and performance when deciding on the appropriate tool for the assembly step. The fast but less accurate assembler Miniasm can be used for quick initial assembly, and further polishing can be applied on top of it to increase the accuracy, which leads to faster overall assembly. (4) The state-of-the-art polishing tool, Racon, generates high-quality consensus sequences while providing a significant speedup over another polishing tool, Nanopolish. We analyze various combinations of different tools and expose the trade-offs between accuracy, performance, memory usage and scalability. We conclude that our observations can guide researchers and practitioners in making conscious

  10. Preliminary High-Throughput Metagenome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Dusheyko, Serge; Furman, Craig; Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank

    2007-03-26

    Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).

  11. Assembling Transgender Moments

    Science.gov (United States)

    Greteman, Adam J.

    2017-01-01

    In this article, the author seeks to assemble moments--scholarly, popular, and aesthetic--in order to explore the possibilities that emerge as moments collect in education's encounters with the needs, struggles, and possibilities of transgender lives and practices. Assembling moments, the author argues, illustrates the value of "moments"…

  12. Centrioles: some self-assembly required.

    Science.gov (United States)

    Song, Mi Hye; Miliaras, Nicholas B; Peel, Nina; O'Connell, Kevin F

    2008-12-01

    Centrioles play an important role in organizing microtubules and are precisely duplicated once per cell cycle. New (daughter) centrioles typically arise in association with existing (mother) centrioles (canonical assembly), suggesting that mother centrioles direct the formation of daughter centrioles. However, under certain circumstances, centrioles can also selfassemble free of an existing centriole (de novo assembly). Recent work indicates that the canonical and de novo pathways utilize a common mechanism and that a mother centriole spatially constrains the self-assembly process to occur within its immediate vicinity. Other recently identified mechanisms further regulate canonical assembly so that during each cell cycle, one and only one daughter centriole is assembled per mother centriole.

  13. Fuel assembly storage pool

    International Nuclear Information System (INIS)

    Hiranuma, Hiroshi.

    1976-01-01

    Object: To remove limitation of the number of storage of fuel assemblies to increase the number of storage thereof so as to relatively reduce the water depth required for shielding radioactive rays. Structure: Fuel assembly storage rack containers for receiving a plurality of spent fuel assembly racks are stacked in multi-layer fashion within a storage pool filled with water for shielding radioactive rays and removing heat. (Furukawa, Y.)

  14. Photonic-structured fibers assembled from cellulose nanocrystals with tunable polarized selective reflection.

    Science.gov (United States)

    Meng, Xin; Pan, Hui; Lu, Tao; Chen, Zhixin; Chen, Yanru; Zhang, Di; Zhu, Shenmin

    2018-05-14

    Fibers with self-assembled photonic structures are of special interest for their unique photonic properties and potential applications in smart textile industry. Inspired by nature, photonic-structured fibers were fabricated through the self-assembly of chiral nematic cellulose nanocrystals (CNC) and the fibers show tunable brilliant and selectively reflected colors under crossed-polarization. A simple wet-spinning method was applied to prepare composite fibers of mixed CNC matrix and polyvinyl alcohol (PVA) additions. During the processing, cholesteric CNC phase formed photonic fibers through a self-assembly process. The selective reflection color of the composite fibers in polarized condition shows a typical red-shift tendency with the increase of the PVA content, which is attributed to the increased helical pitch of the CNC. Furthermore, polarized angle can also alter the reflected colors. Owing to the excellent selective reflection properties under polarized condition, CNC-based photonic fibers are promising as the next-generation smart fibers, applied in the fields of specific display and sensing. © 2018 IOP Publishing Ltd.

  15. A unique highly hydrophobic anticancer prodrug self-assembled nanomedicine for cancer therapy.

    Science.gov (United States)

    Ren, Guolian; Jiang, Mengjuan; Xue, Peng; Wang, Jing; Wang, Yongjun; Chen, Bo; He, Zhonggui

    2016-11-01

    In contrast with common thought, we generated highly hydrophobic anticancer prodrug self-assembled nanoparticles without the aid of surface active substances, based on the conjugation of docetaxel to d-α-tocopherol succinate. The reduction-sensitive prodrug was synthesized with a disulfide bond inserted into the linker and was compared with a control reduction-insensitive prodrug. The morphology and stability of self-assembled nanoparticles were investigated. Cytotoxicity and apoptosis assays showed that the reduction-sensitive nanoparticles had higher anticancer activity than the reduction-insensitive nanoparticles. The reduction-sensitive nanoparticles exhibited favorable in vivo antitumor activity and tolerance compared with docetaxel Tween80-containing formulation and the reduction-insensitive nanoparticles. Taken together, the unique nanomedicine demonstrated a number of advantages: (i) ease and reproducibility of preparation, (ii) high drug payload, (iii) superior stability, (iv) prolonged circulation, and (v) improved therapeutic effect. This highly reproducible molecular assembly strategy should motivate the development of new nanomedicines. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. On the role of the chaperonin CCT in the just-in-time assembly process of APC/CCdc20.

    Science.gov (United States)

    Dekker, Carien

    2010-02-05

    The just-in-time hypothesis relates to the assembly of large multi-protein complexes and their regulation of activation in the cell. Here I postulate that chaperonins may contribute to the timely assembly and activation of such complexes. For the case of anaphase promoting complex/cyclosome(Cdc20) assembly by the eukaryotic chaperonin chaperonin containing Tcp1 it is shown that just-in-time synthesis and chaperone-assisted folding can synergise to generate a highly regulated assembly process of a protein complex that is vital for cell cycle progression. Once dependency has been established transcriptional regulation and chaperonin-dependency may have co-evolved to safeguard the timely activation of important multi-protein complexes. 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  17. ROSA-V large scale test facility (LSTF) system description for the third and fourth simulated fuel assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Mitsuhiro; Nakamura, Hideo; Ohtsu, Iwao [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment] [and others

    2003-03-01

    The Large Scale Test Facility (LSTF) is a full-height and 1/48 volumetrically scaled test facility of the Japan Atomic Energy Research Institute (JAERI) for system integral experiments simulating the thermal-hydraulic responses at full-pressure conditions of a 1100 MWe-class pressurized water reactor (PWR) during small break loss-of-coolant accidents (SBLOCAs) and other transients. The LSTF can also simulate well a next-generation type PWR such as the AP600 reactor. In the fifth phase of the Rig-of-Safety Assessment (ROSA-V) Program, eighty nine experiments have been conducted at the LSTF with the third simulated fuel assembly until June 2001, and five experiments have been conducted with the newly-installed fourth simulated fuel assembly until December 2002. In the ROSA-V program, various system integral experiments have been conducted to certify effectiveness of both accident management (AM) measures in beyond design basis accidents (BDBAs) and improved safety systems in the next-generation reactors. In addition, various separate-effect tests have been conducted to verify and develop computer codes and analytical models to predict non-homogeneous and multi-dimensional phenomena such as heat transfer across the steam generator U-tubes under the presence of non-condensable gases in both current and next-generation reactors. This report presents detailed information of the LSTF system with the third and fourth simulated fuel assemblies for the aid of experiment planning and analyses of experiment results. (author)

  18. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

    Directory of Open Access Journals (Sweden)

    Haznedaroglu Berat Z

    2012-07-01

    Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities

  19. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  20. Generation of consistent nuclear properties of DUPIC fuel by DRAGON with ENDF/B-VI nuclear data library

    International Nuclear Information System (INIS)

    Shen, W.; Rozon, D.

