National Library of Energy BETA

Sample records for dna double strand

  1. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA glycosylase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Schormann, Norbert; Banerjee, Surajit; Ricciardi, Robert; Chattopadhyay, Debasish

    2015-06-02

    Background: Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. Results: This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This alsomore » represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. In comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. Conclusion: The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.« less

  2. Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

    DOE Patents [OSTI]

    Gray, Joe W. (Livermore, CA); Pinkel, Daniel (Walnut Creek, CA)

    1991-01-01

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. Probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations.

  3. Method of preparing and applying single stranded DNA probes to double stranded target DNAs in situ

    DOE Patents [OSTI]

    Gray, J.W.; Pinkel, D.

    1991-07-02

    A method is provided for producing single stranded non-self-complementary nucleic acid probes, and for treating target DNA for use therewith. The probe is constructed by treating DNA with a restriction enzyme and an exonuclease to form template/primers for a DNA polymerase. The digested strand is resynthesized in the presence of labeled nucleoside triphosphate precursor. Labeled single stranded fragments are separated from the resynthesized fragments to form the probe. Target DNA is treated with the same restriction enzyme used to construct the probe, and is treated with an exonuclease before application of the probe. The method significantly increases the efficiency and specificity of hybridization mixtures by increasing effective probe concentration by eliminating self-hybridization between both probe and target DNAs, and by reducing the amount of target DNA available for mismatched hybridizations. No Drawings

  4. Screening Tool for Providers of Double-Stranded DNA - Energy...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Technology Marketing SummaryThe invention screens purchase orders submitted to DNA synthesis companies.DescriptionOrders are screened to find indicators that the ordered DNA...

  5. Spin transport and spin polarization properties in double-stranded DNA

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2013-11-21

    We study the spin-dependent electron transport through a double-stranded DNA (dsDNA) using the Bogoliubov-de Gennes equations and non-equilibrium Green's function method. We calculate the spin-dependent electron conductance and spin-polarization for different lengths, helix angles, twist angles of dsDNA, the environment-induced dephasing factors, and hopping integral. It is shown that the conductance decreases by increasing the length and dephasing factor. Also, we show that the spin-polarization depends on the helical symmetry and the length of DNA. It is shown that the double-stranded DNA can act as a perfect spin filter. Finally, we show that the sign of spin polarization can be inverted from +1 (?1) to ?1 (+1) for some values of hopping integral.

  6. Zinc chromate induces chromosome instability and DNA double strand breaks in human lung cells

    SciTech Connect (OSTI)

    Xie Hong; Holmes, Amie L.; Young, Jamie L.; Qin Qin; Joyce, Kellie; Pelsue, Stephen C.; Peng Cheng; Wise, Sandra S.; Jeevarajan, Antony S.; Wallace, William T.; Hammond, Dianne; Wise, John Pierce E-mail: John.Wise@usm.maine.edu

    2009-02-01

    Hexavalent chromium Cr(VI) is a respiratory toxicant and carcinogen, with solubility playing an important role in its carcinogenic potential. Zinc chromate, a water insoluble or 'particulate' Cr(VI) compound, has been shown to be carcinogenic in epidemiology studies and to induce tumors in experimental animals, but its genotoxicity is poorly understood. Our study shows that zinc chromate induced concentration-dependent increases in cytotoxicity, chromosome damage and DNA double strand breaks in human lung cells. In response to zinc chromate-induced breaks, MRE11 expression was increased and ATM and ATR were phosphorylated, indicating that the DNA double strand break repair system was initiated in the cells. In addition, our data show that zinc chromate-induced double strand breaks were only observed in the G2/M phase population, with no significant amount of double strand breaks observed in G1 and S phase cells. These data will aid in understanding the mechanisms of zinc chromate toxicity and carcinogenesis.

  7. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  8. Double-stranded DNA organization in bacteriophage heads: An alternative toroid-based model

    SciTech Connect (OSTI)

    Hud, N.V.

    1995-10-01

    Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent with all available data. Recently, the authors proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here the authors propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.

  9. The effect of a magnetic field on the spin-selective transport in double-stranded DNA

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-05-28

    Spin-polarization in double-stranded DNA is studied in the presence of a magnetic field applied along its helix axis using the non-equilibrium Green's function method. The spin-polarization could be tuned by changing the magnetic field. In some special cases, the double-stranded DNA behaved as a perfect spin-filter. Furthermore, the dependency of the spin-polarization on the spin-orbit strength and dephasing strength is studied.

  10. Proximity-induced superconductivity effect in a double-stranded DNA

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-02-07

    We study the proximity-induced superconductivity effect in a double-stranded DNA by solving the Bogoliubov-de Gennes equations and taking into account the effect of thermal fluctuations of the twist angle between neighboring base pairs. We show that the electron conductance is spin-dependent and the conductance of spin up (down) increases (decreases) due to the spin-orbit coupling (SOC). It is found that, for T?

  11. Probability of double-strand breaks in genome-sized DNA by {gamma}-ray decreases markedly as the DNA concentration increases

    SciTech Connect (OSTI)

    Shimobayashi, Shunsuke F.; Iwaki, Takafumi; Mori, Toshiaki; Yoshikawa, Kenichi

    2013-05-07

    By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by {gamma}-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P{sub 1}, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.

  12. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Oakland, CA)

    2000-01-01

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

  13. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, A.N.; Benson, S.C.

    1998-07-21

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye. 10 figs.

  14. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Oakland, CA)

    1998-01-01

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a cationic chain. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

  15. Dyes designed for high sensitivity detection of double-stranded DNA

    DOE Patents [OSTI]

    Glazer, Alexander N. (Orinda, CA); Benson, Scott C. (Albany, CA)

    1994-01-01

    Novel fluorescent dyes are provided, characterized by having a fluorophore joined to a polycationic chain of at least two positive charges. The dyes are found to provide for high enhancement upon binding to nucleic acid and have strong binding affinities to the nucleic acid, as compared to the fluorophore without the polycationic chain. The dyes find use in detection of dsDNA in gel electrophoresis and solution at substantially higher sensitivities using substantially less dye.

  16. Homologous recombination contributes to the repair of DNA double-strand breaks induced by high-energy iron ions

    SciTech Connect (OSTI)

    Zafar, Faria; Seidler, Sara B.; Kronenberg, Amy; Schild, David; Wiese, Claudia

    2010-06-29

    To test the contribution of homologous recombinational repair (HRR) in repairing DNA damaged sites induced by high-energy iron ions, we used: (1) HRR-deficient rodent cells carrying a deletion in the RAD51D gene and (2) syngeneic human cells impaired for HRR by RAD51D or RAD51 knockdown using RNA interference. We show that in response to iron ions, HRR contributes to cell survival in rodent cells, and that HRR-deficiency abrogates RAD51 foci formation. Complementation of the HRR defect by human RAD51D rescues both enhanced cytotoxicity and RAD51 foci formation. For human cells irradiated with iron ions, cell survival is decreased, and, in p53 mutant cells, the levels of mutagenesis are increased when HRR is impaired. Human cells synchronized in S phase exhibit more pronounced resistance to iron ions as compared with cells in G1 phase, and this increase in radioresistance is diminished by RAD51 knockdown. These results implicate a role for RAD51-mediated DNA repair (i.e. HRR) in removing a fraction of clustered lesions induced by charged particle irradiation. Our results are the first to directly show the requirement for an intact HRR pathway in human cells in ensuring DNA repair and cell survival in response to high-energy high LET radiation.

  17. Unidirectional Scaffold-Strand Arrangement in DNA Origami

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Unidirectional Scaffold-Strand Arrangement in DNA Origami Authors: Han, D., Jiang, S., Samanta, A., Liu, Y., and Yan, H. Title: Unidirectional Scaffold-Strand Arrangement in DNA...

  18. Induction and Rejoining of DNA Double Strand Breaks Assessed by H2AX Phosphorylation in Melanoma Cells Irradiated with Proton and Lithium Beams

    SciTech Connect (OSTI)

    Ibanez, Irene L.; Bracalente, Candelaria; Molinari, Beatriz L.; Palmieri, Monica A.; Policastro, Lucia; Kreiner, Andres J.; Burlon, Alejandro A.; Valda, Alejandro; Navalesi, Daniela; Davidson, Jorge; Davidson, Miguel; Vazquez, Monica; Ozafran, Mabel; Duran, Hebe

    2009-07-15

    Purpose: The aim of this study was to evaluate the induction and rejoining of DNA double strand breaks (DSBs) in melanoma cells exposed to low and high linear energy transfer (LET) radiation. Methods and Materials: DSBs and survival were determined as a function of dose in melanoma cells (B16-F0) irradiated with monoenergetic proton and lithium beams and with a gamma source. Survival curves were obtained by clonogenic assay and fitted to the linear-quadratic model. DSBs were evaluated by the detection of phosphorylated histone H2AX ({gamma}H2AX) foci at 30 min and 6 h post-irradiation. Results: Survival curves showed the increasing effectiveness of radiation as a function of LET. {gamma}H2AX labeling showed an increase in the number of foci vs. dose for all the radiations evaluated. A decrease in the number of foci was found at 6 h post-irradiation for low LET radiation, revealing the repair capacity of DSBs. An increase in the size of {gamma}H2AX foci in cells irradiated with lithium beams was found, as compared with gamma and proton irradiations, which could be attributed to the clusters of DSBs induced by high LET radiation. Foci size increased at 6 h post-irradiation for lithium and proton irradiations in relation with persistent DSBs, showing a correlation with surviving fraction. Conclusions: Our results showed the response of B16-F0 cells to charged particle beams evaluated by the detection of {gamma}H2AX foci. We conclude that {gamma}H2AX foci size is an accurate parameter to correlate the rejoining of DSBs induced by different LET radiations and radiosensitivity.

  19. Nonenzymatic Role for WRN in Preserving Nascent DNA Strands after Replication Stress

    SciTech Connect (OSTI)

    Su, Fengtao; Mukherjee, Shibani; Yang, Yanyong; Mori, Eiichiro; Bhattacharya, Souparno; Kobayashi, Junya; Yannone, Steven  M.; Chen, David  J.; Asaithamby, Aroumougame

    2014-11-20

    WRN, the protein defective in Werner syndrome (WS), is a multifunctional nuclease involved in DNA damage repair, replication, and genome stability maintenance. It was assumed that the nuclease activities of WRN were critical for these functions. Here, we report a nonenzymatic role for WRN in preserving nascent DNA strands following replication stress. We found that lack of WRN led to shortening of nascent DNA strands after replication stress. Furthermore, we discovered that the exonuclease activity of MRE11 was responsible for the shortening of newly replicated DNA in the absence of WRN. Mechanistically, the N-terminal FHA domain of NBS1 recruits WRN to replication-associated DNA double-stranded breaks to stabilize Rad51 and to limit the nuclease activity of its C-terminal binding partner MRE11. Thus, this previously unrecognized nonenzymatic function of WRN in the stabilization of nascent DNA strands sheds light on the molecular reason for the origin of genome instability in WS individuals.

  20. Solid phase sequencing of double-stranded nucleic acids

    DOE Patents [OSTI]

    Fu, Dong-Jing (Waltham, MA); Cantor, Charles R. (Boston, MA); Koster, Hubert (Concord, MA); Smith, Cassandra L. (Boston, MA)

    2002-01-01

    This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

  1. An intercalation-locked parallel-stranded DNA tetraplex

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Tripathi, S.; Zhang, D.; Paukstelis, P. J.

    2015-01-27

    DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(ACBrUCGGABrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A base pairs betweenmore » adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H–1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

  2. Nonenzymatic Role for WRN in Preserving Nascent DNA Strands after Replication Stress

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Su, Fengtao; Mukherjee, Shibani; Yang, Yanyong; Mori, Eiichiro; Bhattacharya, Souparno; Kobayashi, Junya; Yannone, Steven  M.; Chen, David  J.; Asaithamby, Aroumougame

    2014-11-20

    WRN, the protein defective in Werner syndrome (WS), is a multifunctional nuclease involved in DNA damage repair, replication, and genome stability maintenance. It was assumed that the nuclease activities of WRN were critical for these functions. Here, we report a nonenzymatic role for WRN in preserving nascent DNA strands following replication stress. We found that lack of WRN led to shortening of nascent DNA strands after replication stress. Furthermore, we discovered that the exonuclease activity of MRE11 was responsible for the shortening of newly replicated DNA in the absence of WRN. Mechanistically, the N-terminal FHA domain of NBS1 recruits WRNmore » to replication-associated DNA double-stranded breaks to stabilize Rad51 and to limit the nuclease activity of its C-terminal binding partner MRE11. Thus, this previously unrecognized nonenzymatic function of WRN in the stabilization of nascent DNA strands sheds light on the molecular reason for the origin of genome instability in WS individuals.« less

  3. Synthesis of DNA

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P. (Danville, CA)

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  4. Method for producing labeled single-stranded nucleic acid probes

    DOE Patents [OSTI]

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  5. Method for nucleic acid hybridization using single-stranded DNA binding protein

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1996-01-01

    Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

  6. Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

    SciTech Connect (OSTI)

    Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; Ansong, Charles; Brewer, Heather M.; Bogomolnaya, Lydia; Adams, L. Garry; McClelland, Michael; Adkins, Joshua N.; Andrews-Polymenis, Helene L.; Fang, Ferric C.

    2015-09-14

    Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking its retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.

  7. Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Elfenbein, Johanna R.; Knodler, Leigh A.; Nakayasu, Ernesto S.; Ansong, Charles; Brewer, Heather M.; Bogomolnaya, Lydia; Adams, L. Garry; McClelland, Michael; Adkins, Joshua N.; Andrews-Polymenis, Helene L.; et al

    2015-09-14

    Multicopy single-stranded DNAs (msDNAs) are hybrid RNA-DNA molecules encoded on retroelements called retrons and produced by the action of retron reverse transcriptases. Retrons are widespread in bacteria but the natural function of msDNA has remained elusive despite 30 years of study. The major roadblock to elucidation of the function of these unique molecules has been the lack of any identifiable phenotypes for mutants unable to make msDNA. We report that msDNA of the zoonotic pathogen Salmonella Typhimurium is necessary for colonization of the intestine. Similarly, we observed a defect in intestinal persistence in an enteropathogenic E. coli mutant lacking itsmore » retron reverse transcriptase. Under anaerobic conditions in the absence of msDNA, proteins of central anaerobic metabolism needed for Salmonella colonization of the intestine are dysregulated. We show that the msDNA-deficient mutant can utilize nitrate, but not other alternate electron acceptors in anaerobic conditions. Consistent with the availability of nitrate in the inflamed gut, a neutrophilic inflammatory response partially rescued the ability of a mutant lacking msDNA to colonize the intestine. These findings together indicate that the mechanistic basis of msDNA function during Salmonella colonization of the intestine is proper production of proteins needed for anaerobic metabolism. We further conclude that a natural function of msDNA is to regulate protein abundance, the first attributable function for any msDNA. Our data provide novel insight into the function of this mysterious molecule that likely represents a new class of regulatory molecules.« less

  8. Activation of double-stranded RNA-dependent protein kinase inhibits proliferation of pancreatic ?-cells

    SciTech Connect (OSTI)

    Chen, Shan-Shan [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Jiang, Teng [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China)] [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Wang, Yi; Gu, Li-Ze [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China); Wu, Hui-Wen [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China)] [Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing (China); Tan, Lan [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China)] [Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Nanjing (China); Guo, Jun, E-mail: Guoj@njmu.edu.cn [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China) [Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing (China); Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing (China)

    2014-01-17

    Highlights: PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in ?-cells. Activated PKR inhibited ?-cell proliferation by arresting cell cycle at G1 phase. Activated PKR fully abrogated the pro-proliferative effects of IGF-I on ?-cells. -- Abstract: Double-stranded RNA-dependent protein kinase (PKR) is revealed to participate in the development of insulin resistance in peripheral tissues in type 2 diabetes (T2DM). Meanwhile, PKR is also characterized as a critical regulator of cell proliferation. To date, no study has focused on the impact of PKR on the proliferation of pancreatic ?-cells. Here, we adopted insulinoma cell lines and mice islet ?-cells to investigate: (1) the effects of glucolipotoxicity and pro-inflammatory cytokines on PKR activation; (2) the effects of PKR on proliferation of pancreatic ?-cells and its underlying mechanisms; (3) the actions of PKR on pro-proliferative effects of IGF-I and its underlying pathway. Our results provided the first evidence that PKR can be activated by glucolipitoxicity and pro-inflammatory cytokines in pancreatic ?-cells, and activated PKR significantly inhibited cell proliferation by arresting cell cycle at G1 phase. Reductions in cyclin D1 and D2 as well as increases in p27 and p53 were associated with the anti-proliferative effects of PKR, and proteasome-dependent degradation took part in the reduction of cyclin D1 and D2. Besides, PKR activation abrogated the pro-proliferative effects of IGF-I by activating JNK and disrupting IRS1/PI3K/Akt signaling pathway. These findings indicate that the anti-proliferative actions of PKR on pancreatic ?-cells may contribute to the pathogenesis of T2DM.

  9. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07

    Disclosed is a method for detecting and quantifying clustered damages in DNA. In this method, a first aliquot of the DNA to be tested for clustered damages with one or more lesion-specific cleaving reagents under conditions appropriate for cleavage of the DNA to produce single-strand nicks in the DNA at sites of damage lesions. The number average molecular length (Ln) of double stranded DNA is then quantitatively determined for the treated DNA. The number average molecular length (Ln) of double stranded DNA is also quantitatively determined for a second, untreated aliquot of the DNA. The frequency of clustered damages (.PHI..sub.c) in the DNA is then calculated.

  10. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Synthesis of DNA Citation Details In-Document Search Title: Synthesis of DNA A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined...

  11. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, C.R.; Ito, Takashi; Smith, C.L.

    1996-01-09

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel. 6 figs.

  12. DNA purification by triplex-affinity capture and affinity capture electrophoresis

    DOE Patents [OSTI]

    Cantor, Charles R.; Ito, Takashi; Smith, Cassandra L.

    1996-01-01

    The invention provides a method for purifying or isolating double stranded DNA intact using triple helix formation. The method includes the steps of complexing an oligonucleotide and double stranded DNA to generate a triple helix and immobilization of the triple helix on a solid phase by means of a molecular recognition system such as avidin/biotin. The purified DNA is then recovered intact by treating the solid phase with a reagent that breaks the bonds between the oligonucleotide and the intact double stranded DNA while not affecting the Watson-Crick base pairs of the double helix. The present invention also provides a method for purifying or isolating double stranded DNA intact by complexing the double stranded DNA with a specific binding partner and recovering the complex during electrophoresis by immobilizing it on a solid phase trap imbedded in an electrophoretic gel.

  13. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    DOE Patents [OSTI]

    Soares, M.B.; Fatima Bonaldo, M. de

    1998-12-08

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.

  14. Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

    DOE Patents [OSTI]

    Soares, Marcelo Bento (New York, NY); Bonaldo, Maria de Fatima (New York, NY)

    1998-01-01

    This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods.

  15. Chemical repair of base lesions, AP-sites, and strand breaks on plasmid DNA in dilute aqueous solution by ascorbic acid

    SciTech Connect (OSTI)

    Hata, Kuniki; Advanced Science Research Center, Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1195 ; Urushibara, Ayumi; Yamashita, Shinichi; Shikazono, Naoya; Yokoya, Akinari; Katsumura, Yosuke; Nuclear Professional School, School of Engineering, The University of Tokyo, 2-22 Shirakatashirane, Tokai-mura, Naka-gun, Ibaraki 319-1188

    2013-05-03

    Highlights: We report a novel mechanism of radiation protection of DNA by chemical activity of ascorbic acid. The chemical repair of DNA damage was revealed using biochemical assay and chemical kinetics analysis. We found that ascorbic acid significantly repairs precursors of nucleobase lesions and abasic sites. However, ascorbic acid seldom repairs precursors of DNA-strand breaks. -- Abstract: We quantified the damage yields produced in plasmid DNA by ?-irradiation in the presence of low concentrations (10100 ?M) of ascorbic acid, which is a major antioxidant in living systems, to clarify whether it chemically repairs radiation damage in DNA. The yield of DNA single strand breaks induced by irradiation was analyzed with agarose gel electrophoresis as conformational changes in closed circular plasmids. Base lesions and abasic sites were also observed as additional conformational changes by treating irradiated samples with glycosylase proteins. By comparing the suppression efficiencies to the induction of each DNA lesion, in addition to scavenging of the OH radicals derived from water radiolysis, it was found that ascorbic acid promotes the chemical repair of precursors of AP-sites and base lesions more effectively than those of single strand breaks. We estimated the efficiency of the chemical repair of each lesion using a kinetic model. Approximately 5060% of base lesions and AP-sites were repaired by 10 ?M ascorbic acid, although strand breaks were largely unrepaired by ascorbic acid at low concentrations. The methods in this study will provide a route to understanding the mechanistic aspects of antioxidant activity in living systems.

  16. Flow cytomeric measurement of DNA and incorporated nucleoside analogs

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1989-01-01

    A method is provided for simultaneously measuring total cellular DNA and incorporated nucleoside analog. The method entails altering the cellular DNA of cells grown in the presence of a nucleoside analog so that single stranded and double stranded portions are present. Separate stains are used against the two portions. An immunochemical stain is used against the single stranded portion to provide a measure of incorporated nucleoside analog, and a double strand DNA-specific stain is used against the double stranded portion to simultaneously provide a measure of total cellular DNA. The method permits rapid flow cytometric analysis of cell populations, rapid identification of cycling and noncycling subpopulations, and determination of the efficacy of S phase cytotoxic anticancer agents.

  17. Dna Sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  18. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOE Patents [OSTI]

    Ji, H.; Smith, L.M.

    1997-01-07

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support. 3 figs.

  19. Rapid purification of circular DNA by triplex-mediated affinity capture

    DOE Patents [OSTI]

    Ji, Huamin (4817 Sheboygan Ave., Madison, WI 53705); Smith, Lloyd M. (1115 Amherst Dr., Madison, WI 53705)

    1997-01-01

    A single-step capture of a target supercoiled double-stranded DNA molecule is accomplished by forming a local triple-helix among two strands of the supercoiled circular DNA and an oligonucleotide probe. The oligonucleotide is bound to an immobilizing support which facilitates the immobilization and purification of target DNA molecules. Non-target DNA molecules and other contaminating cellular material are easily removed by washing. The triple-helical structure is destabilized by raising the pH, leaving purified target DNA in the supernatant and reusable affinity capture oligonucleotide secured to the immobilizing support.

  20. Derivatized versions of ligase enzymes for constructing DNA sequences

    DOE Patents [OSTI]

    Mariella, Jr., Raymond P. (Danville, CA); Christian, Allen T. (Tracy, CA); Tucker, James D. (Novi, MN); Dzenitis, John M. (Livermore, CA); Papavasiliou, Alexandros P. (Oakland, CA)

    2006-08-15

    A method of making very long, double-stranded synthetic poly-nucleotides. A multiplicity of short oligonucleotides is provided. The short oligonucleotides are sequentially hybridized to each other. Enzymatic ligation of the oligonucleotides provides a contiguous piece of PCR-ready DNA of predetermined sequence.

  1. Probe and method for DNA detection

    DOE Patents [OSTI]

    Yeh, Hsin-Chih; Werner, James Henry; Sharma, Jaswinder Kumar; Martinez, Jennifer Suzanne

    2013-07-02

    A hybridization probe containing two linear strands of DNA lights up upon hybridization to a target DNA using silver nanoclusters that have been templated onto one of the DNA strands. Hybridization induces proximity between the nanoclusters on one strand and an overhang on the other strand, which results in enhanced fluorescence emission from the nanoclusters.

  2. Photochemistry of psoralen-DNA adducts, biological effects of psoralen-DNA adducts, applications of psoralen-DNA photochemistry

    SciTech Connect (OSTI)

    Shi, Yun-bo

    1988-03-01

    This thesis consists of three main parts and totally eight chapters. In Part I, The author will present studies on the photochemistry of psoralen-DNA adducts, specifically, the wavelength dependencies for the photoreversals of thymidine-HMT (4'-hydroxymethyl-4, 5', 8-trimenthylpsoralen) monoadducts and diadduct and the same adducts incorporated in DNA helices and the wavelength dependecies for the photocrossslinking of thymidine-HMT monoadducts in double-stranded helices. In Part II, The author will report some biological effects of psoralen-DNA adducts, i.e., the effects on double-stranded DNA stability, DNA structure, and transcription by E. coli and T7 RNA polymerases. Finally, The author will focus on the applications of psoralen-DNA photochemistry to investigation of protein-DNA interaction during transcription, which includes the interaction of E. coli and T7 RNA polymerases with DNA in elongation complexes arrested at specific psoralen-DNA adduct sites as revealed by DNase I footprinting experiments. 123 refs., 52 figs., 12 tabs.