    1998-01-01

    DRAGON code with 89-groups ENDF/B-VI cross section library was used in this paper to generate consistent nuclear properties of DUPIC fuel. The reference feed material used for the DUPIC fuel cycle is a 17x17 French standard 900 MWe PWR spent fuel assembly with 3.2 w/o initial enrichment and 32500 MWD/7 discharge burnup. The PWR fuel assembly was modeled by JPMT/SYBILT transport method in DRAGON to generate nuclide fields of spent PWR fuel. The resultant nuclide fields constitute the initial fuel composition files for reference DUPIC fuel which can be accessed by DRAGON for CANDU 2D cluster geometry depletion calculation and 3D supercell calculation. Because of uneven spatial power distribution in PWR assemblies and full core, unexpected transition cycle, and various fuel management strategy, the spent PWR fuel composition is expected to be different from one assembly to the next. This heterogeneity was characterized also by modeling various spent PWR fuel assembly types in the paper. (author)

  1. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

    Science.gov (United States)

    Fonseca, Pedro; Romano, Flavio; Schreck, John S.; Ouldridge, Thomas E.; Doye, Jonathan P. K.; Louis, Ard A.

    2018-04-01

    Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model reproduces a critical temperature for the formation of the assembly that is close to the temperature at which assembly first occurs in experiments. Furthermore, the model allows us to investigate in detail the nucleation barriers and the distribution of critical nucleus shapes for the assembly of a single target structure. The assembly intermediates are compact and highly connected (although not maximally so), and classical nucleation theory provides a good fit to the height and shape of the nucleation barrier at temperatures close to where assembly first occurs.

  2. Supramolecular Nanocomposites Under Confinement: Chiral Optically Active Nanoparticle Assemblies and Beyond

    Science.gov (United States)

    Bai, Peter; Yang, Sui; Bao, Wei; Salmeron, Miquel; Zhang, Xiang; Xu, Ting

    2015-03-01

    Block copolymer-based supramolecules provide a versatile platform to direct the self-assembly of nanoparticles (NPs) into precisely controlled nanostructures in bulk and thin film geometries. A supramolecule, PS-b-P4VP(PDP), composed of the small molecule 3-pentadecylphenol (PDP) hydrogen bonded to a diblock copolymer, polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP), was subjected to 2-D volume confinement in cylindrical anodic aluminum oxide (AAO) membrane pores. TEM and 3-D TEM tomography reveal that the morphologies accessible by the supramolecule and supramolecule/NP composites, such as NP clusters, arrays, stacked rings, and single and double helical ribbons, are significantly different from those in the bulk or thin film. Furthermore, single molecule dark field scattering measurements demonstrate strong chiral optical response of single helical Au NP ribbon nanostructures in the near infrared wavelength regime. These studies demonstrate 2-D confinement to be an effective means to tailor self-assembled NP structure within supramolecule nanocomposites and pave the way for this assembly approach to be applied towards next generation chiral metamaterials and optoelectronic devices.

  3. AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

    Science.gov (United States)

    Correa, Miria C; Deus, Helena F; Vasconcelos, Ana T; Hayashi, Yuki; Ajani, Jaffer A; Patnana, Srikrishna V; Almeida, Jonas S

    2010-10-26

    AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces

  4. AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

    Directory of Open Access Journals (Sweden)

    Hayashi Yuki

    2010-10-01

    Full Text Available Abstract Background AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF, and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. Methods The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. Results We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model. We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally reflected into the configuration of the client's interface application. Conclusions The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general

  5. Novel nanostructures for next generation dye-sensitized solar cells

    KAUST Repository

    Té treault, Nicolas; Grä tzel, Michael

    2012-01-01

    Herein, we review our latest advancements in nanostructured photoanodes for next generation photovoltaics in general and dye-sensitized solar cells in particular. Bottom-up self-assembly techniques are developed to fabricate large-area 3D

  6. Layer-by-Layer-Assembled AuNPs-Decorated First-Generation Poly(amidoamine) Dendrimer with Reduced Graphene Oxide Core as Highly Sensitive Biosensing Platform with Controllable 3D Nanoarchitecture for Rapid Voltammetric Analysis of Ultratrace DNA Hybridization.

    Science.gov (United States)

    Jayakumar, Kumarasamy; Camarada, María Belén; Dharuman, Venkataraman; Rajesh, Rajendiran; Venkatesan, Rengarajan; Ju, Huangxian; Maniraj, Mahalingam; Rai, Abhishek; Barman, Sudipta Roy; Wen, Yangping

    2018-06-12

    The structure and electrochemical properties of layer-by-layer-assembled gold nanoparticles (AuNPs)-decorated first-generation (G1) poly(amidoamine) dendrimer (PD) with reduced graphene oxide (rGO) core as a highly sensitive and label-free biosensing platform with a controllable three-dimensional (3D) nanoarchitecture for the rapid voltammetric analysis of DNA hybridization at ultratrace levels were characterized. Mercaptopropinoic acid (MPA) was self-assembled onto Au substrate, then GG1PD formed by the covalent functionalization between the amino terminals of G1PD and carboxyl terminals of rGO was covalently linked onto MPA, and finally AuNPs were decorated onto GG1PD by strong physicochemical interaction between AuNPs and -OH of rGO in GG1PD, which was characterized through different techniques and confirmed by computational calculation. This 3D controllable thin-film electrode was optimized and evaluated using [Fe(CN) 6 ] 3-/4- as the redox probe and employed to covalently immobilize thiol-functionalized single-stranded DNA as biorecognition element to form the DNA nanobiosensor, which achieved fast, ultrasensitive, and high-selective differential pulse voltammetric analysis of DNA hybridization in a linear range from 1 × 10 -6 to 1 × 10 -13 g m -1 with a low detection limit of 9.07 × 10 -14 g m -1 . This work will open a new pathway for the controllable 3D nanoarchitecture of the layer-by-layer-assembled metal nanoparticles-functionalized lower-generation PD with two-dimensional layered nanomaterials as cores that can be employed as ultrasensitive and label-free nanobiodevices for the fast diagnosis of specific genome diseases in the field of biomedicine.

  7. Advanced gray rod control assembly

    Science.gov (United States)

    Drudy, Keith J; Carlson, William R; Conner, Michael E; Goldenfield, Mark; Hone, Michael J; Long, Jr., Carroll J; Parkinson, Jerod; Pomirleanu, Radu O

    2013-09-17

    An advanced gray rod control assembly (GRCA) for a nuclear reactor. The GRCA provides controlled insertion of gray rod assemblies into the reactor, thereby controlling the rate of power produced by the reactor and providing reactivity control at full power. Each gray rod assembly includes an elongated tubular member, a primary neutron-absorber disposed within the tubular member said neutron-absorber comprising an absorber material, preferably tungsten, having a 2200 m/s neutron absorption microscopic capture cross-section of from 10 to 30 barns. An internal support tube can be positioned between the primary absorber and the tubular member as a secondary absorber to enhance neutron absorption, absorber depletion, assembly weight, and assembly heat transfer characteristics.

  8. Multi-Robot Assembly Strategies and Metrics

    Science.gov (United States)

    MARVEL, JEREMY A.; BOSTELMAN, ROGER; FALCO, JOE

    2018-01-01

    We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies. PMID:29497234

  9. Multi-Robot Assembly Strategies and Metrics.

    Science.gov (United States)

    Marvel, Jeremy A; Bostelman, Roger; Falco, Joe

    2018-02-01

    We present a survey of multi-robot assembly applications and methods and describe trends and general insights into the multi-robot assembly problem for industrial applications. We focus on fixtureless assembly strategies featuring two or more robotic systems. Such robotic systems include industrial robot arms, dexterous robotic hands, and autonomous mobile platforms, such as automated guided vehicles. In this survey, we identify the types of assemblies that are enabled by utilizing multiple robots, the algorithms that synchronize the motions of the robots to complete the assembly operations, and the metrics used to assess the quality and performance of the assemblies.