  3. Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices

    DOE Patents [OSTI]

    Karger, Barry L.; Thilly, William G.; Foret, Frantisek; Khrapko, Konstaintin; Koehavong, Phouthone; Cohen, Aharon S.; Giese, Roger W.

    1997-01-01

    The disclosure relates to a method for resolving double-stranded DNA species differing by at least one base pair. Each of the species is characterized by an iso-melting domain with a unique melting temperature contiguous with a melting domain of higher thermal stability.

  4. Electrophoretic detection and separation of mutant DNA using replaceable polymer matrices

    DOE Patents [OSTI]

    Karger, B.L.; Thilly, W.G.; Foret, F.; Khrapko, K.; Koehavong, P.; Cohen, A.S.; Giese, R.W.

    1997-05-27

    The disclosure relates to a method for resolving double-stranded DNA species differing by at least one base pair. Each of the species is characterized by an iso-melting domain with a unique melting temperature contiguous with a melting domain of higher thermal stability. 18 figs.

  5. DUPLEX: A molecular mechanics program in torsion angle space for computing structures of DNA and RNA

    SciTech Connect (OSTI)

    Hingerty, B.E.

    1992-07-01

    DUPLEX produces energy minimized structures of DNA and RNA of any base sequence for single and double strands. The smallest subunits are deoxydinucleoside monophosphates, and up to 12 residues, single or double stranded can be treated. In addition, it can incorporate NMR derived interproton distances an constraints in the minimizations. Both upper and lower bounds for these distances can be specified. The program has been designed to run on a UNICOS Cray supercomputer, but should run, albeit slowly, on a laboratory computer such as a VAX or a workstation.

  6. An improved DNA force field for ssDNA interactions with gold nanoparticles

    SciTech Connect (OSTI)

    Jiang, Xiankai; Huai, Ping; Fan, Chunhai; Song, Bo E-mail: bosong@sinap.ac.cn; Gao, Jun; Huynh, Tien; Zhou, Ruhong E-mail: bosong@sinap.ac.cn

    2014-06-21

    The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones protecting hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the protection by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

  7. Plasma induced DNA damage: Comparison with the effects of ionizing radiation

    SciTech Connect (OSTI)

    Lazovi?, S.; Maleti?, D.; Pua?, N.; Malovi?, G.; Petrovi?, Z. Lj.; Leskovac, A.; Filipovi?, J.; Joksi?, G.

    2014-09-22

    We use human primary fibroblasts for comparing plasma and gamma rays induced DNA damage. In both cases, DNA strand breaks occur, but of fundamentally different nature. Unlike gamma exposure, contact with plasma predominantly leads to single strand breaks and base-damages, while double strand breaks are mainly consequence of the cell repair mechanisms. Different cell signaling mechanisms are detected confirming this (ataxia telangiectasia mutated - ATM and ataxia telangiectasia and Rad3 related - ATR, respectively). The effective plasma doses can be tuned to match the typical therapeutic doses of 2?Gy. Tailoring the effective dose through plasma power and duration of the treatment enables safety precautions mainly by inducing apoptosis and consequently reduced frequency of micronuclei.

  8. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect (OSTI)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other application papers of sequencing up to this level were also published in the mid 1990's. A major interest of the sequencing community has always been read length. The longer the sequence read per run the more efficient the process as well as the ability to read repeat sequences. We therefore devoted a great deal of time to studying the factors influencing read length in capillary electrophoresis, including polymer type and molecule weight, capillary column temperature, applied electric field, etc. In our initial optimization, we were able to demonstrate, for the first time, the sequencing of over 1000 bases with 90% accuracy. The run required 80 minutes for separation. Sequencing of 1000 bases per column was next demonstrated on a multiple capillary instrument. Our studies revealed that linear polyacrylamide produced the longest read lengths because the hydrophilic single strand DNA had minimal interaction with the very hydrophilic linear polyacrylamide. Any interaction of the DNA with the polymer would lead to broader peaks and lower read length. Another important parameter was the molecular weight of the linear chains. High molecular weight (> 1 MDA) was important to allow the long single strand DNA to reptate through the entangled polymer matrix. In an important paper, we showed an inverse emulsion method to prepare reproducibility linear polyacrylamide polymer with an average MWT of 9MDa. This approach was used in the polymer for sequencing the human genome. Another critical factor in the successful use of capillary electrophoresis for sequencing was the sample preparation method. In the Sanger sequencing reaction, high concentration of salts and dideoxynucleotide remained. Since the sample was introduced to the capillary column by electrokinetic injection, these salt ions would be favorably injected into the column over the sequencing fragments, thus reducing the signal for longer fragments and hence reading read length. In two papers, we examined the role of individual components from the sequencing reaction and then developed a protocol to reduce the deleterio

  9. DNA damage in cells exhibiting radiation-induced genomic instability

    SciTech Connect (OSTI)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesis that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.

  10. DNA damage in cells exhibiting radiation-induced genomic instability

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Keszenman, Deborah J.; Kolodiuk, Lucia; Baulch, Janet E.

    2015-02-22

    Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesismore » that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.« less

  11. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1997-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  12. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3{prime} noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

  13. Neutrino Physics AAPT Strand Day

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Physics AAPT Strand Day NSTA Regional, 2005 Jocelyn Monroe, Columbia University 1. What Is ... quark (FNAL) The Standard Model New Physics (Relatively Speaking) 1900s: e discovered ...

  14. DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    drives achievement in protein structure research September 15, 2014 Computational analysis key to structural understanding of molecular machine that targets viral DNA LOS ALAMOS, N.M., Sept. 15, 2014-When this week's print issue of the journal Science comes out, a collective cheer will go up from New Mexico, Montana and even the Netherlands, thanks to the type of collaborative effort that is more and more the norm in these connected times. Yes, the research was brilliant, and if we're lucky, it

  15. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

    Nolan, John P. (Santa Fe, NM); White, P. Scott (Los Alamos, NM); Cai, Hong (Los Alamos, NM)

    2001-01-01

    DNA polymorphism identity determination using flow cytometry. Primers designed to be immobilized on microspheres are allowed to anneal to the DNA strand under investigation, and are extended by either DNA polymerase using fluorescent dideoxynucleotides or ligated by DNA ligase to fluorescent reporter oligonucleotides. The fluorescence of either the dideoxynucleotide or the reporter oligonucleotide attached to the immobilized primer is measured by flow cytometry, thereby identifying the nucleotide polymorphism on the DNA strand.

  16. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

    SciTech Connect (OSTI)

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; ulc, Petr; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.

    2015-06-21

    We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  17. Using DNA to Build Nanomaterials

    DOE R&D Accomplishments [OSTI]

    Walsh, Karen McNulty

    2011-05-09

    Scientists use complementary strands of synthetic DNA to build functional materials from the bottom up. Future applications include biosensors, optical nano-devices, and new kinds of solar cells.

  18. Radiation-Induced Upregulation of Gene Expression From Adenoviral Vectors Mediated by DNA Damage Repair and Regulation

    SciTech Connect (OSTI)

    Nokisalmi, Petri; Rajecki, Maria; Pesonen, Sari; Escutenaire, Sophie; Soliymani, Rabah; Tenhunen, Mikko; Ahtiainen, Laura; Hemminki, Akseli

    2012-05-01

    Purpose: In the present study, we evaluated the combination of replication-deficient adenoviruses and radiotherapy in vitro. The purpose of the present study was to analyze the mechanism of radiation-mediated upregulation of adenoviral transgene expression. Methods and Materials: Adenoviral transgene expression (luciferase or green fluorescent protein) was studied with and without radiation in three cell lines: breast cancer M4A4-LM3, prostate cancer PC-3MM2, and lung cancer LNM35/enhanced green fluorescent protein. The effect of the radiation dose, modification of the viral capsid, and five different transgene promoters were studied. The cellular responses were studied using mass spectrometry and immunofluorescence analysis. Double strand break repair was modulated by inhibitors of heat shock protein 90, topoisomerase-I, and DNA protein kinase, and transgene expression was measured. Results: We found that a wide range of radiation doses increased adenoviral transgene expression regardless of the cell line, transgene, promoter, or viral capsid modification. Treatment with adenovirus, radiation, and double strand break repair inhibitors resulted in persistence of double strand breaks and subsequent increases in adenovirus transgene expression. Conclusions: Radiation-induced enhancement of adenoviral transgene expression is linked to DNA damage recognition and repair. Radiation induces a global cellular response that results in increased production of RNA and proteins, including adenoviral transgene products. This study provides a mechanistic rationale for combining radiation with adenoviral gene delivery.

  19. Determining orientation and direction of DNA sequences

    DOE Patents [OSTI]

    Goodwin, Edwin H. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)

    2000-01-01

    Determining orientation and direction of DNA sequences. A method by which fluorescence in situ hybridization can be made strand specific is described. Cell cultures are grown in a medium containing a halogenated nucleotide. The analog is partially incorporated in one DNA strand of each chromatid. This substitution takes place in opposite strands of the two sister chromatids. After staining with the fluorescent DNA-binding dye Hoechst 33258, cells are exposed to long-wavelength ultraviolet light which results in numerous strand nicks. These nicks enable the substituted strand to be denatured and solubilized by heat, treatment with high or low pH aqueous solutions, or by immersing the strands in 2.times.SSC (0.3M NaCl+0.03M sodium citrate), to name three procedures. It is unnecessary to enzymatically digest the strands using Exo III or another exonuclease in order to excise and solubilize nucleotides starting at the sites of the nicks. The denaturing/solubilizing process removes most of the substituted strand while leaving the prereplication strand largely intact. Hybridization of a single-stranded probe of a tandem repeat arranged in a head-to-tail orientation will result in hybridization only to the chromatid with the complementary strand present.

  20. Melatonin Protects Human Cells from Clustered DNA Damages, Killing and Acquisition of Soft Agar Growth Induced by X-rays or 970 MeV/n Fe ions

    SciTech Connect (OSTI)

    Das, B.; Sutherland, B.; Bennett, P. V.; Cutter, N. C.; Sutherland, J. C.

    2011-06-01

    We tested the ability of melatonin (N-acetyl-5 methoxytryptamine), a highly effective radical scavenger and human hormone, to protect DNA in solution and in human cells against induction of complex DNA clusters and biological damage induced by low or high linear energy transfer radiation (100 kVp X-rays, 970 MeV/nucleon Fe ions). Plasmid DNA in solution was treated with increasing concentrations of melatonin (0.0-3.5 mM) and were irradiated with X-rays. Human cells (28SC monocytes) were also irradiated with X-rays and Fe ions with and without 2 mM melatonin. Agarose plugs containing genomic DNA were subjected to Contour Clamped Homogeneous Electrophoretic Field (CHEF) followed by imaging and clustered DNA damages were measured by using Number Average length analysis. Transformation experiments on human primary fibroblast cells using soft agar colony assay were carried out which were irradiated with Fe ions with or without 2 mM melatonin. In plasmid DNA in solution, melatonin reduced the induction of single- and double-strand breaks. Pretreatment of human 28SC cells for 24 h before irradiation with 2 mM melatonin reduced the level of X-ray induced double-strand breaks by {approx}50%, of abasic clustered damages about 40%, and of Fe ion-induced double-strand breaks (41% reduction) and abasic clusters (34% reduction). It decreased transformation to soft agar growth of human primary cells by a factor of 10, but reduced killing by Fe ions only by 20-40%. Melatonin's effective reduction of radiation-induced critical DNA damages, cell killing, and striking decrease of transformation suggest that it is an excellent candidate as a countermeasure against radiation exposure, including radiation exposure to astronaut crews in space travel.

  1. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1992-01-01

    An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

  2. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

    Bonaldo, M.D.; Soares, M.B.

    1997-12-30

    This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library. 1 fig.

  3. Procedure for normalization of cDNA libraries

    DOE Patents [OSTI]

    Bonaldo, Maria DeFatima (New York, NY); Soares, Marcelo Bento (New York, NY)

    1997-01-01

    This invention provides a method to normalize a cDNA library constructed in a vector capable of being converted to single-stranded circles and capable of producing complementary nucleic acid molecules to the single-stranded circles comprising: (a) converting the cDNA library in single-stranded circles; (b) generating complementary nucleic acid molecules to the single-stranded circles; (c) hybridizing the single-stranded circles converted in step (a) with complementary nucleic acid molecules of step (b) to produce partial duplexes to an appropriate Cot; (e) separating the unhybridized single-stranded circles from the hybridized single-stranded circles, thereby generating a normalized cDNA library.

  4. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1996-01-09

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form. The method comprises: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. 4 figs.

  5. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1996-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to moderate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library.

  6. Probing the Conformational Distributions of Sub-Persistence Length DNA

    SciTech Connect (OSTI)

    Mastroianni, Alexander; Sivak, David; Geissler, Phillip; Alivisatos, Paul

    2009-06-08

    We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle X-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble FRET) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs (bp) are consistent with a simple worm-like chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 bp) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.

  7. After Cajun, what next for stranded costs?

    SciTech Connect (OSTI)

    Pembroke, J.D.

    1994-10-01

    Members of FERC have said that the Cajun decision does not pose a serious problem to its proposed rulemaking on stranded costs. But the D.C. Circuit`s Cajun decision, criticizing the concept of recovery for stranded investment in broad terms, promises to make that task difficult, if not impossible. The United States Court of Appeals for the District of Columbia Circuit, in its July 12, 1994 opinion in Cajun Electric Power Cooperative, Inc. v. Federal Energy Regulatory Commission, subjected the Entergy Corporations`s transmission tariff`s stranded investment provision to broad and, perhaps, fatal criticism. The Cajun opinion, premised on basic concepts of antitrust law, was issued at a time of substantial industry discussion on the concept of stranded investment and should greatly impact the decisions of both federal and state regulators on stranded investment.

  8. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  9. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  10. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted Print DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for medical and homeland security applications. Like digital chips, DNA

  11. Line narrowing spectroscopic studies of DNA-carcinogen adducts and DNA-dye complexes

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06

    Laser-induced fluorescence line narrowing and non-line narrowing spectroscopic methods were applied to conformational studies of stable DNA adducts of the 7{beta}, 8{alpha}-dihydoxy-9{alpha}, l0{alpha}-epoxy-7,8,9, 10-tetrahydrobenzo[{alpha}]pyrene (anti-BPDE). Stereochemically distinct (+)-trans-, ({minus})-trans-, (+)-cis- and ({minus})-cis adducts of anti-BPDE bound to exocyclic amino group of the central guanine in an 11-mer oligonucleotide, exist in a mixture of conformations in frozen aqueous buffer matrices. The (+)-trans adduct adopts primarily an external conformation with a smaller fraction ( {approximately} 25 %) exists in a partially base-stacked conformation. Both cis adducts were found to be intercalated with significant {pi}-{pi} stacking interactions between the pyrenyl residues and the bases. Conformations of the trans-adduct of (+)-anti -BPDE in 11-mer oligonucleotides were studied as a function of flanking bases. In single stranded form the adduct at G{sub 2} or G{sub 3} (5 ft-flanking, base guanine) adopts a conformation with strong, interaction with the bases. In contrast, the adduct with a 5ft-flanking, thymine exists in a primarily helixexternal conformation. Similar differences were observed in the double stranded oligonucleotides. The nature of the 3ft-flanking base has little influence on the conformational equilibrium of the (+)-trans-anti BPDE-dG adduct. The formation and repair of BPDE-N{sup 2}-dG in DNA isolated from the skin of mice treated topically with benzo[{alpha}]pyrene (BP) was studied. Low-temperature fluorescence spectroscopy of the intact DNA identified the major adduct as (+)-trans-anti-BPDE-N-dG, and the minor adduct fraction consisted mainly of (+)-cis-anti-BPDE-N{sup 2}-dG.

  12. DNA attachment to support structures

    DOE Patents [OSTI]

    Balhorn, Rodney L. (Livermore, CA); Barry, Christopher H. (Fresno, CA)

    2002-01-01

    Microscopic beads or other structures are attached to nucleic acids (DNA) using a terminal transferase. The transferase adds labeled dideoxy nucleotide bases to the ends of linear strands of DNA. The labels, such as the antigens digoxigenin and biotin, bind to the antibody compounds or other appropriate complementary ligands, which are bound to the microscopic beads or other support structures. The method does not require the synthesis of a synthetic oligonucleotide probe. The method can be used to tag or label DNA even when the DNA has an unknown sequence, has blunt ends, or is a very large fragment (e.g., >500 kilobase pairs).

  13. Method for rapid base sequencing in DNA and RNA with two base labeling

    DOE Patents [OSTI]

    Jett, James H.; Keller, Richard A.; Martin, John C.; Posner, Richard G.; Marrone, Babetta L.; Hammond, Mark L.; Simpson, Daniel J.

    1995-01-01

    Method for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand.

  14. Method for rapid base sequencing in DNA and RNA with two base labeling

    DOE Patents [OSTI]

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Posner, R.G.; Marrone, B.L.; Hammond, M.L.; Simpson, D.J.

    1995-04-11

    A method is described for rapid-base sequencing in DNA and RNA with two-base labeling and employing fluorescent detection of single molecules at two wavelengths. Bases modified to accept fluorescent labels are used to replicate a single DNA or RNA strand to be sequenced. The bases are then sequentially cleaved from the replicated strand, excited with a chosen spectrum of electromagnetic radiation, and the fluorescence from individual, tagged bases detected in the order of cleavage from the strand. 4 figures.

  15. Reconstitution of the cellular response to DNA damage in vitro using damage-activated extracts from mammalian cells

    SciTech Connect (OSTI)

    Roper, Katherine; Coverley, Dawn

    2012-03-10

    In proliferating mammalian cells, DNA damage is detected by sensors that elicit a cellular response which arrests the cell cycle and repairs the damage. As part of the DNA damage response, DNA replication is inhibited and, within seconds, histone H2AX is phosphorylated. Here we describe a cell-free system that reconstitutes the cellular response to DNA double strand breaks using damage-activated cell extracts and naieve nuclei. Using this system the effect of damage signalling on nuclei that do not contain DNA lesions can be studied, thereby uncoupling signalling and repair. Soluble extracts from G1/S phase cells that were treated with etoposide before isolation, or pre-incubated with nuclei from etoposide-treated cells during an in vitro activation reaction, restrain both initiation and elongation of DNA replication in naieve nuclei. At the same time, H2AX is phosphorylated in naieve nuclei in a manner that is dependent upon the phosphatidylinositol 3-kinase-like protein kinases. Notably, phosphorylated H2AX is not focal in naieve nuclei, but is evident throughout the nucleus suggesting that in the absence of DNA lesions the signal is not amplified such that discrete foci can be detected. This system offers a novel screening approach for inhibitors of DNA damage response kinases, which we demonstrate using the inhibitors wortmannin and LY294002. -- Highlights: Black-Right-Pointing-Pointer A cell free system that reconstitutes the response to DNA damage in the absence of DNA lesions. Black-Right-Pointing-Pointer Damage-activated extracts impose the cellular response to DNA damage on naieve nuclei. Black-Right-Pointing-Pointer PIKK-dependent response impacts positively and negatively on two separate fluorescent outputs. Black-Right-Pointing-Pointer Can be used to screen for inhibitors that impact on the response to damage but not on DNA repair. Black-Right-Pointing-Pointer LY294002 and wortmannin demonstrate the system's potential as a pathway focused screening approach.

  16. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1998-11-03

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3` noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries. 19 figs.

  17. Method for construction of normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, Marcelo B. (New York, NY); Efstratiadis, Argiris (Englewood, NJ)

    1998-01-01

    This invention provides a method to normalize a directional cDNA library constructed in a vector that allows propagation in single-stranded circle form comprising: (a) propagating the directional cDNA library in single-stranded circles; (b) generating fragments complementary to the 3' noncoding sequence of the single-stranded circles in the library to produce partial duplexes; (c) purifying the partial duplexes; (d) melting and reassociating the purified partial duplexes to appropriate Cot; and (e) purifying the unassociated single-stranded circles, thereby generating a normalized cDNA library. This invention also provides normalized cDNA libraries generated by the above-described method and uses of the generated libraries.

  18. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures Citation Details In-Document Search Title: Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical

  19. Method and apparatus for testing a forward-moving strand

    DOE Patents [OSTI]

    Ducommun, Joel (Chavannes, CH); Vulliens, Philippe (Palezieux-Gare, CH)

    1980-01-01

    In a method for testing a continuously forward-moving strand a light beam which passes along a plane that extends approximately perpendicularly to the longitudinal axis of the strand is introduced into the strand. The brightness value is measured on a place of the strand exterior which is distal from the light incidence place by means of at least one photoelectronic element disposed directly on the strand exterior and the measured result is evaluated in a gating circuit which is electrically connected to the photoelectronic element.

  20. Radiosensitivity profiles from a panel of ovarian cancer cell lines exhibiting genetic alterations in p53 and disparate DNA-dependent protein kinase activities

    SciTech Connect (OSTI)

    Langland, Gregory T.; Yannone, Steven M.; Langland, Rachel A.; Nakao, Aki; Guan, Yinghui; Long, Sydney B.T.; Vonguyen, Lien; Chen, David J.; Gray, Joe W; Chen, Fanqing

    2009-09-07

    The variability of radiation responses in ovarian tumors and tumor-derived cell lines is poorly understood. Since both DNA repair capacity and p53 status can significantly alter radiation sensitivity, we evaluated these factors along with radiation sensitivity in a panel of sporadic human ovarian carcinoma cell lines. We observed a gradation of radiation sensitivity among these sixteen lines, with a five-fold difference in the LD50 between the most radiosensitive and the most radioresistant cells. The DNA-dependent protein kinase (DNA-PK) is essential for the repair of radiation induced DNA double-strand breaks in human somatic cells. Therefore, we measured gene copy number, expression levels, protein abundance, genomic copy and kinase activity for DNA-PK in all of our cell lines. While there were detectable differences in DNA-PK between the cell lines, there was no clear correlation with any of these differences and radiation sensitivity. In contrast, p53 function as determined by two independent methods, correlated well with radiation sensitivity, indicating p53 mutant ovarian cancer cells are typically radioresistant relative to p53 wild-type lines. These data suggest that the activity of regulatory molecules such as p53 may be better indicators of radiation sensitivity than DNA repair enzymes such as DNAPK in ovarian cancer.

  1. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    When DNA Needs to Stand Up and Be Counted When DNA Needs to Stand Up and Be Counted Print Wednesday, 31 May 2006 00:00 DNA microarrays are small metal, glass, or silicon chips covered with patterns of short single-stranded DNA (ssDNA). These "DNA chips" are revolutionizing biotechnology, allowing scientists to identify and count many DNA sequences simultaneously. They are the enabling technology for genomic-based medicine and are a critical component of advanced diagnostic systems for

  2. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

    Krulevitch, Peter A. (Pleasanton, CA); Miles, Robin R. (Danville, CA); Wang, Xiao-Bo (San Diego, CA); Mariella, Raymond P. (Danville, CA); Gascoyne, Peter R. C. (Bellaire, TX); Balch, Joseph W. (Livermore, CA)

    2002-01-01

    Manipulation of DNA molecules in solution has become an essential aspect of genetic analyses used for biomedical assays, the identification of hazardous bacterial agents, and in decoding the human genome. Currently, most of the steps involved in preparing a DNA sample for analysis are performed manually and are time, labor, and equipment intensive. These steps include extraction of the DNA from spores or cells, separation of the DNA from other particles and molecules in the solution (e.g. dust, smoke, cell/spore debris, and proteins), and separation of the DNA itself into strands of specific lengths. Dielectrophoresis (DEP), a phenomenon whereby polarizable particles move in response to a gradient in electric field, can be used to manipulate and separate DNA in an automated fashion, considerably reducing the time and expense involved in DNA analyses, as well as allowing for the miniaturization of DNA analysis instruments. These applications include direct transport of DNA, trapping of DNA to allow for its separation from other particles or molecules in the solution, and the separation of DNA into strands of varying lengths.

  3. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

    Heimer, Brandon W.; Crown, Kevin K.; Bachand, George David

    2005-11-01

    Deoxyribonucleic acid (DNA) molecules represent Nature's genetic database, encoding the information necessary for all cellular processes. From a materials engineering perspective, DNA represents a nanoscale scaffold with highly refined structure, stability across a wide range of environmental conditions, and the ability to interact with a range of biomolecules. The ability to mass-manufacture functionalized DNA strands with Angstrom-level resolution through DNA replication technology, however, has not been explored. The long-term goal of the work presented in this report is focused on exploiting DNA and in vitro DNA replication processes to mass-manufacture nanocomposite materials. The specific objectives of this project were to: (1) develop methods for replicating DNA strands that incorporate nucleotides with ''chemical handles'', and (2) demonstrate attachment of nanocrystal quantum dots (nQDs) to functionalized DNA strands. Polymerase chain reaction (PCR) and primer extension methodologies were used to successfully synthesize amine-, thiol-, and biotin-functionalized DNA molecules. Significant variability in the efficiency of modified nucleotide incorporation was observed, and attributed to the intrinsic properties of the modified nucleotides. Noncovalent attachment of streptavidin-coated nQDs to biotin-modified DNA synthesized using the primer extension method was observed by epifluorescence microscopy. Data regarding covalent attachment of nQDs to amine- and thiol-functionalized DNA was generally inconclusive; alternative characterization tools are necessary to fully evaluate these attachment methods. Full realization of this technology may facilitate new approaches to manufacturing materials at the nanoscale. In addition, composite nQD-DNA materials may serve as novel recognition elements in sensor devices, or be used as diagnostic tools for forensic analyses. This report summarizes the results obtained over the course of this 1-year project.

  4. Methods to estimate stranded commitments for a restructuring US electricity industry

    SciTech Connect (OSTI)

    Hirst, E.; Hadley, S.; Baxter, L.

    1996-01-01

    Estimates of stranded commitments for US investor-owned electric utilities range widely, from as little as $20 billion to as much as $500 billion (more than double the shareholder equity in US utilities). These potential losses are a consequence of the above-market book values for some utility-owned power plants, long-term power-purchase contracts, deferred income taxes, regulatory assets, and public-policy programs. Because of the wide range of estimates and the potentially large dollar amounts involved, state and federal regulators need a clear understanding of the methods used to calculate these estimates. In addition, they may want simple methods that they can use to check the reasonableness of the estimates that utilities and other parties present in regulatory proceedings. This report explains various top-down and bottom-up methods to calculate stranded commitments. The purpose of this analysis is to help regulators and others understand the implications of different analytical approaches to estimating stranded-commitment amounts. Top-down methods, because they use the utility as the unit of analysis, are simple to apply and to understand. However, their aggregate nature makes it difficult to determine what specific assets and liabilities affect their estimates. Bottom-up methods use the individual asset (e.g., power plant) or liability (e.g., power-purchase contract, fuel-supply contract, and deferred income taxes) as the unit of analysis. These methods have substantial data and computational requirements.

  5. Structure of DNA-Bound FEN1 Reveals Mechanism of Action

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    to the template's nucleotides. But before polymerase builds the duplicate strand, an RNA primer must bind to the template acting as a short length of "pseudo-DNA" to whose...

  6. A double-double/double-single computation package

    Energy Science and Technology Software Center (OSTI)

    2004-12-01

    The DDFUNIDSFUN software permits a new or existing Fortran-90 program to utilize double-double precision (approx. 31 digits) or double-single precision (approx. 14 digits) arithmetic. Double-double precision is required by a rapidly expandirtg body of scientific computations in physics and mathematics, for which the conventional 64-bit IEEE computer arithmetic (about 16 decimal digit accuracy) is not sufficient. Double-single precision permits users of systems that do not have hardware 64-bit IEEE arithmetic (such as some game systems)more » to perform arithmetic at a precision nearly as high as that of systems that do. Both packages run significantly faster Than using multiple precision or arbitrary precision software for this purpose. The package includes an extensive set of low-level routines to perform high-precision arithmetic, including routines to calculate various algebraic and transcendental functions, such as square roots, sin, ccc, exp, log and others. In addition, the package includes high-level translation facilities, so that Fortran programs can utilize these facilities by making only a few changes to conventional Fortran programs. In most cases, the only changes that are required are to change the type statements of variables that one wishes to be treated as multiple precision, plus a few other minor changes. The DDFUN package is similar in functionality to the double-double part of the GD package, which was previously written at LBNL. However, the DDFUN package is written exclusively in Fortran-90, thus avoidIng difficulties that some users experience when using GD, which includes both Fortran-90 and C++ code.« less

  7. Gel Electrophoresis of Gold-DNA Nanoconjugates

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pellegrino, T.; Sperling, R. A.; Alivisatos, A. P.; Parak, W. J.

    2007-01-01

    Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effectivemore » diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.« less

  8. Chromosome doubling method

    DOE Patents [OSTI]

    Kato, Akio

    2006-11-14

    The invention provides methods for chromosome doubling in plants. The technique overcomes the low yields of doubled progeny associated with the use of prior techniques for doubling chromosomes in plants such as grasses. The technique can be used in large scale applications and has been demonstrated to be highly effective in maize. Following treatment in accordance with the invention, plants remain amenable to self fertilization, thereby allowing the efficient isolation of doubled progeny plants.

  9. Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA

    SciTech Connect (OSTI)

    Horton, John R.; Borgaro, Janine G.; Griggs, Rose M.; Quimby, Aine; Guan, Shengxi; Zhang, Xing; Wilson, Geoffrey G.; Zheng, Yu; Zhu, Zhenyu; Cheng, Xiaodong

    2014-07-03

    AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves DNA containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ~ 70 , consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ~ 22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.

  10. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

    Wong; Pak C. (Richland, WA), Wong; Kwong K. (Sugar Land, TX), Foote; Harlan P. (Richland, WA)

    2006-06-06

    Current technologies allow the generation of artificial DNA molecules and/or the ability to alter the DNA sequences of existing DNA molecules. With a careful coding scheme and arrangement, it is possible to encode important information as an artificial DNA strand and store it in a living host safely and permanently. This inventive technology can be used to identify origins and protect R&D investments. It can also be used in environmental research to track generations of organisms and observe the ecological impact of pollutants. Today, there are microorganisms that can survive under extreme conditions. As well, it is advantageous to consider multicellular organisms as hosts for stored information. These living organisms can provide as memory housing and protection for stored data or information. The present invention provides well for data storage in a living organism wherein at least one DNA sequence is encoded to represent data and incorporated into a living organism.

  11. Double Flash | Open Energy Information

    Open Energy Info (EERE)

    Double Flash Jump to: navigation, search Retrieved from "http:en.openei.orgwindex.php?titleDoubleFlash&oldid599606...

  12. Method for detecting point mutations in DNA utilizing fluorescence energy transfer

    DOE Patents [OSTI]

    Parkhurst, Lawrence J. (Lincoln, NE); Parkhurst, Kay M. (Lincoln, NE); Middendorf, Lyle (Lincoln, NE)

    2001-01-01

    A method for detecting point mutations in DNA using a fluorescently labeled oligomeric probe and Forster resonance energy transfer (FRET) is disclosed. The selected probe is initially labeled at each end with a fluorescence dye, which act together as a donor/acceptor pair for FRET. The fluorescence emission from the dyes changes dramatically from the duplex stage, wherein the probe is hybridized to the complementary strand of DNA, to the single strand stage, when the probe is melted to become detached from the DNA. The change in fluorescence is caused by the dyes coming into closer proximity after melting occurs and the probe becomes detached from the DNA strand. The change in fluorescence emission as a function of temperature is used to calculate the melting temperature of the complex or T.sub.m. In the case where there is a base mismatch between the probe and the DNA strand, indicating a point mutation, the T.sub.m has been found to be significantly lower than the T.sub.m for a perfectly match probelstand duplex. The present invention allows for the detection of the existence and magnitude of T.sub.m, which allows for the quick and accurate detection of a point mutation in the DNA strand and, in some applications, the determination of the approximate location of the mutation within the sequence.

  13. Factors that affect electric-utility stranded commitments

    SciTech Connect (OSTI)

    Hirst, E.; Hadley, S.; Baxter, L.

    1996-07-01

    Estimates of stranded commitments for U.S. investor-owned utilities range widely, with many falling in the range of $100 to $200 billion. These potential losses exist because some utility-owned power plants, long-term power-purchase contracts and fuel-supply contracts, regulatory assets, and expenses for public-policy programs have book values that exceed their expected market values under full competition. This report quantifies the sensitivity of stranded- commitment estimates to the various factors that lead to these above- market-value estimates. The purpose of these sensitivity analyses is to improve understanding on the part of state and federal regulators, utilities, customers, and other electric-industry participants about the relative importance of the factors that affect stranded- commitment amounts.

  14. Nucleolar exit of RNF8 and BRCA1 in response to DNA damage

    SciTech Connect (OSTI)

    Guerra-Rebollo, Marta; Mateo, Francesca; Franke, Kristin; Huen, Michael S.Y.; Lopitz-Otsoa, Fernando; Rodriguez, Manuel S.; Plans, Vanessa; Thomson, Timothy M.

    2012-11-01

    The induction of DNA double-strand breaks (DSBs) elicits a plethora of responses that redirect many cellular functions to the vital task of repairing the injury, collectively known as the DNA damage response (DDR). We have found that, in the absence of DNA damage, the DSB repair factors RNF8 and BRCA1 are associated with the nucleolus. Shortly after exposure of cells to {gamma}-radiation, RNF8 and BRCA1 translocated from the nucleolus to damage foci, a traffic that was reverted several hours after the damage. RNF8 interacted through its FHA domain with the ribosomal protein RPSA, and knockdown of RPSA caused a depletion of nucleolar RNF8 and BRCA1, suggesting that the interaction of RNF8 with RPSA is critical for the nucleolar localization of these DDR factors. Knockdown of RPSA or RNF8 impaired bulk protein translation, as did {gamma}-irradiation, the latter being partially countered by overexpression of exogenous RNF8. Our results suggest that RNF8 and BRCA1 are anchored to the nucleolus through reversible interactions with RPSA and that, in addition to its known functions in DDR, RNF8 may play a role in protein synthesis, possibly linking the nucleolar exit of this factor to the attenuation of protein synthesis in response to DNA damage. -- Highlights: Black-Right-Pointing-Pointer RNF8 and BRCA1 are associated with the nucleolus of undamaged cells. Black-Right-Pointing-Pointer Upon {gamma}-radiation, RNF8 and BRCA1 are translocated from the nucleolus to damage foci. Black-Right-Pointing-Pointer The ribosomal protein RPSA anchors RNF8 to the nucleolus. Black-Right-Pointing-Pointer RNF8 may play previously unsuspected roles in protein synthesis.

  15. Methods for sequencing GC-rich and CCT repeat DNA templates

    DOE Patents [OSTI]

    Robinson, Donna L.

    2007-02-20

    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  16. Method for fabricating multi-strand superconducting cable

    DOE Patents [OSTI]

    Borden, A.R.

    1985-04-01

    Multi-strand superconducting cables adapted to be used, for example, to wind a magnet are fabricated by directing wire strands inwardly from spools disposed on the perimeter of a rotating disk and wrapping them diagonally around a tapered mandrel with a flattened cross-sectional shape with a core having a wedge-shaped channel. As the cable is pulled axially, flexibly coupled wedge-shaped pieces are continuously passed through the channel in the mandrel and inserted into the cable as an internal support therefor.

  17. Jefferson Lab Hosts Upcoming Science Lectures on DNA and Chocolate |

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Jefferson Lab Upcoming Science Lectures on DNA and Chocolate NEWPORT NEWS, Va., Feb. 24, 2011 - Jefferson Lab will host a public lecture on March 29 titled DNA: The Strand That Connects Us All presented by Matt Kaplan from the Human Origins Genotyping Laboratory, Phoenix, Ariz. Kaplan will discuss how the methods and discoveries of human population genetics studies are applied for personal genealogical reconstruction and anthropological testing. Kaplan will start with a short general review

  18. Induction and Persistence of Large ?H2AX Foci by High Linear Energy Transfer Radiation in DNA-Dependent protein kinaseDeficient Cells

    SciTech Connect (OSTI)

    Bracalente, Candelaria; Ibaez, Irene L.; Molinari, Beatriz; Palmieri, Mnica; Kreiner, Andrs; Valda, Alejandro; and others

    2013-11-15

    Purpose: To evaluate the cell response to DNA double-strand breaks induced by low and high linear energy transfer (LET) radiations when the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), an essential protein of the nonhomologous end-joining repair pathway, lacks kinase activity. Methods and Materials: CHO10B2, a Chinese hamster ovary cell line, and its derived radiosensitive mutant cell line, irs-20, lacking DNA-PKcs activity, were evaluated after 0 to 3 Gy of ?-rays, plateau and Bragg peak protons, and lithium beams by clonogenic assay, and as a measurement of double-strand breaks, phosphorylated H2AX (?H2AX) foci number and size were quantified by immunocytofluorescence. Results: Irs-20 exhibited greater radiosensitivity and a higher amount of ?H2AX foci than CHO10B2 at 6 hours after irradiation for all types of radiations. Remarkably, CHO10B2 and irs-20 maintained their difference in radiosensitivity after high-LET radiation. Six hours after low-LET radiations, irs-20 did not reach basal levels of ?H2AX at high doses, whereas CHO10B2 recovered basal levels for all doses. After high-LET radiation, only CHO10B2 exhibited a reduction in ?H2AX foci, but it never reached basal levels. Persistent foci in irs-20 confirmed a repair deficiency. Interestingly, after 30 minutes of high-LET radiation both cell lines exhibited large foci (size >0.9 ?m{sup 2}) related to the damage nature, whereas at 6 hours irs-20 showed a higher amount of large foci than CHO10B2, with a 7-fold increase at 3 Gy, that could also be associated to radiosensitivity. Conclusions: We demonstrated, for the first time, an association between deficient DNA-PKcs activity and not only high levels of H2AX phosphorylation but also persistence and size increase of ?H2AX foci after high-LET irradiation.

  19. DNA sequencing with pyrophosphatase

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.C.

    1996-03-12

    A kit or solution is disclosed for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule and having a second single-stranded region homologous to the first single-stranded region. The first agent is able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture. The second agent is able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.

  20. DNA sequencing with pyrophosphatase

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles C.

    1996-03-12

    A kit or solution for use in extension of an oligonucleotide primer having a first single-stranded region on a template molecule having a second single-stranded region homologous to the first single-stranded region, comprising a first agent able to cause extension of the first single-stranded region of the primer on the second single-stranded region of the template in a reaction mixture, and a second agent able to reduce the amount of pyrophosphate in the reaction mixture below the amount produced during the extension in the absence of the second agent.

  1. Improvements in strand feeding and its effect of sintering performance

    SciTech Connect (OSTI)

    Beer, H.; Kersting, K.; Werner, P.

    1995-12-01

    Sintering may be considered a rather simple, counter current gas-solid process. A bed of granular solids is moved horizontally on a strand of pallets and suction is applied beneath the grate. Shortly after the sinter mix is fed onto the strand the incorporated solid fuel is ignited in the surface layer and the hot gases are drawn into the bed. The temperature of the top layer is raised high enough to burn the fuel particles while air is sucked down through it. Passing the upper, already sintered part of the bed the air is first preheated then sustains the combustion reaction. The hot, still oxygen-rich combustion gases leave the sintering zone and transfer its heat to the charge below. While the solids are preheated, carbonates, combined water, and moisture are driven off, rapidly cooling the gas. Thus, a flame front propagates through the traveling bed, generating at peak temperatures enough heat to agglomerate the bed of quasi-particles into a sinter cake. The strand speed is adjusted so that the burning through of the combustion zone coincides with the end of the suction area. To ensure stable operation this cross stream reactor has to be kept in a steady state.

  2. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kilina, Svetlana; Yarotski, Dzmitry A.; Talin, A. Alec; Tretiak, Sergei; Taylor, Antoinette J.; Balatsky, Alexander V.

    2011-01-01

    We present a combined approach that relies on computational simulations and scanning tunneling microscopy (STM) measurements to reveal morphological properties and stability criteria of carbon nanotube-DNA (CNT-DNA) constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4 ° and a coiling period of 3.3 nm. Using force field simulations, we determine how the DNA-CNT binding energy depends on the sequence and binding geometry of a single strand DNA. This dependence allows us to quantitatively characterize the stability of a hybrid structure with an optimal π-stacking between DNA nucleotides andmore » the tube surface and better interpret STM data. Our simulations clearly demonstrate the existence of a very stable DNA binding geometry for (6,5) CNT as evidenced by the presence of a well-defined minimum in the binding energy as a function of an angle between DNA strand and the nanotube chiral vector. This novel approach demonstrates the feasibility of CNT-DNA geometry studies with subnanometer resolution and paves the way towards complete characterization of the structural and electronic properties of drug-delivering systems based on DNA-CNT hybrids as a function of DNA sequence and a nanotube chirality.« less

  3. Reduced repair capacity of a DNA clustered damage site comprised of 8-oxo-7,8-dihydro-2'-deoxyguanosine and 2-deoxyribonolactone results in an increased mutagenic potential of these lesions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Cunniffe, Siobhan; O’Neill, Peter; Greenberg, Marc M.; Lomax, Martine E.

    2014-04-01

    A signature of ionizing radiation is the induction of DNA clustered damaged sites. Non-double strand break (DSB) clustered damage has been shown to compromise the base excision repair pathway, extending the lifetimes of the lesions within the cluster, compared to isolated lesions. This increases the likelihood the lesions persist to replication and thus increasing the mutagenic potential of the lesions within the cluster. Lesions formed by ionizing radiation include 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) and 2-deoxyribonolactone (dL). dL poses an additional challenge to the cell as it is not repaired by the short-patch base excision repair pathway. Here we show recalcitrant dL repairmore » is reflected in mutations observed when DNA containing it and a proximal 8-oxodGuo is replicated in Escherichia coli. 8-oxodGuo in close proximity to dL on the opposing DNA strand results in an enhanced frequency of mutation of the lesions within the cluster and a 20 base sequence flanking the clustered damage site in an E. coli based plasmid assay. In vitro repair of a dL lesion is reduced when compared to the repair of an abasic (AP) site and a tetrahydrofuran (THF), and this is due mainly to a reduction in the activity of polymerase β, leading to retarded FEN1 and ligase 1 activities. This study has given insights in to the biological effects of clusters containing dL.« less

  4. Materials, Strands, and Cables for Superconducting Accelerator Magnets. Final Report

    SciTech Connect (OSTI)

    Sumption, Mike D.; Collings, Edward W.

    2014-09-19

    This report focuses on Materials, Strands and Cables for High Energy Physics Particle accelerators. In the materials area, work has included studies of basic reactions, diffusion, transformations, and phase assemblage of Nb3Sn. These materials science aspects have been married to results, in the form of flux pinning, Bc2, Birr, and transport Jc, with an emphasis on obtaining the needed Jc for HEP needs. Attention has also been paid to the intermediate-temperature superconductor, magnesium diboride emphasis being placed on (i) irreversibility field enhancement, (ii) critical current density and flux pinning, and (iii) connectivity. We also report on studies of Bi-2212. The second area of the program has been in the area of Strands in which, aside from the materials aspect of the conductor, its physical properties and their influence on performance have been studied. Much of this work has been in the area of magnetization estimation and flux jump calculation and control. One of the areas of this work was strand instabilities in high-performance Nb3Sn conductors due to combined fields and currents. Additionally, we investigated quench and thermal propagation in YBCO coated conductors at low temperatures and high fields. The last section, Cables, focussed on interstrand contact resistance, ICR, it origins, control, and implications. Following on from earlier work in NbTi, the present work in Nb3Sn has aimed to make ICR intermediate between the two extremes of too little contact (no current sharing) and too much (large and unacceptable magnetization and associated beam de-focussing). Interstrand contact and current sharing measurements are being made on YBCO based Roebel cables using transport current methods. Finally, quench was investigated for YBCO cables and the magnets wound from them, presently with a focus on 50 T solenoids for muon collider applications.

  5. MCM ring hexamerization is a prerequisite for DNA-binding

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Froelich, Clifford A.; Nourse, Amanda; Enemark, Eric J.

    2015-09-13

    The hexameric Minichromosome Maintenance (MCM) protein complex forms a ring that unwinds DNA at the replication fork in eukaryotes and archaea. Our recent crystal structure of an archaeal MCM N-terminal domain bound to single-stranded DNA (ssDNA) revealed ssDNA associating across tight subunit interfaces but not at the loose interfaces, indicating that DNA-binding is governed not only by the DNA-binding residues of the subunits (MCM ssDNA-binding motif, MSSB) but also by the relative orientation of the subunits. We now extend these findings to show that DNA-binding by the MCM N-terminal domain of the archaeal organism Pyrococcus furiosus occurs specifically in themore » hexameric oligomeric form. We show that mutants defective for hexamerization are defective in binding ssDNA despite retaining all the residues observed to interact with ssDNA in the crystal structure. One mutation that exhibits severely defective hexamerization and ssDNA-binding is at a conserved phenylalanine that aligns with the mouse Mcm4(Chaos3) mutation associated with chromosomal instability, cancer, and decreased intersubunit association.« less

  6. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, D.R.

    1982-09-23

    A digital quartz accelerometer includes a pair of spaced double-ended tuning forks fastened at one end to a base and at the other end through a spacer mass. Transverse movement of the resonator members stresses one and compresses the other, providing a differential frequency output which is indicative of acceleration.

  7. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, Dale R.

    1984-01-01

    A digital quartz accelerometer includes a pair of spaced double-ended tuning forks fastened at one end to a base and at the other end through a spacer mass. Transverse movement of the resonator members stresses one and compresses the other, providing a differential frequency output which is indicative of acceleration.

  8. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and

    Office of Scientific and Technical Information (OSTI)

    function (Journal Article) | DOE PAGES Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function « Prev Next » Title: Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2-7 (minichromosome maintenance proteins 2-7) double hexamer. During S phase, each Mcm2-7 hexamer forms the core of a replicative DNA

  9. A Golden Ruler Used to Measure DNA Structure in Solution

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    8 A Golden Ruler Used to Measure DNA Structure in Solution The first crystal structures of DNA double helices appeared in 1979 and directly confirmed the atomic model of Watson-Crick from 25 years earlier. Since then, DNA has been modeled as a relatively rigid polymer. An isotropic elastic rod model of the polymer has proven to be exceptionally good at integrating classical biochemical measurements on DNA with recent single-molecule results for DNA on length scales of 100 nm or longer.

  10. DNA Origami with Complex Curvatures in Three-Dimensional Space

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA Origami with Complex Curvatures in Three-Dimensional Space Authors: Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., and Yan, H. Title: DNA Origami with Complex Curvatures in Three-Dimensional Space Source: Science Year: 2011 Volume: 332 Pages: 342-346 ABSTRACT: We present a strategy to design and construct self-assembling DNA nanostructures that define intricate curved surfaces in three-dimensional (3D) space using the DNA origami folding technique. Double-helical DNA is bent to follow

  11. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levelsmore » of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.« less

  12. Double Beta Decay Experiments

    SciTech Connect (OSTI)

    Nanal, Vandana [Dept. of Nuclear and Atomic Physics, Tata Institute of Fundamental Research, Mumbai 400 005 (India)

    2011-11-23

    At present, neutrinoless double beta decay is perhaps the only experiment that can tell us whether the neutrino is a Dirac or a Majorana particle. Given the significance of the 0{nu}{beta}{beta}, there is a widespread interest for these rare event studies employing a variety of novel techniques. This paper describes the current status of DBD experiments. The Indian effort for an underground NDBD experiment at the upcoming INO laboratory is also presented.

  13. Double Beta Decay

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Double Beta Decay Measuring the Mass of the Neutrino One of the most elusive and exotic subatomic particles being investigated around the world today is the neutrino. Understanding the family of neutrino particles and how they interact with other matter (and among themselves) has become one the most intensive physics research efforts ever attempted by mankind. With a virtually undetectable mass, and without electric charge, these weakly interacting particles have been devilishly difficult to

  14. Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Zhang, Yugang; Pal, Suchetan; Srinivasan, Babji; Vo, Thi; Kumar, Sanat; Gang, Oleg

    2015-05-25

    The rapid development of self-assembly approaches has enabled the creation of materials with desired organization of nanoscale components. However, achieving dynamic control, wherein the system can be transformed on demand into multiple entirely different states, is typically absent in atomic and molecular systems and has remained elusive in designed nanoparticle systems. Here, we demonstrate with in situ small-angle x-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensional lattice of DNA-coated nanoparticles can be switched from an initial 'mother' phase into one of multiple 'daughter' phases. The introduction of different types of re-programming DNA strands modifiesmore » the DNA shells of the nanoparticles within the superlattice, thereby shifting interparticle interactions to drive the transformation into a particular daughter phase. We mapped quantitatively with free-energy calculations the selective re-programming of interactions onto the observed daughter phases.« less

  15. A new structural framework for integrating replication protein A into DNA processing machinery

    SciTech Connect (OSTI)

    Brosey, Chris; Yan, Chunli; Tsutakawa, Susan; Heller, William; Rambo, Robert; Tainer, John; Ivanov, Ivaylo; Chazin, Walter

    2013-01-17

    By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.