  10. Self-assembled morphologies of an amphiphilic Y-shaped weak polyelectrolyte in a thin film.

    Science.gov (United States)

    Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

    2017-11-29

    Different from the self-assembly of neutral polymers, polyelectrolytes self-assemble into smaller aggregates with a more loosely assembled structure, which results from the repulsive forces acting between similar electrical compositions with the introduction of ions. The Y-shaped weak polyelectrolytes self-assemble into a core-shell type cylindrical structure with a hexagonal arrangement in a thin film, whose thickness is smaller than the gyration radius of the polymer chain. The corresponding formation mechanism consists of enrichment of the same components, adjustment of the shape of the aggregate, and the subsequent separation into individual aggregates. With the increase in the thickness of the thin film until it exceeds the gyration radius of the polymer chain, combined with the greater freedom of movement along the direction of thin film thickness, the self-assembled structure changes into a micellar structure. Under confinement, the repulsive force to the polymeric components is weakened by the repulsive forces among polyelectrolyte components with like charges, and this helps in generating aggregates with more uniform size and density distribution. In particular, when the repulsive force between the walls and the core forming components is greater than that between the walls and the shell forming components, such asymmetric confinement produces a crossed-cylindrical structure with nearly perpendicular arrangement of two cylinder arrays. Similarly, a novel three-crossed cylinder morphology is self-assembled upon removal of confinement.

  11. Modular jet impingement assemblies with passive and active flow control for electronics cooling

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Feng; Dede, Ercan Mehmet; Joshi, Shailesh

    2016-09-13

    Power electronics modules having modular jet impingement assembly utilized to cool heat generating devices are disclosed. The modular jet impingement assemblies include a modular manifold having a distribution recess, one or more angled inlet connection tubes positioned at an inlet end of the modular manifold that fluidly couple the inlet tube to the distribution recess and one or more outlet connection tubes positioned at an outlet end of the modular manifold that fluidly coupling the outlet tube to the distribution recess. The modular jet impingement assemblies include a manifold insert removably positioned within the distribution recess and include one or more inlet branch channels each including an impinging slot and one or more outlet branch channels each including a collecting slot. Further a heat transfer plate coupled to the modular manifold, the heat transfer plate comprising an impingement surface including an array of fins that extend toward the manifold insert.

  12. Developing Spent Fuel Assembly for Advanced NDA Instrument Calibration - NGSI Spent Fuel Project

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Jianwei [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Gauld, Ian C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Banfield, James [GE Hitachi Nuclear Energy, Wilmington, NC (United States); Skutnik, Steven [Univ. of Tennessee, Knoxville, TN (United States)

    2014-02-01

    This report summarizes the work by Oak Ridge National Laboratory to investigate the application of modeling and simulation to support the performance assessment and calibration of the advanced nondestructive assay (NDA) instruments developed under the Next Generation Safeguards Initiative Spent Fuel (NGSI-SF) Project. Advanced NDA instrument calibration will likely require reference spent fuel assemblies with well-characterized nuclide compositions that can serve as working standards. Because no reference spent fuel standard currently exists, and the practical ability to obtain direct measurement of nuclide compositions using destructive assay (DA) measurements of an entire fuel assembly is prohibitive in the near term due to the complexity and cost of spent fuel experiments, modeling and simulation will be required to construct such reference fuel assemblies. These calculations will be used to support instrument field tests at the Swedish Interim Storage Facility (Clab) for Spent Nuclear Fuel.

  13. Simulating control rod and fuel assembly motion using moving meshes

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, D. [Department of Electrical and Computer Engineering, McMaster University, 1280 Main Street West, Hamilton Ontario, L8S 4K1 (Canada)], E-mail: gilbertdw1@gmail.com; Roman, J.E. [Departamento de Sistemas Informaticos y Computacion, Universidad Politecnica de Valencia, Camino de Vera s/n, 46022 Valencia (Spain); Garland, Wm. J. [Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton Ontario, L8S 4K1 (Canada); Poehlman, W.F.S. [Department of Computing and Software, McMaster University, 1280 Main Street West, Hamilton Ontario, L8S 4K1 (Canada)

    2008-02-15

    A prerequisite for designing a transient simulation experiment which includes the motion of control and fuel assemblies is the careful verification of a steady state model which computes k{sub eff} versus assembly insertion distance. Previous studies in nuclear engineering have usually approached the problem of the motion of control rods with the use of nonlinear nodal models. Nodal methods employ special approximations for the leading and trailing cells of the moving assemblies to avoid the rod cusping problem which results from the naive volume weighted cell cross-section approximation. A prototype framework called the MOOSE has been developed for modeling moving components in the presence of diffusion phenomena. A linear finite difference model is constructed, solutions for which are computed by SLEPc, a high performance parallel eigenvalue solver. Design techniques for the implementation of a patched non-conformal mesh which links groups of sub-meshes that can move relative to one another are presented. The generation of matrices which represent moving meshes which conserve neutron current at their boundaries, and the performance of the framework when applied to model reactivity insertion experiments is also discussed.

  14. Design and analysis of permanent magnet moving coil type generator used in a micro-CHP generation system

    Science.gov (United States)

    Oros Pop, Susana Teodora; Berinde, Ioan; Vadan, Ioan

    2015-12-01

    This paper presents the design and analysis of a permanent magnet moving coil type generator driven by a free piston Stirling engine. This assemble free piston Stirling engine - permanent magnet moving coil type generator will be used in a combined heat and power (CHP) system for producing heat and power in residential area. The design procedure for moving coil type linear generator starts from the rated power imposed and finally uses the Faraday law of induction. The magneto-static magnetic field generated by permanent magnets is analyzed by means of Reluctance method and Finite Element Method in order to evaluate the magnetic flux density in the air gap, which is a design data imposed in the design stage, and the results are compared.

  15. ASSEMBLY TRANSFER SYSTEM DESCRIPTION DOCUMENT

    International Nuclear Information System (INIS)

    Gorpani, B.

    2000-01-01

    The Assembly Transfer System (ATS) receives, cools, and opens rail and truck transportation casks from the Carrier/Cask Handling System (CCHS). The system unloads transportation casks consisting of bare Spent Nuclear Fuel (SNF) assemblies, single element canisters, and Dual Purpose Canisters (DPCs). For casks containing DPCs, the system opens the DPCs and unloads the SNF. The system stages the assemblies, transfer assemblies to and from fuel-blending inventory pools, loads them into Disposal Containers (DCs), temporarily seals and inerts the DC, decontaminates the DC and transfers it to the Disposal Container Handling System. The system also prepares empty casks and DPCs for off-site shipment. Two identical Assembly Transfer System lines are provided in the Waste Handling Building (WHB). Each line operates independently to handle the waste transfer throughput and to support maintenance operations. Each system line primarily consists of wet and dry handling areas. The wet handling area includes a cask transport system, cask and DPC preparation system, and a wet assembly handling system. The basket transport system forms the transition between the wet and dry handling areas. The dry handling area includes the dry assembly handling system, assembly drying system, DC preparation system, and DC transport system. Both the wet and dry handling areas are controlled by the control and tracking system. The system operating sequence begins with moving transportation casks to the cask preparation area. The cask preparation operations consist of cask cavity gas sampling, cask venting, cask cool-down, outer lid removal, and inner shield plug lifting fixture attachment. Casks containing bare SNF (no DPC) are filled with water and placed in the cask unloading pool. The inner shield plugs are removed underwater. For casks containing a DPC, the cask lid(s) is removed, and the DPC is penetrated, sampled, vented, and cooled. A DPC lifting fixture is attached and the cask is placed

  16. Trajectory generation for two robots cooperating to perform a task

    International Nuclear Information System (INIS)

    Lewis, C.L.

    1995-01-01

    This paper formulates an algorithm for trajectory generation for two robots cooperating to perform an assembly task. Treating the two robots as a single redundant system, this paper derives two Jacobian matrices which relate the joint rates of the entire system to the relative motion of the grippers with respect to one another. The advantage of this formulation over existing methods is that a variety of secondary criteria can be conveniently satisfied using motion in the null-space of the relative Jacobian. This paper presents methods for generating dual-arm joint trajectories which perform assembly tasks while at the same time avoiding obstacles and joint limits, and also maintaining constraints on the absolute position and orientation of the end-effectors

  17. Genome Assembly and Computational Analysis Pipelines for Bacterial Pathogens

    KAUST Repository

    Rangkuti, Farania Gama Ardhina

    2011-06-01

    Pathogens lie behind the deadliest pandemics in history. To date, AIDS pandemic has resulted in more than 25 million fatal cases, while tuberculosis and malaria annually claim more than 2 million lives. Comparative genomic analyses are needed to gain insights into the molecular mechanisms of pathogens, but the abundance of biological data dictates that such studies cannot be performed without the assistance of computational approaches. This explains the significant need for computational pipelines for genome assembly and analyses. The aim of this research is to develop such pipelines. This work utilizes various bioinformatics approaches to analyze the high-­throughput genomic sequence data that has been obtained from several strains of bacterial pathogens. A pipeline has been compiled for quality control for sequencing and assembly, and several protocols have been developed to detect contaminations. Visualization has been generated of genomic data in various formats, in addition to alignment, homology detection and sequence variant detection. We have also implemented a metaheuristic algorithm that significantly improves bacterial genome assemblies compared to other known methods. Experiments on Mycobacterium tuberculosis H37Rv data showed that our method resulted in improvement of N50 value of up to 9697% while consistently maintaining high accuracy, covering around 98% of the published reference genome. Other improvement efforts were also implemented, consisting of iterative local assemblies and iterative correction of contiguated bases. Our result expedites the genomic analysis of virulent genes up to single base pair resolution. It is also applicable to virtually every pathogenic microorganism, propelling further research in the control of and protection from pathogen-­associated diseases.

  18. Storage method for spent fuel assembly

    International Nuclear Information System (INIS)

    Tajiri, Hiroshi.

    1992-01-01

    In the present invention, spent fuel assemblies are arranged at a dense pitch in a storage rack by suppressing the reactivity of the assemblies, to increase storage capacity for the spent fuel assemblies. That is, neutron absorbers are filled in the cladding tube of an absorbing rod, and the diameter thereof is substantially equal with that of a fuel rod. A great amount of the absorbing rods are arranged at the outer circumference of the fuel assembly. Then, they are fixed integrally to the fuel assembly and stored in a storage rack. In this case, the storage rack may be constituted only with angle materials which are inexpensive and installed simply. With such a constitution, in the fuel assembly having absorbing rods wound therearound, neutrons are absorbed by absorbing rods and the reactivity is lowered. Accordingly, the assembly arrangement pitch in the storage rack can be made dense. As a result, the storage capacity for the assemblies is increased. (I.S.)

  19. Nuclear reactor fuel assembly

    International Nuclear Information System (INIS)

    Vikhorev, Yu.V.; Biryukov, G.I.; Kirilyuk, N.A.; Lobanov, V.N.

    1977-01-01

    A fuel assembly is proposed for nuclear reactors allowing remote replacement of control rod bundles or their shifting from one assembly to another, i.e., their multipurpose use. This leads to a significant increase in fuel assembly usability. In the fuel assembly the control rod bundle is placed in guide tube channels to which baffles are attached for fuel element spacing. The remote handling of control rods is provided by a hollow cylinder with openings in its lower bottom through which the control rods pass. All control rods in a bundle are mounted to a cross beam which in turn is mounted in the cylinder and is designed for grasping the whole rod bundle by a remotely controlled telescopic mechanism in bundle replacement or shifting. (Z.M.)

  20. The Relationship between Self-Assembly and Conformal Mappings

    Science.gov (United States)

    Duque, Carlos; Santangelo, Christian

    The isotropic growth of a thin sheet has been used as a way to generate programmed shapes through controlled buckling. We discuss how conformal mappings, which are transformations that locally preserve angles, provide a way to quantify the area growth needed to produce a particular shape. A discrete version of the conformal map can be constructed from circle packings, which are maps between packings of circles whose contact network is preserved. This provides a link to the self-assembly of particles on curved surfaces. We performed simulations of attractive particles on a curved surface using molecular dynamics. The resulting particle configurations were used to generate the corresponding discrete conformal map, allowing us to quantify the degree of area distortion required to produce a particular shape by finding particle configurations that minimize the area distortion.

  1. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    Delafosse, Jacques.

    1977-01-01

    This invention relates to a nuclear fuel assembly for a light or heavy water reactor, or for a fast reactor of the kind with a bundle of cladded pins, maintained parallel to each other in a regular network by an assembly of separate supporting grids, fitted with elastic bearing surfaces on these pins [fr

  2. Fuel cycle and waste management. 2. Design of a BWR Core with Over-moderated MOX Fuel Assemblies

    International Nuclear Information System (INIS)

    Francois, J.L.; Del Campo, C. Martin

    2001-01-01

    The use of uranium-plutonium mixed-oxide (MOX) fuel in light water reactors is a current practice in several countries. Generally one-third of the reactor core is loaded with MOX fuel assemblies, and the other two-thirds is loaded with uranium assemblies. Nevertheless, the plutonium utilization could be more effective if the full core could be loaded with MOX fuel. In this work, the design of a boiling water reactor (BWR) core fully loaded with over-moderated MOX fuel designs was investigated. In previous work, the design of over-moderated BWR MOX fuel assemblies based on a 10 x 10 lattice was presented; these designs improve the neutron spectrum and the plutonium consumption rate, compared with standard MOX assemblies. To increase the moderator-to-fuel ratio (MFR), two approaches were followed. In the first approach, 8 or 12 fuel rods were replaced by water rods in the 10x10 assembly, which increased the MFR from 1.9 to 2.2 and 2.4, respectively. These designs are called MOX-8WR and MOX-12WR, respectively, in this paper. In the second approach, an 11 x 11 lattice with 24 water rods (11 x 11-24WR) was designed, which is a design with a number of active fuel rods (88) very close to the standard MOX assembly (91). The fuel rod diameter is smaller to preserve the assembly dimensions, and in this last case, the MFR is 2.4. The calculations were performed with the CM-PRESTO three-dimensional steady-state simulator. The nuclear data banks were generated with the HELIOS system, and they were processed by TABGEN to produce tables of nuclear cross sections depending on burnup, void, and exposure weighted void (void history), which are used by CM-PRESTO. One base reload pattern was designed for a BWR/5 rated at 1931 MW(thermal), to be used with the different over-moderated assembly designs. The reload pattern has 112 fresh fuel assemblies (FFAs) out of a total of 444 fuel assemblies and was simulated during 20 cycles with the Haling strategy, until an equilibrium cycle of

  3. Steam generator replacement at Surry Power Station

    International Nuclear Information System (INIS)

    McKay, H.S.