  16. Characteristics of Cu stabilized Nb3Al strands with low Cu ratio

    SciTech Connect (OSTI)

    Kikuchi, A.; Yamada, R.; Barzi, E.; Kobayashi, M.; Lamm, M.; Nakagawa, K.; Sasaki, K.; Takeuchi, T.; Turrioni, D.; Zlobin, A.V.; /NIMC, Tsukuba /Fermilab /Hitachi, Tsuchiura Works /KEK, Tsukuba

    2008-12-01

    Characteristics of recently developed F4-Nb{sub 3}Al strand with low Cu ratio are described. The overall J{sub c} of the Nb{sub 3}Al strand could be easily increased by decreasing of the Cu ratio. Although the quench of a pulse-like voltage generation is usually observed in superconducting unstable conductor, the F4 strand with a low Cu ratio of 0.61 exhibited an ordinary critical transition of gradual voltage generation. The F4 strand does not have magnetic instabilities at 4.2 K because of the tantalum interfilament matrix. The overall J{sub c} of the F4 strand achieved was 80-85% of the RRP strand. In the large mechanical stress above 100 MPa, the overall J{sub c} of the F4 strand might be comparable to that of high J{sub c} RRP-Nb{sub 3}Sn strands. The Rutherford cable with a high packing factor of 86.5% has been fabricated using F4 strands. The small racetrack magnet, SR07, was also fabricated by a 14 m F4 cable. The quench current, I{sub q}, of SR07 were obtained 22.4 kA at 4.5 K and 25.2 kA at 2.2 K. The tantalum matrix Nb{sub 3}Al strands are promising for the application of super-cooled high-field magnets as well as 4.2 K operation magnets.

  17. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    SciTech Connect (OSTI)

    sumption, Mike; Majoros, Milan; Collings, E. W.; Van der Laan, D. C.

    2014-11-07

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of IV curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software. Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 m?, (enabling a current sharing of 5% at 1.3Ic ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 1001000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.

  18. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Majoros, M.; Sumption, M. D.; Collings, E. W.; Long, N. J.

    2015-04-08

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less

  19. Inter-strand current sharing and ac loss measurements in superconducting YBCO Roebel cables

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    sumption, Mike; Majoros, Milan; Collings, E. W.; Van der Laan, D. C.

    2014-11-07

    A Roebel cable, one twist pitch long, was modified from its as-received state by soldering copper strips between the strands to provide inter-strand connections enabling current sharing. Various DC transport currents (representing different percentages of its critical current) were applied to a single strand of such a modified cable at 77 K in a liquid nitrogen bath. Simultaneous monitoring of I–V curves in different parts of the strand as well as in its interconnections with other strands was made using a number of sensitive Keithley nanovoltmeters in combination with a multichannel high-speed data acquisition card, all controlled via LabView software.more » Current sharing onset was observed at about 1.02 of strand Ic. At a strand current of 1.3Ic about 5% of the current was shared through the copper strip interconnections. A finite element method modeling was performed to estimate the inter-strand resistivities required to enable different levels of current sharing. The relative contributions of coupling and hysteretic magnetization (and loss) were compared, and for our cable and tape geometry, and at dB/dt=1 T s-1, and our inter-strand resistance of 0.77 mΩ, (enabling a current sharing of 5% at 1.3Ic ) the coupling component was 0.32% of the hysteretic component. However, inter-strand contact resistance values of 100–1000 times smaller (close to those of NbTi and Nb3Sn based accelerator cables) would make the coupling components comparable in size to the hysteretic components.« less

  20. Allostery through protein-induced DNA bubbles

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Traverso, Joseph J.; Manoranjan, Valipuram S.; Bishop, A. R.; Rasmussen, Kim Ø.; Voulgarakis, Nikolaos K.

    2015-03-12

    Allostery through DNA is increasingly recognized as an important modulator of DNA functions. Here, we show that the coalescence of protein-induced DNA bubbles can mediate allosteric interactions that drive protein aggregation. We propose that such allostery may regulate DNA's flexibility and the assembly of the transcription machinery. Mitochondrial transcription factor A (TFAM), a dual-function protein involved in mitochondrial DNA (mtDNA) packaging and transcription initiation, is an ideal candidate to test such a hypothesis owing to its ability to locally unwind the double helix. Numerical simulations demonstrate that the coalescence of TFAM-induced bubbles can explain experimentally observed TFAM oligomerization. The resultingmore » melted DNA segment, approximately 10 base pairs long, around the joints of the oligomers act as flexible hinges, which explains the efficiency of TFAM in compacting DNA. Since mitochondrial polymerase (mitoRNAP) is involved in melting the transcription bubble, TFAM may use the same allosteric interaction to both recruit mitoRNAP and initiate transcription.« less

  1. Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

    SciTech Connect (OSTI)

    Sun, Jingchuan; Li, Huilin; Fernandez-Cid, Alejandra; Riera, Alberto; Tognetti, Sivia; Yuan, Zuanning; Stillman, Bruce; Speck, Christian

    2014-10-15

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm27 (minichromosome maintenance proteins 27) double hexamer. During S phase, each Mcm27 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORCCdc6 function to recruit a single Cdt1Mcm27 heptamer to replication origins prior to Cdt1 release and ORCCdc6Mcm27 complex formation, but how the second Mcm27 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORCCdc6Mcm27 complex and an ORCCdc6Mcm27Mcm27 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm27 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm27 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.

  2. DNA polymerase with modified processivity

    DOE Patents [OSTI]

    Bedford, Ella; Tabor, Stanley; Richardson, Charles C.

    1999-01-01

    Chimeric DNA polymerase having a DNA polymerase domain and processivity factor binding domain not naturally associated with DNA polymerase domain.

  3. Double acting bit holder

    DOE Patents [OSTI]

    Morrell, Roger J. (Blommington, MN); Larson, David A. (Minneapolis, MN); Ruzzi, Peter L. (Eagan, MN)

    1994-01-01

    A double acting bit holder that permits bits held in it to be resharpened during cutting action to increase energy efficiency by reducing the amount of small chips produced. The holder consist of: a stationary base portion capable of being fixed to a cutter head of an excavation machine and having an integral extension therefrom with a bore hole therethrough to accommodate a pin shaft; a movable portion coextensive with the base having a pin shaft integrally extending therefrom that is insertable in the bore hole of the base member to permit the moveable portion to rotate about the axis of the pin shaft; a recess in the movable portion of the holder to accommodate a shank of a bit; and a biased spring disposed in adjoining openings in the base and moveable portions of the holder to permit the moveable portion to pivot around the pin shaft during cutting action of a bit fixed in a turret to allow front, mid and back positions of the bit during cutting to lessen creation of small chip amounts and resharpen the bit during excavation use.

  4. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-08-15

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  5. Magnetization anomaly of Nb3Al strands and instability of Nb3Al Rutherford cables

    SciTech Connect (OSTI)

    Yamada, Ryuji; /Fermilab; Kikuchi, Akihiro; /Tsukuba Magnet Lab; Wake, Masayoshi; /KEK, Tsukuba

    2006-08-01

    Using a Cu stabilized Nb{sub 3}Al strand with Nb matrix, a 30 meter long Nb{sub 3}Al Rutherford cable was made by a collaboration of Fermilab and NIMS. Recently the strand and cable were tested. In both cases instability was observed at around 1.5 Tesla. The magnetization of this Nb{sub 3}Al strand was measured first using a balanced coil magnetometer at 4.2 K. Strands showed an anomalously large magnetization behavior around at 1.6 T, which is much higher than the usual B{sub c2} {approx} 0.5 Tesla (4.2 K) of Nb matrix. This result is compared with the magnetization data of short strand samples using a SQUID magnetometer, in which a flux-jump signal was observed at 0.5 Tesla, but not at higher field. As a possible explanation for this magnetization anomaly, the interfilament coupling through the thin Nb films in the strands is suggested. The instability problem observed in low field tests of the Nb{sub 3}Al Rutherford cables is attributed to this effect.

  6. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

    Gray, Joe W. (San Francisco, CA); Weier, Heinz-Ulrich G. (Oakland, CA)

    1998-01-01

    The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

  7. The influence of TRP53 in the dose response of radiation-induced apoptosis, DNA repair and genomic stability in murine haematopoietic cells

    SciTech Connect (OSTI)

    Lemon, Jennifer A.; Taylor, Kristina; Verdecchia, Kyle; Phan, Nghi; Boreham, Douglas R.

    2014-01-01

    Apoptotic and DNA damage endpoints are frequently used as surrogate markers of cancer risk, and have been well-studied in the Trp53+/- mouse model. We report the effect of differing Trp53 gene status on the dose response of ionizing radiation exposures (0.01-2 Gy), with the unique perspective of determining if effects of gene status remain at extended time points. Here we report no difference in the dose response for radiation-induced DNA double-strand breaks in bone marrow and genomic instability (MN-RET levels) in peripheral blood, between wild-type (Trp53+/+) and heterozygous (Trp53+/-) mice. The dose response for Trp53+/+ mice showed higher initial levels of radiation-induced lymphocyte apoptosis relative to Trp53+/- between 0 and 1 Gy. Although this trend was observed up to 12 hours post-irradiation, both genotypes ultimately reached the same level of apoptosis at 14 hours, suggesting the importance of late-onset p53-independent apoptotic responses in this mouse model. Expected radiation-induced G1 cell cycle delay was observed in Trp53+/+ but not Trp53+/-. Although p53 has an important role in cancer risk, we have shown its influence on radiation dose response can be temporally variable. This research highlights the importance of caution when using haematopoietic endpoints as surrogates to extrapolate radiation-induced cancer risk estimation.

  8. Manganese oxide helices, rings, strands, and films, and methods for their preparation

    DOE Patents [OSTI]

    Suib, Steven L. (Storrs, CT); Giraldo, Oscar (Storrs, CT); Marquez, Manuel (Wheeling, IL); Brock, Stephanie (Detroit, MI)

    2003-01-07

    Methods for the preparation of mixed-valence manganese oxide compositions with quaternary ammonium ions are described. The compositions self-assemble into helices, rings, and strands without any imposed concentration gradient. These helices, rings, and strands, as well as films having the same composition, undergo rapid ion exchange to replace the quaternary ammonium ions with various metal ions. And the metal-ion-containing manganese oxide compositions so formed can be heat treated to form semi-conducting materials with high surface areas.

  9. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, J.J.; Quesada, M.A.; Randesi, M.

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector. The cloning vector has an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe. 1 fig.

  10. Method for introducing unidirectional nested deletions

    DOE Patents [OSTI]

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

    1999-07-27

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  11. DNA tagged microparticles

    DOE Patents [OSTI]

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  12. Minimal Doubling and Point Splitting

    SciTech Connect (OSTI)

    Creutz, M.

    2010-06-14

    Minimally-doubled chiral fermions have the unusual property of a single local field creating two fermionic species. Spreading the field over hypercubes allows construction of combinations that isolate specific modes. Combining these fields into bilinears produces meson fields of specific quantum numbers. Minimally-doubled fermion actions present the possibility of fast simulations while maintaining one exact chiral symmetry. They do, however, introduce some peculiar aspects. An explicit breaking of hyper-cubic symmetry allows additional counter-terms to appear in the renormalization. While a single field creates two different species, spreading this field over nearby sites allows isolation of specific states and the construction of physical meson operators. Finally, lattice artifacts break isospin and give two of the three pseudoscalar mesons an additional contribution to their mass. Depending on the sign of this mass splitting, one can either have a traditional Goldstone pseudoscalar meson or a parity breaking Aoki-like phase.

  13. Endogenous DNA Damage and Risk of Testicular Germ Cell Tumors

    SciTech Connect (OSTI)

    Cook, M B; Sigurdson, A J; Jones, I M; Thomas, C B; Graubard, B I; Korde, L; Greene, M H; McGlynn, K A

    2008-01-18

    Testicular germ cell tumors (TGCT) are comprised of two histologic groups, seminomas and nonseminomas. We postulated that the possible divergent pathogeneses of these histologies may be partially explained by variable endogenous DNA damage. To assess our hypothesis, we conducted a case-case analysis of seminomas and nonseminomas using the alkaline comet assay to quantify single-strand DNA breaks and alkali-labile sites. The Familial Testicular Cancer study and the U.S. Radiologic Technologists cohort provided 112 TGCT cases (51 seminomas & 61 nonseminomas). A lymphoblastoid cell line was cultured for each patient and the alkaline comet assay was used to determine four parameters: tail DNA, tail length, comet distributed moment (CDM) and Olive tail moment (OTM). Odds ratios (OR) and 95% confidence intervals (95%CI) were estimated using logistic regression. Values for tail length, tail DNA, CDM and OTM were modeled as categorical variables using the 50th and 75th percentiles of the seminoma group. Tail DNA was significantly associated with nonseminoma compared to seminoma (OR{sub 50th percentile} = 3.31, 95%CI: 1.00, 10.98; OR{sub 75th percentile} = 3.71, 95%CI: 1.04, 13.20; p for trend=0.039). OTM exhibited similar, albeit statistically non-significant, risk estimates (OR{sub 50th percentile} = 2.27, 95%CI: 0.75, 6.87; OR{sub 75th percentile} = 2.40, 95%CI: 0.75, 7.71; p for trend=0.12) whereas tail length and CDM showed no association. In conclusion, the results for tail DNA and OTM indicate that endogenous DNA damage levels are higher in patients who develop nonseminoma compared with seminoma. This may partly explain the more aggressive biology and younger age-of-onset of this histologic subgroup compared with the relatively less aggressive, later-onset seminoma.

  14. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, Robert S. (Oak Ridge, TN)

    1997-01-01

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  15. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, Robert S. (Oak Ridge, TN)

    1999-01-01

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means.

  16. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, R.S.

    1999-08-31

    A microminiature sequencing apparatus and method provide means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus comprises a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 11 figs.

  17. Large scale DNA microsequencing device

    DOE Patents [OSTI]

    Foote, R.S.

    1997-08-26

    A microminiature sequencing apparatus and method provide a means for simultaneously obtaining sequences of plural polynucleotide strands. The apparatus cosists of a microchip into which plural channels have been etched using standard lithographic procedures and chemical wet etching. The channels include a reaction well and a separating section. Enclosing the channels is accomplished by bonding a transparent cover plate over the apparatus. A first oligonucleotide strand is chemically affixed to the apparatus through an alkyl chain. Subsequent nucleotides are selected by complementary base pair bonding. A target nucleotide strand is used to produce a family of labelled sequencing strands in each channel which are separated in the separating section. During or following separation the sequences are determined using appropriate detection means. 17 figs.

  18. Detection and quantitation of single nucleotide polymorphisms, DNA sequence variations, DNA mutations, DNA damage and DNA mismatches

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

    DNA mutation binding proteins alone and as chimeric proteins with nucleases are used with solid supports to detect DNA sequence variations, DNA mutations and single nucleotide polymorphisms. The solid supports may be flow cytometry beads, DNA chips, glass slides or DNA dips sticks. DNA molecules are coupled to solid supports to form DNA-support complexes. Labeled DNA is used with unlabeled DNA mutation binding proteins such at TthMutS to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by binding which gives an increase in signal. Unlabeled DNA is utilized with labeled chimeras to detect DNA sequence variations, DNA mutations and single nucleotide length polymorphisms by nuclease activity of the chimera which gives a decrease in signal.

  19. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01

    During this year we performed two major projects: I. We developed a detailed theoretical model which complements our experiments on surface DNA electrophoresis. We found that it was possible to enhance the separation of DNA chains by imposing a chemical nanoscale pattern on the surface. This approach utilized the surface interaction effect of the DNA chains with the substrate and is a refinement to our previous method in which DNA chains were separated on homogeneous flat surfaces. By introducing the nano-patterns on the surface, the conformational changes of DNA chains of different lengths can be amplified, which results in the different friction strengths with the substrate surface. Our results also show that, when compared to the DNA electrophoresis performed on homogeneous flat surfaces, nanopatterned surfaces offer a larger window in choosing different surface interactions to achieve separation. II. In collaboration with a large international manufacturer of skin care products we also embarked on a project involving photo toxicity of titanium dioxide nanoparticles, which are a key ingredient in sunscreen and cosmetic lotions. The results clearly implicated the nanoparticles in catalyzing damage to chromosomal DNA. We then used this knowledge to develop a polymer/anti-oxidant coating which prevented the photocatalytic reaction on DNA while still retaining the UV absorptive properties of the nanoparticles. The standard gel electrophoresis was not sufficient in determining the extent of the DNA damage. The conclusions of this study were based predominantly on analysis obtained with the surface electrophoresis method.

  20. Controlling DNA Methylation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Controlling DNA Methylation Though life on earth is composed of a diverse range of organisms, some with many different types of tissues and cells, all these are encoded by a molecule we call DNA. The information required to build a protein is stored in DNA within the cells. Not all the message in the DNA is used in each cell and not all the message is used all the time. During cell differentiation, the cells become dedicated for their specific function which involves selectively activating some

  1. Booster double harmonic setup notes

    SciTech Connect (OSTI)

    Gardner, C. J.

    2015-02-17

    The motivation behind implementing a booster double harmonic include the reduced transverse space charge force from a reduced peak beam current and reduced momentum spread of the beam, both of which can be achieved from flattening the RF bucket. RF capture and acceleration of polarized protons (PP) is first set up in the single harmonic mode with RF harmonic h=1. Once capture and acceleration have been set up in the single harmonic mode, the second harmonic system is brought on and programmed to operate in concert with the single harmonic system.

  2. Evaluation of Juvenile Fall Chinook Stranding on the Hanford Reach, 1997-1999 Interim Report.

    SciTech Connect (OSTI)

    Wagner, Paul; Nugent, John; Price, William

    1999-02-15

    Pilot work conducted in 1997 to aid the development of the study for the 1998 Evaluation of Juvenile Fall Chinook Stranding on The Hanford Reach. The objectives of the 1997 work were to: (1) identify juvenile chinook production and rearing areas..., (2) identify sampling sites and develop the statistical parameters necessary to complete the study, (3) develop a study plan..., (4) conduct field sampling activities...

  3. Double Coil Condenser Apparatus - Energy Innovation Portal

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Double Coil Condenser Apparatus A glass condenser apparatus that allows the user to adjust the rate of condensation during testing Savannah River National Laboratory Contact SRNL About This Technology Double Coil Condenser Apparatus Double Coil Condenser Apparatus Technology Marketing Summary A Glass Technologist at the Savannah River National Laboratory has developed a glass condenser apparatus that allows the user to adjust the rate of condensation during testing. The apparatus consists of a

  4. Double perovskite catalysts for oxidative coupling

    DOE Patents [OSTI]

    Campbell, Kenneth D.

    1991-01-01

    Alkali metal doped double perovskites containing manganese and at least one of cobalt, iron and nickel are useful in the oxidative coupling of alkane to higher hydrocarbons.

  5. Chimeric proteins for detection and quantitation of DNA mutations, DNA sequence variations, DNA damage and DNA mismatches

    DOE Patents [OSTI]

    McCutchen-Maloney, Sandra L. (Pleasanton, CA)

    2002-01-01

    Chimeric proteins having both DNA mutation binding activity and nuclease activity are synthesized by recombinant technology. The proteins are of the general formula A-L-B and B-L-A where A is a peptide having DNA mutation binding activity, L is a linker and B is a peptide having nuclease activity. The chimeric proteins are useful for detection and identification of DNA sequence variations including DNA mutations (including DNA damage and mismatches) by binding to the DNA mutation and cutting the DNA once the DNA mutation is detected.

  6. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12

    The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

  7. The Chromodomains of the Chd1 Chromatin Remodeler Regulate DNA Access to the ATPase Motor

    SciTech Connect (OSTI)

    Hauk, G.; McKnight, J; Nodelman, I; Bowman, G

    2010-01-01

    Chromatin remodelers are ATP-driven machines that assemble, slide, and remove nucleosomes from DNA, but how the ATPase motors of remodelers are regulated is poorly understood. Here we show that the double chromodomain unit of the Chd1 remodeler blocks DNA binding and activation of the ATPase motor in the absence of nucleosome substrates. The Chd1 crystal structure reveals that an acidic helix joining the chromodomains can pack against a DNA-binding surface of the ATPase motor. Disruption of the chromodomain-ATPase interface prevents discrimination between nucleosomes and naked DNA and reduces the reliance on the histone H4 tail for nucleosome sliding. We propose that the chromodomains allow Chd1 to distinguish between nucleosomes and naked DNA by physically gating access to the ATPase motor, and we hypothesize that related ATPase motors may employ a similar strategy to discriminate among DNA-containing substrates.

  8. Cadmium sulfate and CdTe-quantum dots alter DNA repair in zebrafish (Danio rerio) liver cells

    SciTech Connect (OSTI)

    Tang, Song; Cai, Qingsong; Chibli, Hicham; Allagadda, Vinay; Nadeau, Jay L.; Mayer, Gregory D.

    2013-10-15

    Increasing use of quantum dots (QDs) makes it necessary to evaluate their toxicological impacts on aquatic organisms, since their contamination of surface water is inevitable. This study compares the genotoxic effects of ionic Cd versus CdTe nanocrystals in zebrafish hepatocytes. After 24 h of CdSO{sub 4} or CdTe QD exposure, zebrafish liver (ZFL) cells showed a decreased number of viable cells, an accumulation of Cd, an increased formation of reactive oxygen species (ROS), and an induction of DNA strand breaks. Measured levels of stress defense and DNA repair genes were elevated in both cases. However, removal of bulky DNA adducts by nucleotide excision repair (NER) was inhibited with CdSO{sub 4} but not with CdTe QDs. The adverse effects caused by acute exposure of CdTe QDs might be mediated through differing mechanisms than those resulting from ionic cadmium toxicity, and studying the effects of metallic components may be not enough to explain QD toxicities in aquatic organisms. - Highlights: Both CdSO{sub 4} and CdTe QDs lead to cell death and Cd accumulation. Both CdSO{sub 4} and CdTe QDs induce cellular ROS generation and DNA strand breaks. Both CdSO{sub 4} and CdTe QDs induce the expressions of stress defense and DNA repair genes. NER repair capacity was inhibited with CdSO{sub 4} but not with CdTe QDs.

  9. Multiplex analysis of DNA

    DOE Patents [OSTI]

    Church, George M.; Kieffer-Higgins, Stephen

    1992-01-01

    This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

  10. DNA | Open Energy Information

    Open Energy Info (EERE)

    Lead Agency District Office Development Phase(s) Techniques DNA-NV-030-09-03 Dusty Miller LLC BLM BLM Carson City District Office BLM Stillwater Field Office BLM...

  11. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1988-10-11

    A double or multiple bevel culet geometry is used on a diamond anvil in a high pressure cell apparatus to provide increased sample pressure and stability for a given force applied to the diamond tables. Double or multiple bevel culet geometries can also be used for sapphire or other hard crystal anvils. Pressures up to and above 5 Megabars can be reached. 8 figs.

  12. Reliability Estimation for Double Containment Piping

    SciTech Connect (OSTI)

    L. Cadwallader; T. Pinna

    2012-08-01

    Double walled or double containment piping is considered for use in the ITER international project and other next-generation fusion device designs to provide an extra barrier for tritium gas and other radioactive materials. The extra barrier improves confinement of these materials and enhances safety of the facility. This paper describes some of the design challenges in designing double containment piping systems. There is also a brief review of a few operating experiences of double walled piping used with hazardous chemicals in different industries. This paper recommends approaches for the reliability analyst to use to quantify leakage from a double containment piping system in conceptual and more advanced designs. The paper also cites quantitative data that can be used to support such reliability analyses.

  13. Development of double-decker pulse radiolysis

    SciTech Connect (OSTI)

    Kan, K.; Kondoh, T.; Yang, J.; Ogata, A.; Norizawa, K.; Yoshida, Y.

    2012-07-15

    Double-decker pulse radiolysis (DDPR), which utilizes double-decker electron beams, was investigated to develop a new pulse radiolysis with a high time resolution. The double-decker electron beams were generated by injecting two UV pulses into a photocathode radio-frequency gun. In the pulse radiolysis, one electron beam was used as a pump beam, and the other was converted to a probe pulse. Finally, as its first application, the DDPR was successfully used for observing solvated electrons in water, with a 10%-90% rise time of 8.6 ps.

  14. Double-reed exhaust valve engine

    DOE Patents [OSTI]

    Bennett, Charles L.

    2015-06-30

    An engine based on a reciprocating piston engine that extracts work from pressurized working fluid. The engine includes a double reed outlet valve for controlling the flow of low-pressure working fluid out of the engine. The double reed provides a stronger force resisting closure of the outlet valve than the force tending to open the outlet valve. The double reed valve enables engine operation at relatively higher torque and lower efficiency at low speed, with lower torque, but higher efficiency at high speed.