    1982-01-01

    The purposes of the steam generator repair program at Surry Power Station were to repair the tube degradation caused by corrosion-related phenomena and to restore the integrity of the steam generators to a level equivalent to new equipment. The repair program consisted of (1) replacing the existing lower-shell assemblies with new ones and (2) adding new moisture separation equipment to the upper-shell assemblies. These tasks required that several pieces of reactor coolant piping, feedwater piping, main steam piping, and the steam generator be cut and refurbished for reinstallation after the new lower shell was in place. The safety implications and other potential effects of the repair program both during the repair work and after the unit was returned to power were part of the design basis of the repair program. The repair program has been completed on Unit 2 without any adverse effects on the health and safety of the general public or to the personnel engaged in the repair work. Before the Unit 1 repair program began, a review of work procedures and field changes for the Unit 2 repair was conducted. Several major changes were made to avoid recurrence of problems and to streamline procedures. Steam generator replacements was completed on June 1, 1981, and the unit is presently in the startup phase of the outrage

  4. Blade attachment assembly

    Science.gov (United States)

    Garcia-Crespo, Andres Jose; Delvaux, John McConnell; Miller, Diane Patricia

    2016-05-03

    An assembly and method for affixing a turbomachine rotor blade to a rotor wheel are disclosed. In an embodiment, an adaptor member is provided disposed between the blade and the rotor wheel, the adaptor member including an adaptor attachment slot that is complementary to the blade attachment member, and an adaptor attachment member that is complementary to the rotor wheel attachment slot. A coverplate is provided, having a coverplate attachment member that is complementary to the rotor wheel attachment slot, and a hook for engaging the adaptor member. When assembled, the coverplate member matingly engages with the adaptor member, and retains the blade in the adaptor member, and the assembly in the rotor wheel.

  5. Magnetic nanoparticle assemblies

    CERN Document Server

    Trohidou, Kalliopi N

    2014-01-01

    Magnetic nanoparticles with diameters in the range of a few nanometers are today at the cutting edge of modern technology and innovation because of their use in numerous applications ranging from engineering to biomedicine. A great deal of scientific interest has been focused on the functionalization of magnetic nanoparticle assemblies. The understanding of interparticle interactions is necessary to clarify the physics of these assemblies and their use in the development of high-performance magnetic materials. This book reviews prominent research studies on the static and dynamic magnetic properties of nanoparticle assemblies, gathering together experimental and computational techniques in an effort to reveal their optimized magnetic properties for biomedical use and as ultra-high magnetic recording media.

  6. Nuclear fuel assembly

    International Nuclear Information System (INIS)

    Hayashi, Hiroshi; Watari, Yoshio; Hizahara, Hiroshi; Masuoka, Ryuzo.

    1970-01-01

    When exchanging nuclear fuel assemblies during the operation of a nuclear reactor, melting of fuel bodies, and severence of tubular claddings is halted at the time of insertion by furnishing a neutron absorbing material such as B 10 , Cd, Gd or the like at the forward end of the fuel assembly to thereby lower the power peak at the forward ends of the fuel elements to within tolerable levels and thus prevent both fuel liquification and excessive expansion. The neutron absorbing material may be attached in the form of a plate to the fuel assembly forward tie plate, or may be inserted as a pellet into the front end of the tubular cladding. (Owens, K.J.)

  7. Reactor fuel assembly

    International Nuclear Information System (INIS)

    Anthony, A.J.; Groves, M.D.

    1980-01-01

    A nuclear reactor fuel assembly having a lower end fitting and actuating means interacting therewith for holding the assembly down on the core support stand against the upward flow of coolant. Locking means for interacting with projections on the support stand are carried by the lower end fitting and are actuated by the movement of an actuating rod operated from above the top of the assembly. In one embodiment of the invention the downward movement of the actuating rod forces a latched spring to move outward into locking engagement with a shoulder on the support stand projections. In another embodiment, the actuating rod is rotated to effect the locking between the end fitting and the projection. (author)

  8. Fuel assembly inspection device

    International Nuclear Information System (INIS)

    Yaginuma, Yoshitaka

    1998-01-01

    The present invention provides a device suitable to inspect appearance of fuel assemblies by photographing the appearance of fuel assemblies. Namely, the inspection device of the present invention measures bowing of fuel assembly or each of fuel rods or both of them based on the partially photographed images of fuel assembly. In this case, there is disposed a means which flashily projects images in the form of horizontal line from a direction intersecting obliquely relative to a horizontal cross section of the fuel assembly. A first image processing means separates the projected image pictures including projected images and calculates bowing. A second image processing means replaces the projected image pictures of the projected images based on projected images just before and after the photographing. Then, images for the measurement of bowing and images for inspection can be obtained simultaneously. As a result, the time required for the photographing can be shortened, the time for inspection can be shortened and an effect of preventing deterioration of photographing means by radiation rays can be provided. (I.S.)

  9. BAUM: Improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach.

    Science.gov (United States)

    Wang, Anqi; Wang, Zhanyu; Li, Zheng; Li, Lei M

    2018-01-15

    It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the Second Generation Sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the Single-Molecule Real-Time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage. However, current assemblers of SGS data do not sufficiently take advantage of the OLC approach. Aiming at minimizing uncertainty, the proposed method BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-assisted assembly based on the genome of a close species; (2) or improve the results of existing assemblies that are obtained based on short or long sequencing reads. The tests on two eukaryote genomes, a wild rice Oryza longistaminata and a parrot Melopsittacus undulatus, show that BAUM achieved substantial improvement on genome size and continuity. Besides, BAUM reconstructed a considerable amount of repetitive regions that failed to be assembled by existing short read assemblers. We also propose statistical approaches to control the uncertainty in different steps of BAUM. http://www.zhanyuwang.xin/wordpress/index.php/2017/07/21/baum. lilei@amss.ac.cn. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  10. Vertical pump assembly

    International Nuclear Information System (INIS)

    Dohnal, M.; Rosel, J.; Skarka, V.

    1988-01-01

    The mounting is described of the drive assembly of a vertical pump for nuclear power plants in areas with seismic risk. The assembly is attached to the building floor using flexible and damping elements. The design allows producing seismically resistant pumps without major design changes in the existing types of vertical pumps. (E.S.). 1 fig

  11. Technology for assembling and welding of top and bottom nozzles in fuel assembly

    International Nuclear Information System (INIS)

    Xia Chenglie; Wan Longfu

    1989-10-01

    The construction character, technology and sequence of assembling and welding, assembling jig used for preventing from deformation, and acceptance test of welding technology for top and bottom nozzles are presented

  12. LISP software generative compilation within the frame of a SLIP system; La compilation generative de programmes LISP dans le cadre d'un systeme SLIP

    Energy Technology Data Exchange (ETDEWEB)

    Sitbon, Andre

    1968-04-24

    After having outlined the limitations associated with the use of some programming languages (Fortran, Algol, assembler, and so on), and the interest of the use of the LISP structure and its associated language, the author notices that some problems remain regarding the memorisation of the computing process obtained by interpretation. Thus, he introduces a generative compiler which produces an executable programme, and which is written in a language very close to the used machine language, i.e. the FAP assembler language.

  13. Framework to Implement Collaborative Robots in Manual Assembly: A Lean Automation Approach

    DEFF Research Database (Denmark)

    Malik, Ali Ahmad; Bilberg, Arne

    The recent proliferation of smart manufacturing technologies has emerged the concept of hybrid automation for assembly systems utilizing the best of humans and robots in a combination. Based on the ability to work alongside human-workers the next generation of industrial robots (or robotics 2...... of virtual simulations is discussed for validation and optimization of human-robot work environment....