  15. Two-subunit DNA escort mechanism and inactive subunit bypass in an ultra-fast ring ATPase

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Liu, Ninning; Chistol, Gheorghe; Bustamante, Carlos

    2015-10-09

    SpoIIIE is a homo-hexameric dsDNA translocase responsible for completing chromosome segregation in Bacillus subtilis . Here, we use a single-molecule approach to monitor SpoIIIE translocation when challenged with neutral-backbone DNA and non-hydrolyzable ATP analogs. We show that SpoIIIE makes multiple essential contacts with phosphates on the 5'→3' strand in the direction of translocation. Using DNA constructs with two neutral-backbone segments separated by a single charged base pair, we deduce that SpoIIIE’s step size is 2 bp. Finally, experiments with non-hydrolyzable ATP analogs suggest that SpoIIIE can operate with non-consecutive inactive subunits. We propose a two-subunit escort translocation mechanism thatmore » is strict enough to enable SpoIIIE to track one DNA strand, yet sufficiently compliant to permit the motor to bypass inactive subunits without arrest. We speculate that such a flexible mechanism arose for motors that, like SpoIIIE, constitute functional bottlenecks where the inactivation of even a single motor can be lethal for the cell.« less

  16. Double logarithmic asymptotic behavior in quantum chromodynamics

    SciTech Connect (OSTI)

    Kirschner, R.

    1981-08-01

    The double logarithmic contributions to the quark-(anti)quark scattering and annihilation amplitudes are summed to all orders in quantum chromodynamics. The results are a generalization of the calculations of Gorshkov et al. in the case of quantum electrodynamics.

  17. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1987-02-06

    Use of double or multiple bevel culet geometry on a diamond anvil to provide increased sample pressure and stability for a given force applied to the diamond tables. 7 figs.

  18. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in...

  19. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits...

  20. Double Shock Experiments and Reactive Flow Modeling of High Pressure...

    Office of Scientific and Technical Information (OSTI)

    Double Shock Experiments and Reactive Flow Modeling of High Pressure LX-17 Detonation Reaction Product States Citation Details In-Document Search Title: Double Shock Experiments ...

  1. Anomalous dimensions of the double parton fragmentation functions...

    Office of Scientific and Technical Information (OSTI)

    Anomalous dimensions of the double parton fragmentation functions Citation Details In-Document Search Title: Anomalous dimensions of the double parton fragmentation functions ...

  2. What can we learn from neutrinoless double beta decay experiments...

    Office of Scientific and Technical Information (OSTI)

    Title: What can we learn from neutrinoless double beta decay experiments? We assess how well next generation neutrinoless double beta decay and normal neutrino beta decay ...

  3. What can we learn from neutrinoless double beta decay experiments...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: What can we learn from neutrinoless double beta decay experiments? Citation Details In-Document Search Title: What can we learn from neutrinoless double beta decay...

  4. SciTech Connect: "neutrinoless double beta decay"

    Office of Scientific and Technical Information (OSTI)

    neutrinoless double beta decay" Find + Advanced Search Term Search Semantic Search Advanced Search All Fields: "neutrinoless double beta decay" Semantic Semantic Term Title:...

  5. Double shell tank waste analysis plan

    SciTech Connect (OSTI)

    Mulkey, C.H.; Jones, J.M.

    1994-12-15

    Waste analysis plan for the double shell tanks. SD-WM-EV-053 is Superseding SD-WM-EV-057.This document provides the plan for obtaining information needed for the safe waste handling and storage of waste in the Double Shell Tank Systems. In Particular it addresses analysis necessary to manage waste according to Washington Administrative Code 173-303 and Title 40, parts 264 and 265 of the Code of Federal Regulations.

  6. Wavelength-doubling optical parametric oscillator

    DOE Patents [OSTI]

    Armstrong, Darrell J. (Albuquerque, NM); Smith, Arlee V. (Albuquerque, NM)

    2007-07-24

    A wavelength-doubling optical parametric oscillator (OPO) comprising a type II nonlinear optical medium for generating a pair of degenerate waves at twice a pump wavelength and a plurality of mirrors for rotating the polarization of one wave by 90 degrees to produce a wavelength-doubled beam with an increased output energy by coupling both of the degenerate waves out of the OPO cavity through the same output coupler following polarization rotation of one of the degenerate waves.

  7. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25

    A modified gene encoding a modified DNA polymerase is disclosed. The modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase. 6 figs.

  8. DNA polymerase having modified nucleotide binding site for DNA sequencing

    DOE Patents [OSTI]

    Tabor, Stanley; Richardson, Charles

    1997-01-01

    Modified gene encoding a modified DNA polymerase wherein the modified polymerase incorporates dideoxynucleotides at least 20-fold better compared to the corresponding deoxynucleotides as compared with the corresponding naturally-occurring DNA polymerase.

  9. Crystal Structure of a Super Leucine Zipper an Extended Two-Stranded Super Long Coiled Coil

    SciTech Connect (OSTI)

    J Diao

    2011-12-31

    Coiled coil is a ubiquitous structural motif in proteins, with two to seven alpha helices coiled together like the strands of a rope, and coiled coil folding and assembly is not completely understood. A GCN4 leucine zipper mutant with four mutations of K3A, D7A, Y17W, and H18N has been designed, and the crystal structure has been determined at 1.6 {angstrom} resolution. The peptide monomer shows a helix trunk with short curved N- and C-termini. In the crystal, two monomers cross in 35{sup o} and form an X-shaped dimer, and each X-shaped dimer is welded into the next one through sticky hydrophobic ends, thus forming an extended two-stranded, parallel, super long coiled coil rather than a discrete, two-helix coiled coil of the wild-type GCN4 leucine zipper. Leucine residues appear at every seventh position in the super long coiled coil, suggesting that it is an extended super leucine zipper. Compared to the wild-type leucine zipper, the N-terminus of the mutant has a dramatic conformational change and the C-terminus has one more residue Glu 32 determined. The mutant X-shaped dimer has a large crossing angle of 35{sup o} instead of 18{sup o} in the wild-type dimer. The results show a novel assembly mode and oligomeric state of coiled coil, and demonstrate that mutations may affect folding and assembly of the overall coiled coil. Analysis of the formation mechanism of the super long coiled coil may help understand and design self-assembling protein fibers.

  10. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01

    The Fleet DNA project objectives include capturing and quantifying drive cycle and technology variation for the multitude of medium- and heavy-duty vocations; providing a common data storage warehouse for medium- and heavy-duty vehicle fleet data across DOE activities and laboratories; and integrating existing DOE tools, models, and analyses to provide data-driven decision making capabilities. Fleet DNA advantages include: for Government - providing in-use data for standard drive cycle development, R&D, tech targets, and rule making; for OEMs - real-world usage datasets provide concrete examples of customer use profiles; for fleets - vocational datasets help illustrate how to maximize return on technology investments; for Funding Agencies - ways are revealed to optimize the impact of financial incentive offers; and for researchers -a data source is provided for modeling and simulation.

  11. Identification of Human Repetitive DNA Elements

    Energy Science and Technology Software Center (OSTI)

    1995-11-01

    PYTHIA identifies the subfamily membership of Alu sequences, occurrences of repetitive human DNA elements, and simple DNA sequences.

  12. Hardware Controller DNA Synthesizer

    Energy Science and Technology Software Center (OSTI)

    1995-07-27

    The program controls the operation of various hardware components of an automatic 12-channel parrallel oligosynthesizer. This involves accepting information regarding the DNA sequence to be generated and converting this into a series of instructions to I/O ports to actuate the appropriate hardware components. The design and function of the software is specific to a particular hardware platform and has no utility for controlling other configurations.

  13. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment A Microscopic Double-Slit Experiment Print Wednesday, 29 February 2012 00:00 Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using

  14. The double-beta decay: Theoretical challenges

    SciTech Connect (OSTI)

    Horoi, Mihai

    2012-11-20

    Neutrinoless double beta decay is a unique process that could reveal physics beyond the Standard Model of particle physics namely, if observed, it would prove that neutrinos are Majorana particles. In addition, it could provide information regarding the neutrino masses and their hierarchy, provided that reliable nuclear matrix elements can be obtained. The two neutrino double beta decay is an associate process that is allowed by the Standard Model, and it was observed for about ten nuclei. The present contribution gives a brief review of the theoretical challenges associated with these two process, emphasizing the reliable calculation of the associated nuclear matrix elements.

  15. On the neutrinoless double ?{sup +}/EC decays

    SciTech Connect (OSTI)

    Suhonen, Jouni

    2013-12-30

    The neutrinoless double positron-emission/electron-capture (0??{sup +}/EC) decays are studied for the magnitudes of the involved nuclear matrix elements (NMEs). Decays to the ground state, 0{sub gs}{sup +}, and excited 0{sup +} states are discussed. The participant many-body wave functions are evaluated in the framework of the quasiparticle random-phase approximation (QRPA). Effective, G-matrix-derived nuclear forces are used in realistic single-particle model spaces. The channels ?{sup +}?{sup +}, ?{sup +}EC, and the resonant neutrinoless double electron capture (R0?ECEC) are discussed.

  16. Nucleotide cleaving agents and method

    DOE Patents [OSTI]

    Que, Jr., Lawrence (Roseville, MN); Hanson, Richard S. (Falcon Heights, MN); Schnaith, Leah M. T. (Redwing, MN)

    2000-01-01

    The present invention provides a unique series of nucleotide cleaving agents and a method for cleaving a nucleotide sequence, whether single-stranded or double-stranded DNA or RNA, using and a cationic metal complex having at least one polydentate ligand to cleave the nucleotide sequence phosphate backbone to yield a hydroxyl end and a phosphate end.

  17. Double layer capacitor prospects look good

    SciTech Connect (OSTI)

    1995-07-01

    The Fourth International Seminar in Double Layer Capacitors and similar energy devices has been sponsored again by Dr. S.P. Wolsky and Dr. Nikola Marincic. The seminar was held in December 1994, at Deerfield Beach, FL. This report provides a brief description of information on supercapacitors.

  18. Laminar burn rates of gun propellants measured in the high-pressure strand burner

    SciTech Connect (OSTI)

    Reaugh, J. E., LLNL

    1997-10-01

    The pressure dependence of the laminar burn rate of gun propellants plays a role in the design and behavior of high-performance guns. We have begun a program to investigate the effects of processing variables on the laminar burn rates, using our high-pressure strand burner to measure these rates at pressures exceeding 700 MPa. We have burned JA2 and M43 propellant samples, provided by Dr. Arpad Juhasz, ARL, from propellant lots previously used in round-robin tests. Our results at room temperature are in accord with other measurements. In addition, we present results measured for propellant that has been preheated to 50 C before burning. We used our thermochemical equilibrium code, CHEETAH, to help interpret the simultaneous pressure and temperature measurements taken during the testing, and show examples of its use. It has been modified to provide performance measures and equations of state for the products that are familiar to the gun-propellant community users of BLAKE.

  19. Sequential addition of short DNA oligos in DNA-polymerase-based...

    Office of Scientific and Technical Information (OSTI)

    and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of...

  20. Double, Double Toil and Trouble: Tungsten Burns and Helium Bubbles | U.S.

    Office of Science (SC) Website

    DOE Office of Science (SC) Double, Double Toil and Trouble: Tungsten Burns and Helium Bubbles Advanced Scientific Computing Research (ASCR) ASCR Home About Research Facilities Science Highlights Benefits of ASCR Funding Opportunities Advanced Scientific Computing Advisory Committee (ASCAC) Community Resources Contact Information Advanced Scientific Computing Research U.S. Department of Energy SC-21/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-7486 F: (301)

  1. Double, Double Toil and Trouble: Tungsten Burns and Helium Bubbles | U.S.

    Office of Science (SC) Website

    DOE Office of Science (SC) Double, Double Toil and Trouble: Tungsten Burns and Helium Bubbles Fusion Energy Sciences (FES) FES Home About Research Facilities Science Highlights Benefits of FES Funding Opportunities Fusion Energy Sciences Advisory Committee (FESAC) Community Resources Contact Information Fusion Energy Sciences U.S. Department of Energy SC-24/Germantown Building 1000 Independence Ave., SW Washington, DC 20585 P: (301) 903-4941 F: (301) 903-8584 E: Email Us More Information »

  2. The Promiscuity of [beta]-Strand Pairing Allows for Rational Design of [beta]-Sheet Face Inversion

    SciTech Connect (OSTI)

    Makabe, Koki; Koide, Shohei

    2009-06-17

    Recent studies suggest the dominant role of main-chain H-bond formation in specifying {beta}-sheet topology. Its essentially sequence-independent nature implies a large degree of freedom in designing {beta}-sheet-based nanomaterials. Here we show rational design of {beta}-sheet face inversions by incremental deletions of {beta}-strands from the single-layer {beta}-sheet of Borrelia outer surface protein A. We show that a {beta}-sheet structure can be maintained when a large number of native contacts are removed and that one can design large-scale conformational transitions of a {beta}-sheet such as face inversion by exploiting the promiscuity of strand-strand interactions. High-resolution X-ray crystal structures confirmed the success of the design and supported the importance of main-chain H-bonds in determining {beta}-sheet topology. This work suggests a simple but effective strategy for designing and controlling nanomaterials based on {beta}-rich peptide self-assemblies.

  3. National CHP Roadmap: Doubling Combined Heat and Power Capacity...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    CHP Roadmap: Doubling Combined Heat and Power Capacity in the United States by 2010, March 2001 National CHP Roadmap: Doubling Combined Heat and Power Capacity in the United States ...

  4. Sensitivity of CUORE to Neutrinoless Double-Beta Decay (Journal...

    Office of Scientific and Technical Information (OSTI)

    Sensitivity of CUORE to Neutrinoless Double-Beta Decay Citation Details In-Document Search Title: Sensitivity of CUORE to Neutrinoless Double-Beta Decay In this paper, we study the...

  5. Sensitivity of CUORE to Neutrinoless Double-Beta Decay (Journal...

    Office of Scientific and Technical Information (OSTI)

    Sensitivity of CUORE to Neutrinoless Double-Beta Decay Citation Details In-Document Search Title: Sensitivity of CUORE to Neutrinoless Double-Beta Decay You are accessing a...

  6. Machine learning bandgaps of double perovskites

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Pilania, G.; Mannodi-Kanakkithodi, A.; Uberuaga, B. P.; Ramprasad, R.; Gubernatis, J. E.; Lookman, T.

    2016-01-19

    The ability to make rapid and accurate predictions on bandgaps of double perovskites is of much practical interest for a range of applications. While quantum mechanical computations for high-fidelity bandgaps are enormously computation-time intensive and thus impractical in high throughput studies, informatics-based statistical learning approaches can be a promising alternative. Here we demonstrate a systematic feature-engineering approach and a robust learning framework for efficient and accurate predictions of electronic bandgaps of double perovskites. After evaluating a set of more than 1.2 million features, we identify lowest occupied Kohn-Sham levels and elemental electronegativities of the constituent atomic species as the mostmore » crucial and relevant predictors. As a result, the developed models are validated and tested using the best practices of data science and further analyzed to rationalize their prediction performance.« less

  7. Double-clad nuclear fuel safety rod

    DOE Patents [OSTI]

    McCarthy, William H. (Los Altos, CA); Atcheson, Donald B. (Cupertino, CA); Vaidyanathan, Swaminathan (San Jose, CA)

    1984-01-01

    A device for shutting down a nuclear reactor during an undercooling or overpower event, whether or not the reactor's scram system operates properly. This is accomplished by double-clad fuel safety rods positioned at various locations throughout the reactor core, wherein melting of a secondary internal cladding of the rod allows the fuel column therein to shift from the reactor core to place the reactor in a subcritical condition.

  8. Monitoring of Double Stud Wall Moisture Conditions in the Northeast

    SciTech Connect (OSTI)

    Ueno, K.

    2015-03-01

    Double-stud walls insulated with cellulose or low-density spray foam can have R-values of 40 or higher. However, double stud walls have a higher risk of interior-sourced condensation moisture damage, when compared with high-R approaches using exterior insulating sheathing.; Moisture conditions in double stud walls were monitored in Zone 5A (Massachusetts); three double stud assemblies were compared.

  9. Double-Difference Tomography for Sequestration MVA

    SciTech Connect (OSTI)

    Westman, Erik

    2008-12-31

    Analysis of synthetic data was performed to determine the most cost-effective tomographic monitoring system for a geologic carbon sequestration injection site. Double-difference tomographic inversion was performed on 125 synthetic data sets: five stages of CO2 plume growth, five seismic event regions, and five geophone arrays. Each resulting velocity model was compared quantitatively to its respective synthetic velocity model to determine an accuracy value. The results were examined to determine a relationship between cost and accuracy in monitoring, verification, and accounting applications using double-difference tomography. The geophone arrays with widely-varying geophone locations, both laterally and vertically, performed best. Additionally, double difference seismic tomography was performed using travel time data from a carbon sequestration site at the Aneth oil field in southeast Utah as part of a Department of Energy initiative on monitoring, verification, and accounting (MVA) of sequestered CO2. A total of 1,211 seismic events were recorded from a borehole array consisting of 22 geophones. Artificial velocity models were created to determine the ease with which different CO2 plume locations and sizes can be detected. Most likely because of the poor geophone arrangement, a low velocity zone in the Desert Creek reservoir can only be detected when regions of test site containing the highest ray path coverage are considered. MVA accuracy and precision may be improved through the use of a receiver array that provides more comprehensive ray path coverage.

  10. Titanium subhydride potassium perchlorate (TiH1.65/KClO4) burn rates from hybrid closed bomb-strand burner experiments.

    SciTech Connect (OSTI)

    Cooper, Marcia A.; Oliver, Michael S.

    2012-08-01

    A hybrid closed bomb-strand burner is used to measure the burning behavior of the titanium subhydride potassium perchlorate pyrotechnic with an equivalent hydrogen concentration of 1.65. This experimental facility allows for simultaneous measurement of the closed bomb pressure rise and pyrotechnic burn rate as detected by electrical break wires over a range of pressures. Strands were formed by pressing the pyrotechnic powders to bulk densities between 60% and 90% theoretical maximum density. The burn rate dependance on initial density and vessel pressure are measured. At all initial strand densities, the burn is observed to transition from conductive to convective burning within the strand. The measured vessel pressure history is further analyzed following the closed bomb analysis methods developed for solid propellants.

  11. *NEW!* Doubling Geothermal Generation Capacity by 2020: A Strategic

    Office of Environmental Management (EM)

    Analysis | Department of Energy *NEW!* Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis *NEW!* Doubling Geothermal Generation Capacity by 2020: A Strategic Analysis PDF icon NREL Doubling Geothermal Capacity.pdf More Documents & Publications Geothermal Exploration Policy Mechanisms Offshore Wind Jobs and Economic Development Impacts in the United States: Four Regional Scenarios track 1: systems analysis | geothermal 2015 peer review

  12. Protection of cisplatin-induced spermatotoxicity, DNA damage and chromatin abnormality by selenium nano-particles

    SciTech Connect (OSTI)

    Rezvanfar, Mohammad Amin; Rezvanfar, Mohammad Ali; Shahverdi, Ahmad Reza; Ahmadi, Abbas; Baeeri, Maryam; Mohammadirad, Azadeh; Abdollahi, Mohammad

    2013-02-01

    Cisplatin (CIS), an anticancer alkylating agent, induces DNA adducts and effectively cross links the DNA strands and so affects spermatozoa as a male reproductive toxicant. The present study investigated the cellular/biochemical mechanisms underlying possible protective effect of selenium nano-particles (Nano-Se) as an established strong antioxidant with more bioavailability and less toxicity, on reproductive toxicity of CIS by assessment of sperm characteristics, sperm DNA integrity, chromatin quality and spermatogenic disorders. To determine the role of oxidative stress (OS) in the pathogenesis of CIS gonadotoxicity, the level of lipid peroxidation (LPO), antioxidant enzymes including superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GSH-Px) and peroxynitrite (ONOO) as a marker of nitrosative stress (NS) and testosterone (T) concentration as a biomarker of testicular function were measured in the blood and testes. Thirty-two male Wistar rats were equally divided into four groups. A single IP dose of CIS (7 mg/kg) and protective dose of Nano-Se (2 mg/kg/day) were administered alone or in combination. The CIS-exposed rats showed a significant increase in testicular and serum LPO and ONOO level, along with a significant decrease in enzymatic antioxidants levels, diminished serum T concentration and abnormal histologic findings with impaired sperm quality associated with increased DNA damage and decreased chromatin quality. Coadministration of Nano-Se significantly improved the serum T, sperm quality, and spermatogenesis and reduced CIS-induced free radical toxic stress and spermatic DNA damage. In conclusion, the current study demonstrated that Nano-Se may be useful to prevent CIS-induced gonadotoxicity through its antioxidant potential. Highlights: ? Cisplatin (CIS) affects spermatozoa as a male reproductive toxicant. ? Effect of Nano-Se on CIS-induced spermatotoxicity was investigated. ? CIS-exposure induces oxidative sperm DNA damage and impairs steroidogenesis. ? Nano-Se retained sperm quality against CIS-induced free radicals toxic stress.

  13. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known...

  14. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the...

  15. Challenges and opportunities for structural DNA nanotechnology

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Challenges and opportunities for structural DNA nanotechnology Authors: Pinheiro, A. V., Han, D., Shih, W. M., and Yan, H. Title: Challenges and opportunities for structural DNA...

  16. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, S.K.

    1998-03-24

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example, the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei. 25 figs.

  17. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K.

    1998-01-01

    The present invention is a rapid sequence-independent amplification procedure (SIA). Even minute amounts of DNA from various sources can be amplified independent of any sequence requirements of the DNA or any a priori knowledge of any sequence characteristics of the DNA to be amplified. This method allows, for example the sequence independent amplification of microdissected chromosomal material and the reliable construction of high quality fluorescent in situ hybridization (FISH) probes from YACs or from other sources. These probes can be used to localize YACs on metaphase chromosomes but also--with high efficiency--in interphase nuclei.

  18. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  19. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  20. Neutrinoless double beta decay and neutrino masses

    SciTech Connect (OSTI)

    Duerr, Michael [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany)

    2012-07-27

    Neutrinoless double beta decay (0{nu}{beta}{beta}) is a promising test for lepton number violating physics beyond the standard model (SM) of particle physics. There is a deep connection between this decay and the phenomenon of neutrino masses. In particular, we will discuss the relation between 0{nu}{beta}{beta} and Majorana neutrino masses provided by the so-called Schechter-Valle theorem in a quantitative way. Furthermore, we will present an experimental cross check to discriminate 0{nu}{beta}{beta} from unknown nuclear background using only one isotope, i.e., within one experiment.

  1. Optical double-slit particle measuring system

    DOE Patents [OSTI]

    Tichenor, D.A.; Wang, J.C.F.; Hencken, K.R.

    1982-03-25

    A method for in situ measurement of particle size is described. The size information is obtained by scanning an image of the particle across a double-slit mask and observing the transmitted light. This method is useful when the particle size of primary interest is 3..mu..m and larger. The technique is well suited to applications in which the particles are non-spherical and have unknown refractive index. It is particularly well suited to high temperature environments in which the particle incandescence provides the light source.

  2. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  3. A Microscopic Double-Slit Experiment

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Microscopic Double-Slit Experiment Print Two centuries ago, Thomas Young performed the classic demonstration of the wave nature of light. He placed a screen with two tiny slits in front of a single light source, effectively converting it into a two-centered source. On a second screen far away, he saw a pattern of light and dark diffraction fringes, a well-known hallmark of wave interference. Along with later studies using particles instead of light, the experiment played a crucial role in

  4. Double acting stirling engine phase control

    DOE Patents [OSTI]

    Berchowitz, David M. (Scotia, NY)

    1983-01-01

    A mechanical device for effecting a phase change between the expansion and compression volumes of a double-acting Stirling engine uses helical elements which produce opposite rotation of a pair of crankpins when a control rod is moved, so the phase between two pairs of pistons is changed by +.psi. and the phase between the other two pairs of pistons is changed by -.psi.. The phase can change beyond .psi.=90.degree. at which regenerative braking and then reversal of engine rotation occurs.

  5. Optical double-slit particle measuring system

    DOE Patents [OSTI]

    Hencken, Kenneth R. (Pleasanton, CA); Tichenor, Daniel A. (Freemont, CA); Wang, James C. F. (Livermore, CA)

    1984-01-01

    A method for in situ measurement of particle size is described. The size information is obtained by scanning an image of the particle across a double-slit mask and observing the transmitted light. This method is useful when the particle size of primary interest is 3 .mu.m and larger. The technique is well suited to applications in which the particles are non-spherical and have unknown refractive index. It is particularly well suited to high temperature environments in which the particle incandescence provides the light source.

  6. The double contact nature of TT Herculis

    SciTech Connect (OSTI)

    Terrell, Dirk; Nelson, Robert H. E-mail: bob.nelson@shaw.ca

    2014-03-01

    We present new radial velocities and photometry of the short-period Algol TT Herculis. Previous attempts to model the light curves of the system have met with limited success, primarily because of the lack of a reliable mass ratio. Our spectroscopic observations are the first to result in radial velocities for the secondary star, and thus provide a spectroscopic mass ratio. Simultaneous analysis of the radial velocities and new photometry shows that the system is a double contact binary, with a rapidly rotating primary that fills its limiting lobe.

  7. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach in the Columbia River, 1998 Interim Report.

    SciTech Connect (OSTI)

    Nugent, John; Newsome, Todd; Nugent, Michael

    2001-07-27

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the second year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fish species, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 1998 field season.

  8. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 2000 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John; Nugent, Michael; Brock, Wendy

    2002-05-29

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the fourth year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 2000 field season.

  9. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 2001 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John; Nugent, Michael; Brock, Wendy

    2002-05-29

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach of the Columbia River. The evaluation, in the fifth year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 2001 field season.

  10. Evaluation of Juvenile Fall Chinook Salmon Stranding on the Hanford Reach of the Columbia River, 1999 Annual Report.

    SciTech Connect (OSTI)

    Nugent, John

    2002-01-24

    The Washington Department of Fish and Wildlife (WDFW) has been contracted through the Bonneville Power Administration (BPA) and the Grant County Public Utility District (GCPUD) to perform an evaluation of juvenile fall chinook salmon (Oncorhynchus tshawytscha) stranding on the Hanford Reach. The evaluation, in the third year of a multi-year study, has been developed to assess the impacts of water fluctuations from Priest Rapids Dam on rearing juvenile fall chinook salmon, other fishes, and benthic macroinvertebrates of the Hanford Reach. This document provides the results of the 1999 field season.

  11. Studies of ${\\rm Nb}_{3}{\\rm Sn}$ Strands Based on the Restacked-Rod Process for High Field Accelerator Magnets

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Barzi, E.; Bossert, M.; Gallo, G.; Lombardo, V.; Turrioni, D.; Yamada, R.; Zlobin, A. V.

    2011-12-21

    A major thrust in Fermilab's accelerator magnet R&D program is the development of Nb3Sn wires which meet target requirements for high field magnets, such as high critical current density, low effective filament size, and the capability to withstand the cabling process. The performance of a number of strands with 150/169 restack design produced by Oxford Superconducting Technology was studied for round and deformed wires. To optimize the maximum plastic strain, finite element modeling was also used as an aid in the design. Results of mechanical, transport and metallographic analyses are presented for round and deformed wires.

  12. Double Retort System for Materials Compatibility Testing

    SciTech Connect (OSTI)

    V. Munne; EV Carelli

    2006-02-23

    With Naval Reactors (NR) approval of the Naval Reactors Prime Contractor Team (NRPCT) recommendation to develop a gas cooled reactor directly coupled to a Brayton power conversion system as the Space Nuclear Power Plant (SNPP) for Project Prometheus (References a and b) there was a need to investigate compatibility between the various materials to be used throughout the SNPP. Of particular interest was the transport of interstitial impurities from the nickel-base superalloys, which were leading candidates for most of the piping and turbine components to the refractory metal alloys planned for use in the reactor core. This kind of contamination has the potential to affect the lifetime of the core materials. This letter provides technical information regarding the assembly and operation of a double retort materials compatibility testing system and initial experimental results. The use of a double retort system to test materials compatibility through the transfer of impurities from a source to a sink material is described here. The system has independent temperature control for both materials and is far less complex than closed loops. The system is described in detail and the results of three experiments are presented.

  13. Quantitative Analysis of Clustered DNA Damages Induced by Silicon Beams of Different Kinetic Energy

    SciTech Connect (OSTI)

    Keszenman D. J.; Keszenman, D.J.; Bennett, P.V.; Sutherland, B.M.; Wilson, P.F.

    2013-05-14

    Humans may b exposed to highly energetic charged particle radiation as a result of medical treatments, occupational activitie or accidental events. In recent years, our increasing presence and burgeoning interest in space exploration beyond low Earth orbit has led to a large increase in the research of the biological effects ofcharged particle radiation typical of that encountered in the space radiation environment. The study of the effects of these types of radiation qualities in terms ofDNA damage induction and repair is fundamental to understand mechanisms both underlying their greater biological effectiveness as we)) as the short and long term risks of health effects such as carcinogenesis, degen rative diseases and premature aging. Charged particle radiation induces a variety of DNA alterations, notably bistranded clustered damages, defined as two or more closely-opposed strand break , oxidized bases or abasic sites within a few helical turns. The induction of such highly complex DNA damage enhances the probability of incorrect or incomplete repair and thus constitutes greater potential for genomic instability, cell death and transformation.

  14. Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec

    SciTech Connect (OSTI)

    Safo, Martin K.; Ko, Tzu-Ping; Musayev, Faik N.; Zhao, Qixun; Archer, Gordon L.

    2006-04-01

    The up-and-down binding of dimeric MecI to mecA dyad DNA may account for the cooperative effect of the repressor. The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of β-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Å resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI–mec complex, but unlike the MecI–bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.

  15. DNA analysis conference in Santa Fe

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA analysis conference in Santa Fe DNA analysis conference in Santa Fe Los Alamos National Laboratory is hosting a DNA sequence analysis and bioinformatics event, the 10th annual Sequencing, Finishing and Analysis in the Future (SFAF) workshop. May 27, 2015 DNA extracted from a soil sample is stored in a small vial of clear liquid. In general, living cells function by using the sequences of bases in their DNA as a blueprint for assembling proteins. A particularly important type of protein is

  16. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01

    This volume contains the proceedings of the conference entitled Cellular Responses to Environmental DNA Damage held in Banff,Alberta December 1--6, 1991. The conference addresses various aspects of DNA repair in sessions titled DNA repair; Basic Mechanisms; Lesions; Systems; Inducible Responses; Mutagenesis; Human Population Response Heterogeneity; Intragenomic DNA Repair Heterogeneity; DNA Repair Gene Cloning; Aging; Human Genetic Disease; and Carcinogenesis. Individual papers are represented as abstracts of about one page in length.

  17. Neutron Interactions in the CUORE Neutrinoless Double Beta Decay Experiment

    Office of Scientific and Technical Information (OSTI)

    (Thesis/Dissertation) | SciTech Connect Thesis/Dissertation: Neutron Interactions in the CUORE Neutrinoless Double Beta Decay Experiment Citation Details In-Document Search Title: Neutron Interactions in the CUORE Neutrinoless Double Beta Decay Experiment Neutrinoless double beta decay (0{nu}DBD) is a lepton-number violating process that can occur only for a massive Majorana neutrino. The search for 0{nu}DBD is currently the only practical experimental way to determine whether neutrinos are

  18. Optical transmission through double-layer, laterally shifted metallic

    Office of Scientific and Technical Information (OSTI)

    subwavelength hole arrays (Journal Article) | SciTech Connect Journal Article: Optical transmission through double-layer, laterally shifted metallic subwavelength hole arrays Citation Details In-Document Search Title: Optical transmission through double-layer, laterally shifted metallic subwavelength hole arrays We measure the transmission of infra-red radiation through double-layer metal lms with periodic arrays of subwavelength holes. When the two metal lms are placed in su ciently close

  19. Neutrinoless double beta decay search with the NEMO 3 experiment

    SciTech Connect (OSTI)

    Nasteva, Irina [Particle Physics Group, School of Physics and Astronomy, University of Manchester, Manchester, M13 9PL (United Kingdom)

    2008-11-23

    The NEMO 3 experiment searches for neutrinoless double beta decay and makes precision measurements of two-neutrino double beta decay in seven isotopes. The latest two-neutrino half-life results are presented, together with the limits on neutrinoless half-lives and the corresponding effective Majorana neutrino masses. Also given are the limits obtained on neutrinoless double beta decay mediated by R{sub p}-violating SUSY, right-hand currents and different Majoron emission modes.

  20. Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Hierarchy with Bolometric Detectors (Journal Article) | SciTech Connect Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino Hierarchy with Bolometric Detectors Citation Details In-Document Search Title: Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino Hierarchy with Bolometric Detectors Neutrinoless double beta decay (0nubb) is one of the most sensitive probes for physics beyond the Standard Model, providing unique information on the nature of

  1. Status Update of the Majorana Demonstrator Neutrinoless Double Beta Decay

    Office of Scientific and Technical Information (OSTI)

    Experiment (Technical Report) | SciTech Connect Status Update of the Majorana Demonstrator Neutrinoless Double Beta Decay Experiment Citation Details In-Document Search Title: Status Update of the Majorana Demonstrator Neutrinoless Double Beta Decay Experiment Neutrinoless double beta decay searches play a major role in determining neutrino properties, in particular the Majorana or Dirac nature of the neutrino and the absolute scale of the neutrino mass. The consequences of these searches go

  2. The Majorana Double Beta Decay Experiment: Present Status (Conference) |

    Office of Scientific and Technical Information (OSTI)

    SciTech Connect Majorana Double Beta Decay Experiment: Present Status Citation Details In-Document Search Title: The Majorana Double Beta Decay Experiment: Present Status The Majorana collaboration is actively pursuing research and development aimed at a tonne-scale 76Ge neutrinoless double-beta decay experiment, an R&D effort that will field approximately 40 kg of germanium detectors with mixed enrichment levels. This article provides a status update on the construction of the

  3. DUF6 Project Doubles Production in 2013 | Department of Energy

    Office of Environmental Management (EM)

    Doubles Production in 2013 DUF6 Project Doubles Production in 2013 November 26, 2013 - 12:00pm Addthis LEXINGTON, Ky. - The conversion plants at EM's Paducah and Portsmouth sites surpassed a fiscal year 2013 goal by converting 13,679 metric tons of depleted uranium hexafluoride (DUF6), more than doubling production a year earlier. EM's Portsmouth Paducah Project Office (PPPO) and contractor Babcock & Wilcox Conversion Services LLC (BWCS) began operations in 2011 to convert the nation's

  4. Correlations and the neutrinoless double beta decay

    SciTech Connect (OSTI)

    Menendez, J.; Poves, A. [Departamento de Fisica Teorica, and IFT, UAM-CSIC, Universidad Autonoma de Madrid, 28049-Madrid (Spain); Caurier, E.; Nowacki, F. [IPHC, IN2P3-CNRS/Universite Louis Pasteur, 67037-Strasbourg (France)

    2009-11-09

    We explore the influence of the deformation on the nuclear matrix elements of the neutrinoless double beta decay (NME), concluding that the difference in deformation -or more generally on the amount of quadrupole correlations- between parent and grand daughter nuclei quenchs strongly the decay. We discuss how varies the nuclear matrix element of {sup 76}Ge decay when the wave functions of the two nuclei involved in the transition are constrained to reproduce the experimental occupancies. In the Interacting Shell Model description the value of the NME is enhanced about 15% compared to previous calculations, whereas in the QRPA the NME's are reduced by 20%-30%, thus, the discrepancies between both approaches diminish.

  5. Double-rotor rotary engine and turbine

    SciTech Connect (OSTI)

    Lin, A.S.

    1990-04-03

    This patent describes a double-rotor engine. It comprises: a base; a housing rotatably mounted to the base and forming a radial cylinder; an output shaft rotatably mounted concentric with the housing and having an arm rigidly extending therefrom within the housing; a piston slidingly engaging the cylinder and forming a combustion chamber with the cylinder; means for admitting a fuel-air mixture into the cylinder; means for releasing combustion products from the cylinder following operation of the expanding means; turbine means operatively connected between the base and the housing, the turbine means providing a torque reaction against the housing in response to flow of the combustion products from the releasing means; and stop means on the shaft for limiting the relative movement between the shaft and the housing.

  6. Solid Double-Layered Hydroxide Catalysts for Lignin Decomposition...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Biomass and Biofuels Biomass and Biofuels Find More Like This Return to Search Solid Double-Layered Hydroxide Catalysts for Lignin Decomposition National Renewable Energy...

  7. Simulations of Cyclic Voltammetry for Electric Double Layers...

    Office of Scientific and Technical Information (OSTI)

    Simulations of Cyclic Voltammetry for Electric Double Layers in Asymmetric Electrolytes: A Generalized Modified PoissonNernstPlanck Model Citation Details In-Document Search...

  8. Systematics of quarkonium production at the LHC and double parton...

    Office of Scientific and Technical Information (OSTI)

    Systematics of quarkonium production at the LHC and double parton fragmentation Citation Details In-Document Search Title: Systematics of quarkonium production at the LHC and ...

  9. Radiochemical tracers as a mix diagnostic for the ignition double...

    Office of Scientific and Technical Information (OSTI)

    for the ignition double-shell capsule One of the most important challenges confronting laser-driven capsule implosion experiments will be a quantitative evaluation of the...

  10. Neutron Interactions in the CUORE Neutrinoless Double Beta Decay...

    Office of Scientific and Technical Information (OSTI)

    Interactions in the CUORE Neutrinoless Double Beta Decay Experiment Dolinski, M J 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; 73 NUCLEAR PHYSICS AND RADIATION PHYSICS;...

  11. Optical transmission through double-layer, laterally shifted...

    Office of Scientific and Technical Information (OSTI)

    shifted metallic subwavelength hole arrays We measure the transmission of infra-red radiation through double-layer metal lms with periodic arrays of subwavelength holes....

  12. DOE Science Showcase - Neutrinoless Double Beta Decay | OSTI...

    Office of Scientific and Technical Information (OSTI)

    In the OSTI Collections: Neutrinoless Double Beta Decay--Are Neutrinos and Antineutrinos the same?, Dr. William Watson DOE PAGESBeta - journal articles and accepted manuscripts ...

  13. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

    Douthart, R.J.; Crowell, S.L.

    1996-05-07

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection. 18 figs.

  14. Apparatus for improved DNA sequencing

    DOE Patents [OSTI]

    Douthart, Richard J. (Richland, WA); Crowell, Shannon L. (Eltopia, WA)

    1996-01-01

    This invention is a means for the rapid sequencing of DNA samples. More specifically, it consists of a new design direct blotting electrophoresis unit. The DNA sequence is deposited on a membrane attached to a rotating drum. Initial data compaction is facilitated by the use of a machined multi-channeled plate called a ribbon channel plate. Each channel is an isolated mini gel system much like a gel filled capillary. The system as a whole, however, is in a slab gel like format with the advantages of uniformity and easy reusability. The system can be used in different embodiments. The drum system is unique in that after deposition the drum rotates the deposited DNA into a large non-buffer open space where processing and detection can occur. The drum can also be removed in toto to special workstations for downstream processing, multiplexing and detection.

  15. Method for double-sided processing of thin film transistors

    DOE Patents [OSTI]

    Yuan, Hao-Chih (Madison, WI); Wang, Guogong (Madison, WI); Eriksson, Mark A. (Madison, WI); Evans, Paul G. (Madison, WI); Lagally, Max G. (Madison, WI); Ma, Zhenqiang (Middleton, WI)

    2008-04-08

    This invention provides methods for fabricating thin film electronic devices with both front- and backside processing capabilities. Using these methods, high temperature processing steps may be carried out during both frontside and backside processing. The methods are well-suited for fabricating back-gate and double-gate field effect transistors, double-sided bipolar transistors and 3D integrated circuits.

  16. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

    Moyzis, Robert K. (Los Alamos, NM); Meyne, Julianne (Los Alamos, NM)

    1991-01-01

    A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

  17. Structure of the Mecl Repressor from Staphylococcus aureus in Complex with the Cognate DNA Operator of mec

    SciTech Connect (OSTI)

    Safo,M.; Ko, T.; Musayev, F.; Zhao, Q.; Wang, A.; Archer, G.

    2006-01-01

    The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of {beta}-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Angstroms resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI-mec complex, but unlike the MecI-bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.

  18. Coronal electron confinement by double layers

    SciTech Connect (OSTI)

    Li, T. C.; Drake, J. F.; Swisdak, M.

    2013-12-01

    In observations of flare-heated electrons in the solar corona, a longstanding problem is the unexplained prolonged lifetime of the electrons compared to their transit time across the source. This suggests confinement. Recent particle-in-cell (PIC) simulations, which explored the transport of pre-accelerated hot electrons through ambient cold plasma, showed that the formation of a highly localized electrostatic potential drop, in the form of a double layer (DL), significantly inhibited the transport of hot electrons. The effectiveness of confinement by a DL is linked to the strength of the DL as defined by its potential drop. In this work, we investigate the scaling of the DL strength with the hot electron temperature by PIC simulations and find a linear scaling. We demonstrate that the strength is limited by the formation of parallel shocks. Based on this, we analytically determine the maximum DL strength, and also find a linear scaling with the hot electron temperature. The DL strength obtained from the analytic calculation is comparable to that from the simulations. At the maximum strength, the DL is capable of confining a significant fraction of hot electrons in the source.

  19. Pionic contribution to neutrinoless double beta decay

    SciTech Connect (OSTI)

    Vergados, J. D. [Physics Department, University of Ioannina, Ioannina, GR 451 10 (Greece); Theory Division, CERN, Geneva (Switzerland); Faessler, Amand [Institute fuer Theoretische Physik, Universitaet Tuebingen (Germany); Toki, H. [RCNP, Osaka University, Osaka, 567-0047 (Japan)

    2010-02-01

    It is well known that neutrinoless double decay is going to play a crucial role in settling the neutrino properties, which cannot be extracted from the neutrino oscillation data. It is, in particular, expected to settle the absolute scale of neutrino mass and determine whether the neutrinos are Majorana particles, i.e. they coincide with their own antiparticles. In order to extract the average neutrino mass from the data, one must be able to estimate the contribution of all possible high mass intermediate particles. The latter, which occur in practically all extensions of the standard model, can, in principle, be differentiated from the usual mass term, if data from various targets are available. One, however, must first be able to reliably calculate the corresponding nuclear matrix elements. Such calculations are extremely difficult since the effective transition operators are very short ranged. For such operators processes like pionic contributions, which are usually negligible, turn out to be dominant. We study such an effect in a nonrelativistic quark model for the pion and the nucleon.

  20. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M. (Oak Ridge, TN)

    1997-01-01

    An internal combustion, liquid metal (LM) magnetohydrodynamic (MHD) engine and an alternating current (AC) magnetohydrodynamic generator, are used in combination to provide useful AC electric energy output. The engine design has four pistons and a double duct configuration, with each duct containing sodium potassium liquid metal confined between free pistons located at either end of the duct. The liquid metal is forced to flow back and forth in the duct by the movement of the pistons, which are alternatively driven by an internal combustion process. In the MHD generator, the two LM-MHD ducts pass in close proximity through a Hartmann duct with output transformer. AC power is produced by operating the engine with the liquid metal in the two generator ducts always flowing in counter directions. The amount of liquid metal maintained in the ducts may be varied. This provides a variable stroke length for the pistons. The engine/generator provides variable AC power at variable frequencies that correspond to the power demands of the vehicular propulsion. Also the engine should maintain nearly constant efficiency throughout the range of power usage. Automobiles and trucks could be powered by the invention, with no transmission or power converter devices being required.

  1. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M. (Oak Ridge, TN)

    1995-01-01

    An internal combustion, liquid metal (LM) magnetohydrodynamic (MHD) engine and an alternating current (AC) magnetohydrodynamic generator, are used in combination to provide useful AC electric energy output. The engine design has-four pistons and a double duct configuration, with each duct containing sodium potassium liquid metal confined between free pistons located at either end of the duct. The liquid metal is forced to flow back and forth in the duct by the movement of the pistons, which are alternatively driven by an internal combustion process. In the MHD generator, the two LM-MHD ducts pass in close proximity through a Hartmann duct with output transformer. AC power is produced by operating the engine with the liquid metal in the two generator ducts always flowing in counter directions. The amount of liquid metal maintained in the ducts may be varied. This provides a variable stroke length for the pistons. The engine/generator provides variable AC power at variable frequencies that correspond to the power demands of the vehicular propulsion. Also the engine should maintain nearly constant efficiency throughout the range of power usage. Automobiles and trucks could be powered by the invention, with no transmission or power converter devices being required.

  2. Interconnecting gold islands with DNA origami

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Interconnecting gold islands with DNA origami Authors: Ding, B., Wu, H., Xu, W., Zhao, Z., Liu, Y., Yu, H., and Yan, H. Title: Interconnecting gold islands with DNA origami Source:...

  3. A DNA tweezer-actuated enzyme nanoreactor

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A DNA tweezer-actuated enzyme nanoreactor Authors: Liu, M., Fu, J., Hejesen, C., Yang, Y., Woodbury, N.W., Gothelf, K., Liu, Y., and Yan, H. Title: A DNA tweezer-actuated enzyme...

  4. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

    Christian, Allen T.; Coleman, Matthew A.; Tucker, James D.

    2002-01-01

    Amplification of chromosomal DNA in situ to increase the amount of DNA associated with a chromosome or chromosome region is described. The amplification of chromosomal DNA in situ provides for the synthesis of Fluorescence in situ Hybridization (FISH) painting probes from single dissected chromosome fragments, the production of cDNA libraries from low copy mRNAs and improved in Comparative Genomic Hybridization (CGH) procedures.

  5. DNA Origami: A History and Current Perspective

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Origami: A History and Current Perspective Authors: Nangreave, J., Han, D., Liu, Y., and Yan, H. Title: DNA Origami: A History and Current Perspective Source: Current Opinion in Chemical Biology Year: 2010 Volume: 14 Pages: 608-615 ABSTRACT: Researchers have been using DNA for the rational design and construction of nanoscale objects for nearly 30 years. Recently, [`]scaffolded DNA origami' has emerged as one of the most promising assembly techniques in DNA nanotechnology with a broad range of

  6. Structure of Rhodococcus equi virulence-associated protein B (VapB) reveals an eight-stranded antiparallel ?-barrel consisting of two Greek-key motifs

    SciTech Connect (OSTI)

    Geerds, Christina; Wohlmann, Jens; Haas, Albert; Niemann, Hartmut H.

    2014-06-18

    The structure of VapB, a member of the Vap protein family that is involved in virulence of the bacterial pathogen R. equi, was determined by SAD phasing and reveals an eight-stranded antiparallel ?-barrel similar to avidin, suggestive of a binding function. Made up of two Greek-key motifs, the topology of VapB is unusual or even unique. Members of the virulence-associated protein (Vap) family from the pathogen Rhodococcus equi regulate virulence in an unknown manner. They do not share recognizable sequence homology with any protein of known structure. VapB and VapA are normally associated with isolates from pigs and horses, respectively. To contribute to a molecular understanding of Vap function, the crystal structure of a protease-resistant VapB fragment was determined at 1.4 resolution. The structure was solved by SAD phasing employing the anomalous signal of one endogenous S atom and two bound Co ions with low occupancy. VapB is an eight-stranded antiparallel ?-barrel with a single helix. Structural similarity to avidins suggests a potential binding function. Unlike other eight- or ten-stranded ?-barrels found in avidins, bacterial outer membrane proteins, fatty-acid-binding proteins and lysozyme inhibitors, Vaps do not have a next-neighbour arrangement but consist of two Greek-key motifs with strand order 41238567, suggesting an unusual or even unique topology.

  7. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-07-11

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  8. NV-020-08-DNA-52 | Open Energy Information

    Open Energy Info (EERE)

    DNA-52 Jump to: navigation, search NEPA Document Collection for: NV-020-08-DNA-52 DNA for GeothermalExploration, DNA for Thermal Gradient Hole at Gavvs Valley for Geothermal...

  9. Fabrication and Measurements of 500 MHz Double Spoke Cavity

    SciTech Connect (OSTI)

    Park, HyeKyoung; Hopper, Christopher S.; Delayen, Jean R.

    2014-12-01

    A 500 MHz ?0=1 double spoke cavity has been designed and optimized for a high velocity application such as a compact electron accelerator at the Center for Accelerator Science at Old Dominion University [1] and the fabrication was recently completed at Jefferson Lab. The geometry specific to the double spoke cavity required a variety of tooling and fixtures. Also a number of asymmetric weld joints were expected to make it difficult to maintain minimal geometric deviation from the design. This paper will report the fabrication procedure, resulting tolerance from the design, initial test results and the lessons learned from the first ?0=1 double spoke cavity fabrication.

  10. Nebraska: Company More than Doubles Annual Sales and Employees | Department

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Energy Nebraska: Company More than Doubles Annual Sales and Employees Nebraska: Company More than Doubles Annual Sales and Employees August 21, 2013 - 12:38pm Addthis Hexagon Lincoln, of Lincoln, Nebraska, has more than doubled its workforce and added a fourth shift for 24-hour/7-days-a-week operation to accommodate growing demand for its carbon fiber composite tanks. With EERE support, Hexagon developed a new trailer that uses high-strength composite vessels to carry more than 720 kg of

  11. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01

    The Fleet DNA Project - designed by the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) in partnership with Oak Ridge National Laboratory - aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel consumption, and emissions. At the heart of the Fleet DNA Project is a clearinghouse of medium- and heavy-duty commercial fleet transportation data for optimizing the design of advanced vehicle technologies or for selecting a given technology to invest in. An easy-to-access online database will help vehicle manufacturers and fleets understand the broad operational range for many of today's commercial vehicle vocations.