  14. High-voltage nanosecond Marx generator with quasi-rectangular pulses

    International Nuclear Information System (INIS)

    Bulan, V.V.; Grabovskij, E.V.; Gribov, A.N.; Luzhnov, V.G.

    1999-01-01

    The automated high-voltage nanosecond generator, forming single pulses of any polarity on the load of 17 Ohm with polarity voltage from 100 up to 300 kV at the semiheight of 80 ns and the front of 7 ns is described. The generator is assembled on the basis of low-inductive capacitors, which by discharge form the pulse, close by form to rectangular one [ru

  15. A translator writing system for microcomputer high-level languages and assemblers

    Science.gov (United States)

    Collins, W. R.; Knight, J. C.; Noonan, R. E.

    1980-01-01

    In order to implement high level languages whenever possible, a translator writing system of advanced design was developed. It is intended for routine production use by many programmers working on different projects. As well as a fairly conventional parser generator, it includes a system for the rapid generation of table driven code generators. The parser generator was developed from a prototype version. The translator writing system includes various tools for the management of the source text of a compiler under construction. In addition, it supplies various default source code sections so that its output is always compilable and executable. The system thereby encourages iterative enhancement as a development methodology by ensuring an executable program from the earliest stages of a compiler development project. The translator writing system includes PASCAL/48 compiler, three assemblers, and two compilers for a subset of HAL/S.

  16. X-Ray Assembler Data

    Data.gov (United States)

    U.S. Department of Health & Human Services — Federal regulations require that an assembler who installs one or more certified components of a diagnostic x-ray system submit a report of assembly. This database...

  17. Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

    Science.gov (United States)

    Budak, Hikmet; Kantar, Melda

    2015-07-01

    MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

  18. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Parween, Sabiha; Nawaz, Kashif; Roy, Riti; Pole, Anil K; Venkata Suresh, B; Misra, Gopal; Jain, Mukesh; Yadav, Gitanjali; Parida, Swarup K; Tyagi, Akhilesh K; Bhatia, Sabhyata; Chattopadhyay, Debasis

    2015-08-11

    Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.

  19. Reiterative Recombination for the in vivo assembly of libraries of multigene pathways.

    Science.gov (United States)

    Wingler, Laura M; Cornish, Virginia W

    2011-09-13

    The increasing sophistication of synthetic biology is creating a demand for robust, broadly accessible methodology for constructing multigene pathways inside of the cell. Due to the difficulty of rationally designing pathways that function as desired in vivo, there is a further need to assemble libraries of pathways in parallel, in order to facilitate the combinatorial optimization of performance. While some in vitro DNA assembly methods can theoretically make libraries of pathways, these techniques are resource intensive and inherently require additional techniques to move the DNA back into cells. All previously reported in vivo assembly techniques have been low yielding, generating only tens to hundreds of constructs at a time. Here, we develop "Reiterative Recombination," a robust method for building multigene pathways directly in the yeast chromosome. Due to its use of endonuclease-induced homologous recombination in conjunction with recyclable markers, Reiterative Recombination provides a highly efficient, technically simple strategy for sequentially assembling an indefinite number of DNA constructs at a defined locus. In this work, we describe the design and construction of the first Reiterative Recombination system in Saccharomyces cerevisiae, and we show that it can be used to assemble multigene constructs. We further demonstrate that Reiterative Recombination can construct large mock libraries of at least 10(4) biosynthetic pathways. We anticipate that our system's simplicity and high efficiency will make it a broadly accessible technology for pathway construction and render it a valuable tool for optimizing pathways in vivo.

  20. On the adequacy of Cartesian geometry discrete ordinates solutions for assembly calculations

    International Nuclear Information System (INIS)

    Schunert, S.; Azmy, Y. Y.

    2009-01-01

    The current generation of lattice codes employs the method of Collision Probabilities (CP), the Method of Characteristics (MOC) or methods derived thereof to solve the two-dimensional multigroup transport equation on the assembly level. We compare the attainable solution accuracy of the lattice code DRAGON to the accuracy of the Discrete Ordinates (DO) code DORT on the basis of the two-dimensional GE-13 assembly in order to determine if the DO on Cartesian meshes is suitable as flux solver in future lattice codes. If DO exhibits high accuracy for assembly configurations, the next question is at what computational expense compared to traditional assembly codes. For this purpose DORT and DRAGON are required to converge to a reference solution, obtained by a multigroup MCNP calculation, with increasing angular quadrature order and decreasing spatial cell size; additionally for DRAGON the reference solution must be approached with increasing tracking density. The convergence of the two codes is judged via the multiplication factor, the pin wise relative error in the fission production rate, it's RMS and the maximum of it's absolute value over all pins. Additionally the computational cost of the obtained solutions is judged via the user CPU time. Although the multiplication factor computed by both codes converges with refinement of the employed meshes, the maximum deviation error of the fission production rate in the central region of the assembly remains unsatisfactorily high for CP and MOC. (authors)

  1. Electrical Programming of Soft Matter: Using Temporally Varying Electrical Inputs To Spatially Control Self Assembly.

    Science.gov (United States)

    Yan, Kun; Liu, Yi; Zhang, Jitao; Correa, Santiago O; Shang, Wu; Tsai, Cheng-Chieh; Bentley, William E; Shen, Jana; Scarcelli, Giuliano; Raub, Christopher B; Shi, Xiao-Wen; Payne, Gregory F

    2018-02-12

    The growing importance of hydrogels in translational medicine has stimulated the development of top-down fabrication methods, yet often these methods lack the capabilities to generate the complex matrix architectures observed in biology. Here we show that temporally varying electrical signals can cue a self-assembling polysaccharide to controllably form a hydrogel with complex internal patterns. Evidence from theory and experiment indicate that internal structure emerges through a subtle interplay between the electrical current that triggers self-assembly and the electrical potential (or electric field) that recruits and appears to orient the polysaccharide chains at the growing gel front. These studies demonstrate that short sequences (minutes) of low-power (∼1 V) electrical inputs can provide the program to guide self-assembly that yields hydrogels with stable, complex, and spatially varying structure and properties.

  2. Nuclear fuel assembly seismic amplitude limiter

    International Nuclear Information System (INIS)

    Anthony, A.J.

    1977-01-01

    The ability of a nuclear reactor to withstand high seismic loading is enhanced by including, on each fuel assembly, at least one seismic grid which reduces the magnitude of the possible lateral deflection of the individual fuel elements and the entire fuel assembly. The reduction in possible deflection minimizes the possibility of impact of the spacer grids of one fuel assembly on those of an adjacent fuel assembly and reduces the magnitude of forces associated with any such impact thereby minimizing the possibility of fuel assembly damage as a result of high seismic loading. The seismic grid is mounted from the fuel assembly guide tubes, has greater external dimensions when compared to the fuel assembly spacer grids and normally does not support or otherwise contact the fuel elements. The reduction in possible deflection is achieved through reduction of the clearance between adjacent fuel assemblies made possible by the use in the seismic grid of a high strength material characterized by favorable thermal expansion characteristics and minimal irradiation induced expansion

  3. Zseq: An Approach for Preprocessing Next-Generation Sequencing Data.

    Science.gov (United States)

    Alkhateeb, Abedalrhman; Rueda, Luis

    2017-08-01

    Next-generation sequencing technology generates a huge number of reads (short sequences), which contain a vast amount of genomic data. The sequencing process, however, comes with artifacts. Preprocessing of sequences is mandatory for further downstream analysis. We present Zseq, a linear method that identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq finds the complexity of the sequences by counting the number of unique k-mers in each sequence as its corresponding score and also takes into the account other factors such as ambiguous nucleotides or high GC-content percentage in k-mers. Based on a z-score threshold, Zseq sweeps through the sequences again and filters those with a z-score less than the user-defined threshold. Zseq algorithm is able to provide a better mapping rate; it reduces the number of ambiguous bases significantly in comparison with other methods. Evaluation of the filtered reads has been conducted by aligning the reads and assembling the transcripts using the reference genome as well as de novo assembly. The assembled transcripts show a better discriminative ability to separate cancer and normal samples in comparison with another state-of-the-art method. Moreover, de novo assembled transcripts from the reads filtered by Zseq have longer genomic sequences than other tested methods. Estimating the threshold of the cutoff point is introduced using labeling rules with optimistic results.

  4. Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence.

    Science.gov (United States)

    Evans, Teri; Johnson, Andrew D; Loose, Matthew

    2018-01-12

    Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download from https://tinyurl.com/y8gydc6n . The software pipeline is available from https://github.com/LooseLab/iterassemble .

  5. The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction

    Directory of Open Access Journals (Sweden)

    Garzón-Martínez Gina A

    2012-04-01

    Full Text Available Abstract Background Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry. Results We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs, using 454 GS FLX Titanium technology. ESTs, with an average length of 371 bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638 bp and 354 bp, respectively. Functional annotation was performed using NCBI’s BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato and Solanum tuberosum (potato. We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs. Conclusions We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the

  6. The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction.

    Science.gov (United States)

    Garzón-Martínez, Gina A; Zhu, Z Iris; Landsman, David; Barrero, Luz S; Mariño-Ramírez, Leonardo

    2012-04-25

    Physalis peruviana commonly known as Cape gooseberry is a member of the Solanaceae family that has an increasing popularity due to its nutritional and medicinal values. A broad range of genomic tools is available for other Solanaceae, including tomato and potato. However, limited genomic resources are currently available for Cape gooseberry. We report the generation of a total of 652,614 P. peruviana Expressed Sequence Tags (ESTs), using 454 GS FLX Titanium technology. ESTs, with an average length of 371 bp, were obtained from a normalized leaf cDNA library prepared using a Colombian commercial variety. De novo assembling was performed to generate a collection of 24,014 isotigs and 110,921 singletons, with an average length of 1,638 bp and 354 bp, respectively. Functional annotation was performed using NCBI's BLAST tools and Blast2GO, which identified putative functions for 21,191 assembled sequences, including gene families involved in all the major biological processes and molecular functions as well as defense response and amino acid metabolism pathways. Gene model predictions in P. peruviana were obtained by using the genomes of Solanum lycopersicum (tomato) and Solanum tuberosum (potato). We predict 9,436 P. peruviana sequences with multiple-exon models and conserved intron positions with respect to the potato and tomato genomes. Additionally, to study species diversity we developed 5,971 SSR markers from assembled ESTs. We present the first comprehensive analysis of the Physalis peruviana leaf transcriptome, which will provide valuable resources for development of genetic tools in the species. Assembled transcripts with gene models could serve as potential candidates for marker discovery with a variety of applications including: functional diversity, conservation and improvement to increase productivity and fruit quality. P. peruviana was estimated to be phylogenetically branched out before the divergence of five other Solanaceae family members, S

  7. Chemical reactions directed Peptide self-assembly.

    Science.gov (United States)

    Rasale, Dnyaneshwar B; Das, Apurba K

    2015-05-13

    Fabrication of self-assembled nanostructures is one of the important aspects in nanoscience and nanotechnology. The study of self-assembled soft materials remains an area of interest due to their potential applications in biomedicine. The versatile properties of soft materials can be tuned using a bottom up approach of small molecules. Peptide based self-assembly has significant impact in biology because of its unique features such as biocompatibility, straight peptide chain and the presence of different side chain functionality. These unique features explore peptides in various self-assembly process. In this review, we briefly introduce chemical reaction-mediated peptide self-assembly. Herein, we have emphasised enzymes, native chemical ligation and photochemical reactions in the exploration of peptide self-assembly.

  8. Benchmark assemblies of the Los Alamos critical assemblies facility

    International Nuclear Information System (INIS)

    Dowdy, E.J.

    1986-01-01

    Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described. (author)

  9. Benchmark assemblies of the Los Alamos Critical Assemblies Facility

    International Nuclear Information System (INIS)

    Dowdy, E.J.

    1985-01-01

    Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described

  10. Benchmark assemblies of the Los Alamos critical assemblies facility

    International Nuclear Information System (INIS)

    Dowdy, E.J.

    1985-01-01

    Several critical assemblies of precisely known materials composition and easily calculated and reproducible geometries have been constructed at the Los Alamos National Laboratory. Some of these machines, notably Jezebel, Flattop, Big Ten, and Godiva, have been used as benchmark assemblies for the comparison of the results of experimental measurements and computation of certain nuclear reaction parameters. These experiments are used to validate both the input nuclear data and the computational methods. The machines and the applications of these machines for integral nuclear data checks are described

  11. Molecular self-assembly advances and applications

    CERN Document Server

    Dequan, Alex Li

    2012-01-01

    In the past several decades, molecular self-assembly has emerged as one of the main themes in chemistry, biology, and materials science. This book compiles and details cutting-edge research in molecular assemblies ranging from self-organized peptide nanostructures and DNA-chromophore foldamers to supramolecular systems and metal-directed assemblies, even to nanocrystal superparticles and self-assembled microdevices

  12. SP-100 nuclear assembly test: Test assembly functional requirements and system arrangement

    International Nuclear Information System (INIS)

    Fallas, T.T.; Gluck, R.; Motwani, K.; Clay, H.; O'Neill, G.

    1991-01-01

    This paper describes the functional requirements and the system that will be tested to validate the reactor, flight shield, and flight controller of the SP-100 Generic Flight System (GFS). The Nuclear Assembly Test (NAT) consists of the test article (SP-100 reactor with control devices and the flight shield) and its supporting systems. The NAT test assembly is being designed by GE. Westinghouse Hanford Company (WHC) is designing the test cell and vacuum vessel system that will contain the NAT test assembly (Renkey et al. 1989). Preliminary design reviews have been completed and the final design is under way

  13. Fuel assembly guide tube

    International Nuclear Information System (INIS)

    Jabsen, F.S.

    1979-01-01

    This invention is directed toward a nuclear fuel assembly guide tube arrangement which restrains spacer grid movement due to coolant flow and which offers secondary means for supporting a fuel assembly during handling and transfer operations

  14. The states of the art of the nondestructive assay of spent nuclear fuel assemblies. A critical review of the Spent Fuel NDA Project of the U.S. Department of Energy's Next Generation Safeguards Initiative

    International Nuclear Information System (INIS)

    Bolind, Alan Michael; Seya, Michio

    2015-12-01

    The state of the art of the nondestructive assay of spent nuclear fuel assemblies is represented by the results of the Spent Fuel Nondestructive Assay Project of the Next Generation Safeguards Initiative (NGSI) of the U.S. Department of Energy / National Nuclear Security Administration. This report surveys the fourteen advanced nondestructive assay (NDA) techniques that were examined by the NGSI. For each technique, it explains how the technique operates, the NGSI's design of an instrument that uses the technique, how the data are analyzed, and the technique's chief limitations. After this survey of the NDA techniques, the report then discusses and critiques the current paradigm of the practice of NDA of spent fuel assemblies. It shows how the current main problem in the NDA of spent fuel assemblies—namely, an unacceptably large uncertainty in the assay results—is caused primarily by using too few independent NDA measurements. Because the physics of the NDA of spent fuel assemblies is three dimensional, at least three independent NDA measurements are required. Thus, NDA results should be able to be improved dramatically by combining the fourteen advanced NDA techniques plus other existing NDA techniques into appropriate combinations of three techniques. This report evaluates the NGSI's proposed NDA combinations according to these principles. (author)

  15. Magnetic self-assembly of small parts

    Science.gov (United States)

    Shetye, Sheetal B.