  12. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13

    An electrophoretic device separates and detects particles such as DNA fragments, proteins, and the like. The device has a capillary which is coated with a coating with a low refractive index such as Teflon.RTM. AF. A sample of particles is fluorescently labeled and injected into the capillary. The capillary is filled with an electrolyte buffer solution. An electrical field is applied across the capillary causing the particles to migrate from a first end of the capillary to a second end of the capillary. A detector light beam is then scanned along the length of the capillary to detect the location of the separated particles. The device is amenable to a high throughput system by providing additional capillaries. The device can also be used to determine the actual size of the particles and for DNA sequencing.

  13. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication The Initiation of Bacterial DNA Replication Print Wednesday, 31 January 2007 00:00 For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA

  14. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, Andrew M. (Oakland, CA); Dawson, John (Pacific Palisades, CA)

    1993-01-01

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source.

  15. Channel plate for DNA sequencing

    DOE Patents [OSTI]

    Douthart, R.J.; Crowell, S.L.

    1998-01-13

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface. 15 figs.

  16. Channel plate for DNA sequencing

    DOE Patents [OSTI]

    Douthart, Richard J. (Richland, WA); Crowell, Shannon L. (Eltopia, WA)

    1998-01-01

    This invention is a channel plate that facilitates data compaction in DNA sequencing. The channel plate has a length, a width and a thickness, and further has a plurality of channels that are parallel. Each channel has a depth partially through the thickness of the channel plate. Additionally an interface edge permits electrical communication across an interface through a buffer to a deposition membrane surface.

  17. EA-1136: Double Tracks Test Site, Nye County, Nevada

    Broader source: Energy.gov [DOE]

    This EA evaluates the environmental impacts of the proposal for the U.S. Department of Energy Nevada Operations Office to conduct environmental restoration operations at the Double Tracks test site...

  18. Double Shell Tank (DST) Monitor and Control Subsystem Specification

    SciTech Connect (OSTI)

    BAFUS, R.R.

    2000-11-03

    This specification revises the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Monitor and Control Subsystem that supports the first phase of Waste Feed Delivery.

  19. Performance of a double pass solar air collector

    SciTech Connect (OSTI)

    Ramani, B.M.; Gupta, Akhilesh; Kumar, Ravi

    2010-11-15

    Double pass counter flow solar air collector with porous material in the second air passage is one of the important and attractive design improvement that has been proposed to improve the thermal performance. This paper presents theoretical and experimental analysis of double pass solar air collector with and without porous material. A mathematical model has been developed based on volumetric heat transfer coefficient. Effects of various parameters on the thermal performance and pressure drop characteristics have been discussed. Comparison of results reveals that the thermal efficiency of double pass solar air collector with porous absorbing material is 20-25% and 30-35% higher than that of double pass solar air collector without porous absorbing material and single pass collector respectively. (author)

  20. Evaluation of Double-moment Microphysical Parameterization with...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    model?" Because of the lack of data with detailed MCS cloud components, a detailed evaluation of double-moment schemes has not yet been undertaken. During April and May of 2011,...

  1. Mechanisms of radiation-induced gene responses

    SciTech Connect (OSTI)

    Woloschak, G.E.; Paunesku, T.

    1996-10-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5` region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3` region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process.

  2. Energy levels of double triangular graphene quantum dots

    SciTech Connect (OSTI)

    Liang, F. X.; Jiang, Z. T. Zhang, H. Y.; Li, S.; Lv, Z. T.

    2014-09-28

    We investigate theoretically the energy levels of the coupled double triangular graphene quantum dots (GQDs) based on the tight-binding Hamiltonian model. The double GQDs including the ZZ-type, ZA-type, and AA-type GQDs with the two GQDs having the zigzag or armchair boundaries can be coupled together via different interdot connections, such as the direct coupling, the chains of benzene rings, and those of carbon atoms. It is shown that the energy spectrum of the coupled double GQDs is the amalgamation of those spectra of the corresponding two isolated GQDs with the modification triggered by the interdot connections. The interdot connection is inclined to lift up the degeneracies of the energy levels in different degree, and as the connection changes from the direct coupling to the long chains, the removal of energy degeneracies is suppressed in ZZ-type and AA-type double GQDs, which indicates that the two coupled GQDs are inclined to become decoupled. Then we consider the influences on the spectra of the coupled double GQDs induced by the electric fields applied on the GQDs or the connection, which manifests as the global spectrum redistribution or the local energy level shift. Finally, we study the symmetrical and asymmetrical energy spectra of the double GQDs caused by the substrates supporting the two GQDs, clearly demonstrating how the substrates affect the double GQDs' spectrum. This research elucidates the energy spectra of the coupled double GQDs, as well as the mechanics of manipulating them by the electric field and the substrates, which would be a significant reference for designing GQD-based devices.

  3. No-neutrino double beta decay: more than one neutrino

    SciTech Connect (OSTI)

    Rosen, S.P.

    1983-01-01

    Interference effects between light and heavy Majorana neutrinos in the amplitude for no-neutrino double beta decay are discussed. The effects include an upper bound on the heavy neutrino mass, and an A dependence for the effective mass extracted from double beta decay. Thus the search for the no-neutrino decay mode should be pursued in several nuclei, and particularly in Ca/sup 48/, where the effective mass may be quite large.

  4. Effect of nuclear deformation on double beta decay

    SciTech Connect (OSTI)

    Rodin, Vadim [Institute fuer Theoretische Physik der Universitaet Tuebingen, D-72076 Tuebingen (Germany)

    2009-11-09

    The existing ways of accounting for deformation in recent calculations of neutrinoless double beta decay matrix elements are discussed. From an analysis of relevant experimental data it is argued that only {sup 150}Nd reveals convincing evidences of strong static deformation, which should eventually be taken into account in QRPA calculations. A proposal which allows in principle to measure the neutrino less double beta decay Fermi matrix element is briefly described.

  5. Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino

    Office of Scientific and Technical Information (OSTI)

    Hierarchy with Bolometric Detectors (Journal Article) | SciTech Connect Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino Hierarchy with Bolometric Detectors Citation Details In-Document Search Title: Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino Hierarchy with Bolometric Detectors × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information

  6. Anomalous dimensions of the double parton fragmentation functions (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect Anomalous dimensions of the double parton fragmentation functions Citation Details In-Document Search Title: Anomalous dimensions of the double parton fragmentation functions Authors: Fleming, Sean ; Leibovich, Adam K. ; Mehen, Thomas ; Rothstein, Ira Z. Publication Date: 2013-04-23 OSTI Identifier: 1102128 Type: Publisher's Accepted Manuscript Journal Name: Physical Review D Additional Journal Information: Journal Volume: 87; Journal Issue: 7; Journal ID: ISSN

  7. Status Update of the Majorana Demonstrator Neutrinoless Double Beta Decay

    Office of Scientific and Technical Information (OSTI)

    Experiment (Technical Report) | SciTech Connect Technical Report: Status Update of the Majorana Demonstrator Neutrinoless Double Beta Decay Experiment Citation Details In-Document Search Title: Status Update of the Majorana Demonstrator Neutrinoless Double Beta Decay Experiment × You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a product of DOE's Office of Scientific and Technical Information (OSTI) and is provided as a public service. Visit

  8. Systematics of quarkonium production at the LHC and double parton

    Office of Scientific and Technical Information (OSTI)

    fragmentation (Journal Article) | SciTech Connect Systematics of quarkonium production at the LHC and double parton fragmentation Citation Details In-Document Search Title: Systematics of quarkonium production at the LHC and double parton fragmentation Authors: Fleming, Sean ; Leibovich, Adam K. ; Mehen, Thomas ; Rothstein, Ira Z. Publication Date: 2012-11-06 OSTI Identifier: 1101291 Type: Publisher's Accepted Manuscript Journal Name: Physical Review D Additional Journal Information: Journal

  9. DNA

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    C. Terwilliger, Randy J. Read, Blake Wiedenheft. Crystal structure of the CRISPR RNA- guided surveillance complex from Escherichia coli. Science, 2014 DOI: 10.1126 science.1256328...

  10. A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Authors: Zhao, Z., Yan, H., and Liu, Y. Title: A Route to Scale up DNA Origami Using DNA Tiles as Folding Staples Source: Angewandte Chemie International Edition Year: 2010 Volume: 49 Pages: 1414-1417 ABSTRACT: A new strategy is presented to scale up DNA origami using multi-helical DNA tiles as folding staples. Atomic force microscopy images (see picture) demonstrate the two-dimensional structures formed by using this strategy.

  11. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

    Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey. Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

  12. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

    Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel

    2013-07-16

    In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.

  13. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  14. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  15. The Initiation of Bacterial DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The Initiation of Bacterial DNA Replication Print For the first time, scientists have determined the structure of the initiator of bacterial DNA replication. It is already known that such replication is controlled by a protein known as DnaA, a member of the AAA+ superfamily of ATPases. What has now been discovered is that the core of the initiator is not the closed-ring structure expected for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates

  16. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

    Caldwell, Karin D. (Salt Lake City, UT); Chu, Tun-Jen (Salt Lake City, UT); Pitt, William G. (Orem, UT)

    1992-01-01

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through said smino groups contained on the surface thereof. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to said target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membrances may be reprobed numerous times.

  17. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

    Caldwell, K.D.; Chu, T.J.; Pitt, W.G.

    1992-05-12

    A method for the multiplex sequencing on DNA is disclosed which comprises the electroblotting or specific base terminated DNA fragments, which have been resolved by gel electrophoresis, onto the surface of a neutral non-aromatic polymeric microporous membrane exhibiting low background fluorescence which has been surface modified to contain amino groups. Polypropylene membranes are preferably and the introduction of amino groups is accomplished by subjecting the membrane to radio or microwave frequency plasma discharge in the presence of an aminating agent, preferably ammonia. The membrane, containing physically adsorbed DNA fragments on its surface after the electroblotting, is then treated with crosslinking means such as UV radiation or a glutaraldehyde spray to chemically bind the DNA fragments to the membrane through amino groups contained on the surface. The DNA fragments chemically bound to the membrane are subjected to hybridization probing with a tagged probe specific to the sequence of the DNA fragments. The tagging may be by either fluorophores or radioisotopes. The tagged probes hybridized to the target DNA fragments are detected and read by laser induced fluorescence detection or autoradiograms. The use of aminated low fluorescent background membranes allows the use of fluorescent detection and reading even when the available amount of DNA to be sequenced is small. The DNA bound to the membranes may be reprobed numerous times. No Drawings

  18. Mechanism of homologous recombination from the RecA-ssDNA/dsDNA...

    Office of Scientific and Technical Information (OSTI)

    The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The ...

  19. Double wall vacuum tubing and method of manufacture

    DOE Patents [OSTI]

    Stahl, Charles R. (Scotia, NY); Gibson, Michael A. (Houston, TX); Knudsen, Christian W. (Houston, TX)

    1989-01-01

    An evacuated double wall tubing is shown together with a method for the manufacture of such tubing which includes providing a first pipe of predetermined larger diameter and a second pipe having an O.D. substantially smaller than the I.D. of the first pipe. An evacuation opening is then in the first pipe. The second pipe is inserted inside the first pipe with an annular space therebetween. The pipes are welded together at one end. A stretching tool is secured to the other end of the second pipe after welding. The second pipe is then prestressed mechanically with the stretching tool an amount sufficient to prevent substantial buckling of the second pipe under normal operating conditions of the double wall pipe. The other ends of the first pipe and the prestressed second pipe are welded together, preferably by explosion welding, without the introduction of mechanical spacers between the pipes. The annulus between the pipes is evacuated through the evacuation opening, and the evacuation opening is finally sealed. The first pipe is preferably of steel and the second pipe is preferably of titanium. The pipes may be of a size and wall thickness sufficient for the double wall pipe to be structurally load bearing or may be of a size and wall thickness insufficient for the double wall pipe to be structurally load bearing, and the double wall pipe positioned with a sliding fit inside a third pipe of a load-bearing size.

  20. HANFORD DOUBLE SHELL TANK THERMAL AND SEISMIC PROJECT SEISMIC ANALYSIS OF HANFORD DOUBLE SHELL TANKS

    SciTech Connect (OSTI)

    MACKEY TC; RINKER MW; CARPENTER BG; HENDRIX C; ABATT FG

    2009-01-15

    M&D Professional Services, Inc. (M&D) is under subcontract to Pacific Northwest National Laboratories (PNNL) to perform seismic analysis of the Hanford Site Double-Shell Tanks (DSTs) in support of a project entitled Double-Shell Tank (DST) Integrity Project - DST Thermal and Seismic Analyses. The original scope of the project was to complete an up-to-date comprehensive analysis of record of the DST System at Hanford in support of Tri-Party Agreement Milestone M-48-14. The work described herein was performed in support of the seismic analysis of the DSTs. The thermal and operating loads analysis of the DSTs is documented in Rinker et al. (2004). Although Milestone M-48-14 has been met, Revision I is being issued to address external review comments with emphasis on changes in the modeling of anchor bolts connecting the concrete dome and the steel primary tank. The work statement provided to M&D (PNNL 2003) required that a nonlinear soil structure interaction (SSI) analysis be performed on the DSTs. The analysis is required to include the effects of sliding interfaces and fluid sloshing (fluid-structure interaction). SSI analysis has traditionally been treated by frequency domain computer codes such as SHAKE (Schnabel, et al. 1972) and SASSI (Lysmer et al. 1999a). Such frequency domain programs are limited to the analysis of linear systems. Because of the contact surfaces, the response of the DSTs to a seismic event is inherently nonlinear and consequently outside the range of applicability of the linear frequency domain programs. That is, the nonlinear response of the DSTs to seismic excitation requires the use of a time domain code. The capabilities and limitations of the commercial time domain codes ANSYS{reg_sign} and MSC Dytran{reg_sign} for performing seismic SSI analysis of the DSTs and the methodology required to perform the detailed seismic analysis of the DSTs has been addressed in Rinker et al (2006a). On the basis of the results reported in Rinker et al. (2006a), it is concluded that time-domain SSI analysis using ANSYS{reg_sign} is justified for predicting the global response of the DSTs. The most significant difference between the current revision (Revision 1) of this report and the original issue (Revision 0) is the treatment of the anchor bolts that tie the steel dome of the primary tank to the concrete tank dome.

  1. HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT SEISMIC ANALYSIS OF HANFORD DOUBLE SHELL TANKS

    SciTech Connect (OSTI)

    MACKEY, T.C.

    2006-03-17

    M&D Professional Services, Inc. (M&D) is under subcontract to Pacific Northwest National Laboratory (PNNL) to perform seismic analysis of the Hanford Site double-shell tanks (DSTs) in support of a project entitled ''Double-Shell Tank (DSV Integrity Project--DST Thermal and Seismic Analyses)''. The overall scope of the project is to complete an up-to-date comprehensive analysis of record of the DST system at Hanford in support of Tri-Party Agreement Milestone M-48-14, The work described herein was performed in support of the seismic analysis of the DSTs. The thermal and operating loads analysis of the DSTs is documented in Rinker et al. (2004). The work statement provided to M&D (PNNL 2003) required that the seismic analysis of the DSTs assess the impacts of potentially non-conservative assumptions in previous analyses and account for the additional soil mass due to the as-found soil density increase, the effects of material degradation, additional thermal profiles applied to the full structure including the soil-structure response with the footings, the non-rigid (low frequency) response of the tank roof, the asymmetric seismic-induced soil loading, the structural discontinuity between the concrete tank wall and the support footing and the sloshing of the tank waste. The seismic analysis considers the interaction of the tank with the surrounding soil and the effects of the primary tank contents. The DSTs and the surrounding soil are modeled as a system of finite elements. The depth and width of the soil incorporated into the analysis model are sufficient to obtain appropriately accurate analytical results. The analyses required to support the work statement differ from previous analysis of the DSTs in that the soil-structure interaction (SSI) model includes several (nonlinear) contact surfaces in the tank structure, and the contained waste must be modeled explicitly in order to capture the fluid-structure interaction behavior between the primary tank and contained waste.

  2. Spin projection with double hybrid density functional theory

    SciTech Connect (OSTI)

    Thompson, Lee M.; Hratchian, Hrant P.

    2014-07-21

    A spin projected double-hybrid density functional theory is presented that accounts for different scaling of opposite and same spin terms in the second order correction. This method is applied to three dissociation reactions which in the unprojected formalism exhibit significant spin contamination with higher spin states. This gives rise to a distorted potential surface and can lead to poor geometries and energies. The projected method presented is shown to improve the description of the potential over unprojected double hybrid density functional theory. Comparison is made with the reference states of the two double hybrid functionals considered here (B2PLYP and mPW2PLYP) in which the projected potential surface is degraded by an imbalance in the description of dynamic and static correlation.

  3. Mechanical seal having a double-tier mating ring

    DOE Patents [OSTI]

    Khonsari, Michael M.; Somanchi, Anoop K.

    2005-09-13

    An apparatus and method to enhance the overall performance of mechanical seals in one of the following ways: by reducing seal face wear, by reducing the contact surface temperature, or by increasing the life span of mechanical seals. The apparatus is a mechanical seal (e.g., single mechanical seals, double mechanical seals, tandem mechanical seals, bellows, pusher mechanical seals, and all types of rotating and reciprocating machines) comprising a rotating ring and a double-tier mating ring. In a preferred embodiment, the double-tier mating ring comprises a first and a second stationary ring that together form an agitation-inducing, guided flow channel to allow for the removal of heat generated at the seal face of the mating ring by channeling a coolant entering the mating ring to a position adjacent to and in close proximity with the interior surface area of the seal face of the mating ring.

  4. A prototype silicon double quantum dot with dispersive microwave readout

    SciTech Connect (OSTI)

    Schmidt, A. R. Henry, E.; Namaan, O.; Siddiqi, I.; Lo, C. C.; Wang, Y.-T.; Bokor, J.; Yablonovitch, E.; Li, H.; Greenman, L.; Whaley, K. B.; Schenkel, T.

    2014-07-28

    We present a unique design and fabrication process for a lateral, gate-confined double quantum dot in an accumulation mode metal-oxide-semiconductor (MOS) structure coupled to an integrated microwave resonator. All electrostatic gates for the double quantum dot are contained in a single metal layer, and use of the MOS structure allows for control of the location of the two-dimensional electron gas via the location of the accumulation gates. Numerical simulations of the electrostatic confinement potential are performed along with an estimate of the coupling of the double quantum dot to the microwave resonator. Prototype devices are fabricated and characterized by transport measurements of electron confinement and reflectometry measurements of the microwave resonator.

  5. Double-{beta} decay Q value of {sup 150}Nd

    SciTech Connect (OSTI)

    Kolhinen, V. S.; Eronen, T.; Gorelov, D.; Hakala, J.; Jokinen, A.; Kankainen, A.; Moore, I. D.; Rissanen, J.; Saastamoinen, A.; Suhonen, J.; Aeystoe, J. [Department of Physics, P. O. Box 35 (YFL), FI-40014 University of Jyvaeskylae (Finland)

    2010-08-15

    The double-{beta} decay Q value of {sup 150}Nd was determined by using the JYFLTRAP Penning trap mass spectrometer. The measured mass difference between {sup 150}Nd and {sup 150}Sm is 3371.38(20) keV. This new value deviates by 3.7 keV from the previously adopted value of 3367.7(22) keV and is a factor of 10 more precise. Accurate knowledge of this Q value is important because {sup 150}Nd is a primary candidate to be used in the search for neutrinoless double-{beta} decay modes in several experiments.

  6. Consistency test of neutrinoless double beta decay with one isotope

    SciTech Connect (OSTI)

    Duerr, Michael; Lindner, Manfred [Max-Planck-Institut fuer Kernphysik, Postfach 10 39 80, 69029 Heidelberg (Germany); Zuber, Kai [Technical University Dresden, Institut fuer Kern- und Teilchenphysik, 01069 Dresden (Germany)

    2011-11-01

    We discuss a consistency test which makes it possible to discriminate unknown nuclear background lines from neutrinoless double beta decay with only one isotope. By considering both the transition to the ground state and to the first excited 0{sup +} state, a sufficiently large detector can reveal if neutrinoless double beta decay or some other nuclear physics process is at work. Such a detector could therefore simultaneously provide a consistency test for a certain range of Majorana masses and be sensitive to lower values of the effective Majorana mass .

  7. Double layer -- a particle accelerator in the magnetosphere

    SciTech Connect (OSTI)

    Fu, Xiangrong

    2015-07-16

    Slides present the material under the following topics: Introduction (What is a double layer (DL)? Why is it important? Key unsolved problems); Theory -- time-independent solutions of 1D Vlasov--Poisson system; Particle-in-cell simulations (Current-driven DLs); and Electron acceleration by DL (Betatron acceleration). Key problems include the generation mechanism, stability, and electron acceleration. In summary, recent observations by Van Allen Probes show large number of DLs in the outer radiation belt, associated with enhanced flux of relativistic electrons. Simulations show that ion acoustic double layers can be generated by field-aligned currents. Thermal electrons can gain energy via betatron acceleration in a dipole magnetic field.

  8. Implementation of Double-Waist Chicane Optics in SPEAR3

    SciTech Connect (OSTI)

    Corbett, J.; Cornacchia, M.; Dao, T.; Dell'Orco, D.; Rafael, F.; Harrington, D.; Hettel, R.; Huang, X.; Nosochkov, Y.; Rabedeau, T.; Rarback, H.; Ringwall, A.; Safranek, J.; Scott, B.; Sebek, J.; Tanabe, J.; Terebilo, A.; Wermelskirchen, C.; Widmeyer, M.; Yoon, Moohyun; /POSTECH

    2006-08-16

    The SPEAR3 accelerator upgrade opened up two 7.6m racetrack straights in the magnet lattice. In one of these straights, we recently added a magnetic chicane to separate two insertion device (ID) beam lines by 10mrad. A quadrupole triplet in the center creates a ''double focus'' optics with {beta}y = 1.6m at the middle of each ID, hence the term ''double-waist chicane''. The new optics also reduced {beta}y in the four matching straights adjacent to the racetrack straights to 2.5m. In this paper, we outline design features of the optics and physical implementation of the lattice.

  9. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    Rambosek, J.; Piddington, C.S.; Kovacevich, B.R.; Young, K.D.; Denome, S.A.

    1994-10-18

    This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous. 13 figs.

  10. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

    Rambosek, John (Seattle, WA); Piddington, Chris S. (Seattle, WA); Kovacevich, Brian R. (Seattle, WA); Young, Kevin D. (Grand Forks, ND); Denome, Sylvia A. (Thompson, ND)

    1994-01-01

    This invention relates to a recombinant DNA molecule containing a gene or genes which encode a biocatalyst capable of desulfurizing a fossil fuel which contains organic sulfur molecules. For example, the present invention encompasses a recombinant DNA molecule containing a gene or genes of a strain of Rhodococcus rhodochrous.

  11. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

    Nasarabadi,Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Round Rock, TX)

    2011-07-05

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM.TM. on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA.TM., on the 5' end.

  12. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, A.M.; Dawson, J.

    1993-12-14

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

  13. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

    Nasarabadi, Shanavaz (Livermore, CA); Langlois, Richard G. (Livermore, CA); Venkateswaran, Kodumudi S. (Livermore, CA)

    2006-08-01

    Disclosed herein are two methods for rapid multiplex analysis to determine the presence and identity of target DNA sequences within a DNA sample. Both methods use reporting DNA sequences, e.g., modified conventional Taqman.RTM. probes, to combine multiplex PCR amplification with microsphere-based hybridization using flow cytometry means of detection. Real-time PCR detection can also be incorporated. The first method uses a cyanine dye, such as, Cy3.TM., as the reporter linked to the 5' end of a reporting DNA sequence. The second method positions a reporter dye, e.g., FAM, on the 3' end of the reporting DNA sequence and a quencher dye, e.g., TAMRA, on the 5' end.

  14. The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

    SciTech Connect (OSTI)

    Stella, Stefano; Cascio, Duilio; Johnson, Reid C.

    2010-06-21

    The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of {approx}65{sup o}, and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.