    Modern society's propensity for miniaturized end-user products is compelling electronic manufacturers to assemble and package different micro-scale, multi-technology components in more efficient and cost-effective manners. As the size of the components gets smaller, issues such as part sticking and alignment precision create challenges that slow the throughput of conventional robotic pick-n-place systems. As an alternative, various self-assembly approaches have been proposed to manipulate micro to millimeter scale components in a parallel fashion without human or robotic intervention. In this dissertation, magnetic self-assembly (MSA) is demonstrated as a highly efficient, completely parallel process for assembly of millimeter scale components. MSA is achieved by integrating permanent micromagnets onto component bonding surfaces using wafer-level microfabrication processes. Embedded bonded powder methods are used for fabrication of the magnets. The magnets are then magnetized using pulse magnetization methods, and the wafers are then singulated to form individual components. When the components are randomly mixed together, self-assembly occurs when the intermagnetic forces overcome the mixing forces. Analytical and finite element methods (FEM) are used to study the force interactions between the micromagnets. The multifunctional aspects of MSA are presented through demonstration of part-to-part and part-to-substrate assembly of 1 mm x 1mm x 0.5 mm silicon components. Part-to-part assembly is demonstrated by batch assembly of free-floating parts in a liquid environment with the assembly yield of different magnetic patterns varying from 88% to 90% in 20 s. Part-to-substrate assembly is demonstrated by assembling an ordered array onto a fixed substrate in a dry environment with the assembly yield varying from 86% to 99%. In both cases, diverse magnetic shapes/patterns are used to control the alignment and angular orientation of the components. A mathematical model is

  16. Mechanical Self-Assembly Science and Applications

    CERN Document Server

    2013-01-01

    Mechanical Self-Assembly: Science and Applications introduces a novel category of self-assembly driven by mechanical forces. This book discusses self-assembly in various types of small material structures including thin films, surfaces, and micro- and nano-wires, as well as the practice's potential application in micro and nanoelectronics, MEMS/NEMS, and biomedical engineering. The mechanical self-assembly process is inherently quick, simple, and cost-effective, as well as accessible to a large number of materials, such as curved surfaces for forming three-dimensional small structures. Mechanical self-assembly is complementary to, and sometimes offer advantages over, the traditional micro- and nano-fabrication. This book also: Presents a highly original aspect of the science of self-assembly Describes the novel methods of mechanical assembly used to fabricate a variety of new three-dimensional material structures in simple and cost-effective ways Provides simple insights to a number of biological systems and ...

  17. Directed Self-Assembly of Nanodispersions

    Energy Technology Data Exchange (ETDEWEB)

    Furst, Eric M [University of Delaware

    2013-11-15

    Directed self-assembly promises to be the technologically and economically optimal approach to industrial-scale nanotechnology, and will enable the realization of inexpensive, reproducible and active nanostructured materials with tailored photonic, transport and mechanical properties. These new nanomaterials will play a critical role in meeting the 21st century grand challenges of the US, including energy diversity and sustainability, national security and economic competitiveness. The goal of this work was to develop and fundamentally validate methods of directed selfassembly of nanomaterials and nanodispersion processing. The specific aims were: 1. Nanocolloid self-assembly and interactions in AC electric fields. In an effort to reduce the particle sizes used in AC electric field self-assembly to lengthscales, we propose detailed characterizations of field-driven structures and studies of the fundamental underlying particle interactions. We will utilize microscopy and light scattering to assess order-disorder transitions and self-assembled structures under a variety of field and physicochemical conditions. Optical trapping will be used to measure particle interactions. These experiments will be synergetic with calculations of the particle polarizability, enabling us to both validate interactions and predict the order-disorder transition for nanocolloids. 2. Assembly of anisotropic nanocolloids. Particle shape has profound effects on structure and flow behavior of dispersions, and greatly complicates their processing and self-assembly. The methods developed to study the self-assembled structures and underlying particle interactions for dispersions of isotropic nanocolloids will be extended to systems composed of anisotropic particles. This report reviews several key advances that have been made during this project, including, (1) advances in the measurement of particle polarization mechanisms underlying field-directed self-assembly, and (2) progress in the

  18. Self-Assembly of Flux-Closure Polygons from Magnetite Nanocubes.

    Science.gov (United States)

    Szyndler, Megan W; Corn, Robert M

    2012-09-06

    Well-defined nanoscale flux-closure polygons (nanogons) have been fabricated on hydrophilic surfaces from the face-to-face self-assembly of magnetite nanocubes. Uniform ferrimagnetic magnetite nanocubes (∼86 nm) were synthesized and characterized with a combination of electron microscopy, diffraction, and magnetization measurements. The nanocubes were subsequently cast onto hydrophilic substrates, wherein the cubes lined up face-to-face and formed a variety of polygons due to magnetostatic and hydrophobic interactions. The generated surfaces consist primarily of three- and four-sided nanogons; polygons ranging from two to six sides were also observed. Further examination of the nanogons showed that the constraints of the face-to-face assembly of nanocubes often led to bowed sides, strained cube geometries, and mismatches at the acute angle vertices. Additionally, extra nanocubes were often present at the vertices, suggesting the presence of external magnetostatic fields at the polygon corners. These nanogons are inimitable nanoscale magnetic structures with potential applications in the areas of magnetic memory storage and high-frequency magnetics.

  19. De novo transcriptome assembly associated with fumonisin production by the rice pathogen Fusarium fujikuroi

    Directory of Open Access Journals (Sweden)

    Keerthi S. Guruge

    2018-06-01

    Full Text Available The present study employed a next-generation sequencing method to assemble a de novo transcriptome database designed to distinguish gene expression changes exhibited by the fumonisin-producing fungus Fusarium fujikuroi when grown under ‘fumonisin-producing’ compared to ‘non-fumonisin-producing’ conditions. The raw data of this study have been deposited at DNA Data Bank of Japan (DDBJ under the accession ID DRA006146. Keywords: Fusarium fujikuroi, Fumonisin, Next-generation sequencing, Transcriptome, Gene-expression

  20. Inverse Problem in Self-assembly

    Science.gov (United States)

    Tkachenko, Alexei

    2012-02-01

    By decorating colloids and nanoparticles with DNA, one can introduce highly selective key-lock interactions between them. This leads to a new class of systems and problems in soft condensed matter physics. In particular, this opens a possibility to solve inverse problem in self-assembly: how to build an arbitrary desired structure with the bottom-up approach? I will present a theoretical and computational analysis of the hierarchical strategy in attacking this problem. It involves self-assembly of particular building blocks (``octopus particles''), that in turn would assemble into the target structure. On a conceptual level, our approach combines elements of three different brands of programmable self assembly: DNA nanotechnology, nanoparticle-DNA assemblies and patchy colloids. I will discuss the general design principles, theoretical and practical limitations of this approach, and illustrate them with our simulation results. Our crucial result is that not only it is possible to design a system that has a given nanostructure as a ground state, but one can also program and optimize the kinetic pathway for its self-assembly.