  15. Structural insight into dynamic bypass of the major cisplatin-DNA adduct by Y-family polymerase Dpo4

    SciTech Connect (OSTI)

    Wong, Jimson H.Y.; Brown, Jessica A.; Suo, Zucai; Blum, Paul; Nohmi, Takehiko; Ling, Hong

    2010-08-23

    Y-family DNA polymerases bypass Pt-GG, the cisplatin-DNA double-base lesion, contributing to the cisplatin resistance in tumour cells. To reveal the mechanism, we determined three structures of the Y-family DNA polymerase, Dpo4, in complex with Pt-GG DNA. The crystallographic snapshots show three stages of lesion bypass: the nucleotide insertions opposite the 3{prime}G (first insertion) and 5{prime}G (second insertion) of Pt-GG, and the primer extension beyond the lesion site. We observed a dynamic process, in which the lesion was converted from an open and angular conformation at the first insertion to a depressed and nearly parallel conformation at the subsequent reaction stages to fit into the active site of Dpo4. The DNA translocation-coupled conformational change may account for additional inhibition on the second insertion reaction. The structures illustrate that Pt-GG disturbs the replicating base pair in the active site, which reduces the catalytic efficiency and fidelity. The in vivo relevance of Dpo4-mediated Pt-GG bypass was addressed by a dpo-4 knockout strain of Sulfolobus solfataricus, which exhibits enhanced sensitivity to cisplatin and proteomic alterations consistent with genomic stress.

  16. Rapid Detection and Identification of a Pathogen's DNA Using Phi29 DNA Polymerase

    SciTech Connect (OSTI)

    Xu, Y.; Dunn, J.; Gao, S.; Bruno, J. F.; Luft, B. J.

    2008-10-31

    Zoonotic pathogens including those transmitted by insect vectors are some of the most deadly of all infectious diseases known to mankind. A number of these agents have been further weaponized and are widely recognized as being potentially significant biothreat agents. We describe a novel method based on multiply-primed rolling circle in vitro amplification for profiling genomic DNAs to permit rapid, cultivation-free differential detection and identification of circular plasmids in infectious agents. Using Phi29 DNA polymerase and a two-step priming reaction we could reproducibly detect and characterize by DNA sequencing circular DNA from Borrelia burgdorferi B31 in DNA samples containing as little as 25 pg of Borrelia DNA amongst a vast excess of human DNA. This simple technology can ultimately be adapted as a sensitive method to detect specific DNA from both known and unknown pathogens in a wide variety of complex environments.

  17. Property:NEPA DNA Worksheet | Open Energy Information

    Open Energy Info (EERE)

    DNA Worksheet Jump to: navigation, search Property Name NEPA DNA Worksheet Property Type Page Description DNA Worksheet files for NEPA Docs. This is a property of type Page. It...

  18. First experiment with the double solenoid RIBRAS system

    SciTech Connect (OSTI)

    Lichtenthaeler, R.; Condori, R. Pampa; Lepine-Szily, A.; Pires, K. C. C.; Morais, M. C.; Leistenschneider, E.; Scarduelli, V. B.; Gasques, L. R.; Faria, P. N. de; Mendes, D. R. Jr.; Shorto, J. M. B.

    2013-05-06

    A description of the double solenoid system (RIBRAS) operating since 2004 in one of the beam lines of the Pelletron Laboratory of the Institute of Physics of the University of Sao Paulo is presented. The recent installation of the secondary scattering chamber after the second solenoid is reported and the first experiment in RIBRAS using both solenoids is described.

  19. Inner-shell and double ionization potentials of aminophenol isomers.

    SciTech Connect (OSTI)

    Kryzhevoi, N. V.; Santra, R.; Cederbaum, L. S.

    2011-01-01

    A comprehensive study of single and double core ionization potentials of the aminophenol molecule is reported. The role of relaxation, correlation, relativistic, and basis set effects in these potentials is clarified. Special attention is paid to the isomer dependence of the single and double core ionization potentials. Some of them are also compared with the respective values of the phenol and aniline molecules. It is shown that the core level single ionization potentials of the para-, meta-, and ortho-aminophenol molecules differ only slightly from each other, rendering these structural isomers challenging to distinguish for conventional x-ray photoelectron spectroscopy. In contrast, the energy needed to remove two core electrons from different atoms depends noticeably on the mutual arrangement and even on the relative orientations of the hydroxyl and amine groups. Together with the electrostatic repulsion between the two core holes, relaxation effects accompanying double core ionization play a crucial role here. The pronounced sensitivity of the double ionization potentials, therefore, enables a spectroscopic characterization of the electronic structure of aminophenol isomers by means of x-ray two-photon photoelectron spectroscopy.

  20. Mixer pump test plan for double shell tank AZ-101

    SciTech Connect (OSTI)

    STAEHR, T.W.

    1999-05-12

    Mixer pump systems have been chosen as the method for retrieval of tank wastes contained in double shell tanks at Hanford. This document describes the plan for testing and demonstrating the ability of two 300 hp mixer pumps to mobilize waste in tank AZ-101. The mixer pumps, equipment and instrumentation to monitor the test were installed by Project W-151.

  1. The Los Alamos National Laboratory precision double crystal spectrometer

    SciTech Connect (OSTI)

    Morgan, D.V.; Stevens, C.J.; Liefield, R.J.

    1994-03-01

    This report discusses the following topics on the LANL precision double crystal X-ray spectrometer: Motivation for construction of the instrument; a brief history of the instrument; mechanical systems; motion control systems; computer control system; vacuum system; alignment program; scan programs; observations of the copper K{alpha} lines; and characteristics and specifications.

  2. Computer code for double beta decay QRPA based calculations

    SciTech Connect (OSTI)

    Barbero, C. A.; Mariano, A.; Krmpoti?, F.; Samana, A. R.; Ferreira, V. dos Santos; Bertulani, C. A.

    2014-11-11

    The computer code developed by our group some years ago for the evaluation of nuclear matrix elements, within the QRPA and PQRPA nuclear structure models, involved in neutrino-nucleus reactions, muon capture and ?{sup } processes, is extended to include also the nuclear double beta decay.

  3. Double Shell Tank AY-102 Radioactive Waste Leak Investigation

    SciTech Connect (OSTI)

    Washenfelder, Dennis J.

    2014-04-10

    PowerPoint. The objectives of this presentation are to: Describe Effort to Determine Whether Tank AY-102 Leaked; Review Probable Causes of the Tank AY-102 Leak; and, Discuss Influence of Leak on Hanfords Double-Shell Tank Integrity Program.

  4. Pd/Ni-WO3 anodic double layer gasochromic device

    DOE Patents [OSTI]

    Lee, Se-Hee; Tracy, C. Edwin; Pitts, J. Roland; Liu, Ping

    2004-04-20

    An anodic double layer gasochromic sensor structure for optical detection of hydrogen in improved response time and with improved optical absorption real time constants, comprising: a glass substrate; a tungsten-doped nickel oxide layer coated on the glass substrate; and a palladium layer coated on the tungsten-doped nickel oxide layer.

  5. Bound states in a hyperbolic asymmetric double-well

    SciTech Connect (OSTI)

    Hartmann, R. R.

    2014-01-15

    We report a new class of hyperbolic asymmetric double-well whose bound state wavefunctions can be expressed in terms of confluent Heun functions. An analytic procedure is used to obtain the energy eigenvalues and the criterion for the potential to support bound states is discussed.

  6. EA-1905: Double Eagle Water System, Carlsbad, New Mexico

    Broader source: Energy.gov [DOE]

    This EA, prepared by the U.S. Department of the Interiors Bureau of Land Management Carlsbad Field Office and adopted by DOE, evaluates the expansion and upgrade of the City of Carlsbads Double Eagle Water System.

  7. Scaling factor inconsistencies in neutrinoless double beta decay

    SciTech Connect (OSTI)

    Cowell, S. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2006-02-15

    The modern theory of neutrinoless double beta decay includes a scaling factor that has often been treated inconsistently in the literature. The nuclear contribution to the decay half-life can be suppressed by 15%-20% when scaling factors are mismatched. Correspondingly, is overestimated.

  8. Majorana neutrino masses and the neutrinoless double-beta decay

    SciTech Connect (OSTI)

    Faessler, A. [University of Tuebingen, Institute of Theoretical Physics (Germany)], E-mail: amand.faessler@uni-tuebingen.de

    2006-12-15

    Neutrinoless double-beta decay is forbidden in the Standard Model of electroweak and strong interaction but allowed in most Grand Unified Theories (GUTs). Only if the neutrino is a Majorana particle (identical with its antiparticle) and if it has a mass is neutrinoless double-beta decay allowed. Apart from one claim that the neutrinoless double-beta decay in {sup 76}Ge is measured, one has only upper limits for this transition probability. But even the upper limits allow one to give upper limits for the electron Majorana neutrino mass and upper limits for parameters of GUTs and the minimal R-parity-violating supersymmetric model. One further can give lower limits for the vector boson mediating mainly the right-handed weak interaction and the heavy mainly right-handed Majorana neutrino in left-right symmetric GUTs. For that, one has to assume that the specific mechanism is the leading one for neutrinoless double-beta decay and one has to be able to calculate reliably the corresponding nuclear matrix elements. In the present work, one discusses the accuracy of the present status of calculating of the nuclear matrix elements and the corresponding limits of GUTs and supersymmetric parameters.

  9. Neutrinoless Double Beta Decay and {nu}-Mass Determination

    SciTech Connect (OSTI)

    Pedretti, M. [Universita dell Insubria, Via Vallegio 11, 22100 Como (Italy)

    2005-10-12

    The search for Neutrinoless Double Beta Decay could improve our knowledge on neutrino properties. After a brief discussion on the implications of the observation of this rare process, I will introduce the experimental approaches and review the prospects of the search for this nuclear transition.

  10. Neutrinoless double-{beta} decay: Status and future

    SciTech Connect (OSTI)

    Bilenky, S. M. [Joint Institute for Nuclear Research (Russian Federation)], E-mail: bilenky@he.sissa.it

    2006-12-15

    A brief summary of the status of neutrino masses, mixing, and oscillations is presented. Neutrinoless double {beta} decay is considered. Predictions for the effective Majorana mass are reviewed. A possible test of the calculations of nuclear matrix elements of the 0{nu}{beta}{beta} decay is proposed.

  11. New Advances in Neutrinoless Double Beta Decay Matrix Elements

    SciTech Connect (OSTI)

    Munoz, Jose Barea [Instituto de Estructura de la Materia, C.S.I.C. Unidad Asociada al Departamento de Fisica Atomica, Molecular y Nuclear, Facultad de Fisica, Universidad de Sevilla, Apartado 1065, 41080 Sevilla (Spain)

    2010-08-04

    We present the matrix elements necessary to evaluate the half-life of some neutrinoless double beta decay candidates in the framework of the microscopic interacting boson model (IBM). We compare our results with those from other models and extract some simple features of the calculations.

  12. Neutrinoless double beta decay in the microscopic interacting boson model

    SciTech Connect (OSTI)

    Iachello, F. [Center for Theoretical Physics, Sloane Physics Laboratory Yale University New Haven, CT 06520-8120 (United States)

    2009-11-09

    The results of a calculation of the nuclear matrix elements for neutrinoless double beta decay in the closure approximation in several nuclei within the framework of the microscopic interacting boson model (IBM-2) are presented and compared with those calculated in the shell model (SM) and quasiparticle random phase approximation (QRPA)

  13. Conditions for detecting CP violation via neutrinoless double beta decay

    SciTech Connect (OSTI)

    Joniec, A.; Zralek, M. [Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland)

    2006-02-01

    Neutrinoless double beta decay data, together with information on the absolute neutrino masses obtained from the future KATRIN experiment and/or astrophysical measurements, provide a chance to find CP violation in the lepton sector with Majorana neutrinos. We derive and discuss necessary conditions which make discovery of such CP violation possible for the future neutrino oscillation and mass measurements data.

  14. Period-doubling reconstructions of semiconductor partial dislocations

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Park, Ji -Sang; Huang, Bing; Wei, Su -Huai; Kang, Joongoo; McMahon, William E.

    2015-09-18

    Atomic-scale understanding and control of dislocation cores is of great technological importance, because they act as recombination centers for charge carriers in optoelectronic devices. Using hybrid density-functional calculations, we present period-doubling reconstructions of a 90° partial dislocation in GaAs, for which the periodicity of like-atom dimers along the dislocation line varies from one to two, to four dimers. The electronic properties of a dislocation change drastically with each period doubling. The dimers in the single-period dislocation are able to interact, to form a dispersive one-dimensional band with deep-gap states. However, the inter-dimer interaction for the double-period dislocation becomes significantly reduced;more » hence, it is free of mid-gap states. The Ga core undergoes a further period-doubling transition to a quadruple-period reconstruction induced by the formation of small hole polarons. Lastly, the competition between these dislocation phases suggests a new passivation strategy via population manipulation of the detrimental single-period phase.« less

  15. Dual-cone double-helical downhole logging device

    DOE Patents [OSTI]

    Yu, Jiunn S. (Albuquerque, NM)

    1984-01-01

    A broadband downhole logging device includes a double-helix coil wrapped over a dielectric support and surrounded by a dielectric shield. The device may also include a second coil longitudinally aligned with a first coil and enclosed within the same shield for measuring magnetic permeability of downhole formations and six additional coils for accurately determining downhole parameters.

  16. Heat exchanger with leak detecting double wall tubes

    DOE Patents [OSTI]

    Bieberbach, George (Tampa, FL); Bongaards, Donald J. (Seminole, FL); Lohmeier, Alfred (Tampa, FL); Duke, James M. (St. Petersburg, all of, FL)

    1981-01-01

    A straight shell and tube heat exchanger utilizing double wall tubes and three tubesheets to ensure separation of the primary and secondary fluid and reliable leak detection of a leak in either the primary or the secondary fluids to further ensure that there is no mixing of the two fluids.

  17. Industrial mixing techniques for Hanford double-shell tanks

    SciTech Connect (OSTI)

    Daymo, E.A.

    1997-09-01

    Jet mixer pumps are currently the baseline technology for sludge mobilization and mixing in one-million gallon double-shell tanks at the Hanford and Savannah River Sites. Improvements to the baseline jet mixer pump technology are sought because jet mixer pumps have moving parts that may fail or require maintenance. Moreover, jet mixers are relatively expensive, they heat the waste, and, in some cases, may not mobilize enough of the sludge. This report documents a thorough literature search for commercially available applicable mixing technologies that could be used for double-shell tank sludge mobilization and mixing. Textbooks, research articles, conference proceedings, mixing experts, and the Thomas Register were consulted to identify applicable technologies. While there are many commercial methods that could be used to mobilize sludge or mix the contents of a one-million gallon tank, few will work given the geometrical constraints (e.g., the mixer must fit through a 1.07-m-diameter riser) or the tank waste properties (e.g., the sludge has such a high yield stress that it generally does not flow under its own weight). Pulsed fluid jets and submersible Flygt mixers have already been identified at Hanford and Savannah River Sites for double-shell tank mixing applications. While these mixing technologies may not be applicable for double-shell tanks that have a thick sludge layer at the bottom (since too many of these mixers would need to be installed to mobilize most of the sludge), they may have applications in tanks that do not have a settled solids layer. Retrieval projects at Hanford and other U.S. Department of Energy sites are currently evaluating the effectiveness of these mixing techniques for tank waste applications. The literature search did not reveal any previously unknown technologies that should be considered for sludge mobilization and mixing in one-million gallon double-shell tanks.

  18. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked...

  19. 6.7 Engineered Enzyme Accelerates DNA Sequencing

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and Richardson, C. C. (1995) "A single residue in DNA polymerases of the Escherichia coli DNA polymerase I family is critical for distinguishing between deoxy- and...

  20. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    scientists. Schematic of DNA structures in various conformations on a gold surface. Differences in overall structure and orientation are emphasized by color-coding of DNA...

  1. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of genomic integrity and responses to DNA damage relevant to pathogens and cancer development. DNA Repair Switch A process similar in spirit to that of a railroad...

  2. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C.; Kuske, Cheryl R.; Mullen, Kenneth I.

    2002-01-01

    A method for quantitating dsDNA in an aqueous sample solution containing an unknown amount of dsDNA. A first aqueous test solution containing a known amount of a fluorescent dye-dsDNA complex and at least one fluorescence-attenutating contaminant is prepared. The fluorescence intensity of the test solution is measured. The first test solution is diluted by a known amount to provide a second test solution having a known concentration of dsDNA. The fluorescence intensity of the second test solution is measured. Additional diluted test solutions are similarly prepared until a sufficiently dilute test solution having a known amount of dsDNA is prepared that has a fluorescence intensity that is not attenuated upon further dilution. The value of the maximum absorbance of this solution between 200-900 nanometers (nm), referred to herein as the threshold absorbance, is measured. A sample solution having an unknown amount of dsDNA and an absorbance identical to that of the sufficiently dilute test solution at the same chosen wavelength is prepared. Dye is then added to the sample solution to form the fluorescent dye-dsDNA-complex, after which the fluorescence intensity of the sample solution is measured and the quantity of dsDNA in the sample solution is determined. Once the threshold absorbance of a sample solution obtained from a particular environment has been determined, any similarly prepared sample solution taken from a similar environment and having the same value for the threshold absorbance can be quantified for dsDNA by adding a large excess of dye to the sample solution and measuring its fluorescence intensity.

  3. DNA fragment sizing and sorting by laser-induced fluorescence

    DOE Patents [OSTI]

    Hammond, Mark L.; Jett, James H.; Keller, Richard A.; Marrone, Babetta L.; Martin, John C.

    1996-01-01

    A method is provided for sizing DNA fragments using high speed detection systems, such as flow cytometry to determine unique characteristics of DNA pieces from a sample. In one characterization the DNA piece is fragmented at preselected sites to produce a plurality of DNA fragments. The DNA piece or the resulting DNA fragments are treated with a dye effective to stain stoichiometrically the DNA piece or the DNA fragments. The fluorescence from the dye in the stained fragments is then examined to generate an output functionally related to the number of nucleotides in each one of the DNA fragments. In one embodiment, the intensity of the fluorescence emissions from each fragment is linearly related to the fragment length. The distribution of DNA fragment sizes forms a characterization of the DNA piece for use in forensic and research applications.

  4. Studies of Nb3Sn Strands Based on the Restacked-Rod Process for High-Field Accelerator Magnets Nb3Sn

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Barzi, E; Bossert, M; Gallo, G; Lombardo, V; Turrioni, D; Yamada, R; Zlobin, A V

    2012-06-01

    A major thrust in Fermilab's accelerator magnet R&D program is the development of Nb3Sn wires which meet target requirements for high field magnets, such as high critical current density, low effective filament size, and the capability to withstand the cabling process. The performance of a number of strands with 150/169 restack design produced by Oxford Superconducting Technology was studied for round and deformed wires. To optimize the maximum plastic strain, finite element modeling was also used as an aid in the design. Results of mechanical, transport and metallographic analyses are presented for round and deformed wires.

  5. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N; Mariella, Jr., Raymond P; Christian, Allen T; Young, Jennifer A; Clague, David S

    2013-06-25

    A method of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths.

  6. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08

    Building on the idea of using DNA to link up nanoparticles scientists at Brookhaven National Lab have designed a molecular assembly line for high-precision nano-construction. Nanofabrication is essential for exploiting the unique properties of nanoparticl

  7. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9...

  8. Extracting biological knowledge from DNA sequences

    SciTech Connect (OSTI)

    De La Vega, F.M.; Thieffry, D.; Collado-Vides, J.

    1996-12-31

    This session describes the elucidation of information from dna sequences and what challenges computational biologists face in their task of summarizing and deciphering the human genome. Techniques discussed include methods from statistics, information theory, artificial intelligence and linguistics. 1 ref.

  9. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, Richard A. (Contra Costa County, CA); Huang, Xiaohua C. (Mt. View, CA); Quesada, Mark A. (San Francisco, CA)

    1995-01-01

    A DNA sequencing method described which uses single lane or channel electrophoresis. Sequencing fragments are separated in said lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radio-isotope labels.

  10. Multiple tag labeling method for DNA sequencing

    DOE Patents [OSTI]

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  11. DOE Zero Energy Ready Home Case Study: KB Home, Double ZeroHouse...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Double ZeroHouse 3.0, El Dorado Hill, CA DOE Zero Energy Ready Home Case Study: KB Home, Double ZeroHouse 3.0, El Dorado Hill, CA Case study of a DOE 2015 Housing Innovation Award ...

  12. Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless Double-Beta Decay in 136Xe with EXO-200 Citation Details In-Document Search Title: Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200 Authors: Auger, M. ;...

  13. The H2 Double-Slit Experiment: Where Quantum and Classical Physics...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The H2 Double-Slit Experiment: Where Quantum and Classical Physics Meet Print For the first time, an international research team carried out a double-slit experiment in H2, the...

  14. Double Beta Decay in Xenon-136: Measuring the Neutrino-Emitting...

    Office of Scientific and Technical Information (OSTI)

    Double Beta Decay in Xenon-136: Measuring the Neutrino-Emitting Mode and Searching for Majoron-Emitting Modes Citation Details In-Document Search Title: Double Beta Decay in...

  15. Search for Neutrinoless Double-Beta Decay in $^{136}$Xe with...

    Office of Scientific and Technical Information (OSTI)

    Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200 Citation Details In-Document Search Title: Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200...

  16. Neutrinoless Double Beta Decay in Light of SNO Salt Data (Journal...

    Office of Scientific and Technical Information (OSTI)

    Neutrinoless Double Beta Decay in Light of SNO Salt Data Citation Details In-Document Search Title: Neutrinoless Double Beta Decay in Light of SNO Salt Data In the SNO data from...

  17. Search for Neutrinoless Double-Beta Decay in $^{136}$Xe with...

    Office of Scientific and Technical Information (OSTI)

    Journal Article: Search for Neutrinoless Double-Beta Decay in 136Xe with EXO-200 Citation Details In-Document Search Title: Search for Neutrinoless Double-Beta Decay in...

  18. Double beta decay, Majorana neutrinos, and neutrino mass

    SciTech Connect (OSTI)

    Avignone, Frank T. III; Elliott, Steven R.; Engel, Jonathan [Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208 (United States); Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Department of Physics and Astronomy, University of North Carolina, Chapel Hill, North Carolina 27599-3255 (United States)

    2008-04-15

    The theoretical and experimental issues relevant to neutrinoless double beta decay are reviewed. The impact that a direct observation of this exotic process would have on elementary particle physics, nuclear physics, astrophysics, and cosmology is profound. Now that neutrinos are known to have mass and experiments are becoming more sensitive, even the nonobservation of neutrinoless double beta decay will be useful. If the process is actually observed, we will immediately learn much about the neutrino. The status and discovery potential of proposed experiments are reviewed in this context, with significant emphasis on proposals favored by recent panel reviews. The importance of and challenges in the calculation of nuclear matrix elements that govern the decay are considered in detail. The increasing sensitivity of experiments and improvements in nuclear theory make the future exciting for this field at the interface of nuclear and particle physics.

  19. Complementarity of Neutrinoless Double Beta Decay and Cosmology

    SciTech Connect (OSTI)

    Dodelson, Scott; Lykken, Joseph

    2014-03-20

    Neutrinoless double beta decay experiments constrain one combination of neutrino parameters, while cosmic surveys constrain another. This complementarity opens up an exciting range of possibilities. If neutrinos are Majorana particles, and the neutrino masses follow an inverted hierarchy, then the upcoming sets of both experiments will detect signals. The combined constraints will pin down not only the neutrino masses but also constrain one of the Majorana phases. If the hierarchy is normal, then a beta decay detection with the upcoming generation of experiments is unlikely, but cosmic surveys could constrain the sum of the masses to be relatively heavy, thereby producing a lower bound for the neutrinoless double beta decay rate, and therefore an argument for a next generation beta decay experiment. In this case as well, a combination of the phases will be constrained.

  20. Neutrinoless double {beta}-decay and neutrino mass hierarchies

    SciTech Connect (OSTI)

    Bilenky, S. M. [Scuola Internazionale Superiore di Studi Avanzati, I-34014 Trieste (Italy); Faessler, Amand; Gutsche, Thomas; Simkovic, Fedor [Institute fuer Theoretische Physik der Universitaet Tuebingen, D-72076 Tuebingen (Germany)

    2005-09-01

    In the framework of the seesaw mechanism the normal hierarchy is favorable for the neutrino mass spectrum. For this spectrum we present a detailed calculation of the half-lives of neutrinoless double {beta}-decay for several nuclei of experimental interest. The half-lives are evaluated by considering the most comprehensive nuclear matrix elements, which were obtained within the renormalized quasiparticle random phase approximation by the Bratislava-Caltech-Tuebingen group. The dependence of the half-lives on sin{sup 2}{theta}{sub 13} and the lightest neutrino mass is studied. We present also the results of the calculations of the half-lives of neutrinoless double {beta}-decay in the case of the inverted hierarchy of neutrino masses.

  1. Results of the double beta decay experiment NEMO-3

    SciTech Connect (OSTI)

    Tretyak, V. I. [Joint Institute for Nuclear Research, 6 Joliot Curie, Dubna (Russian Federation); Collaboration: NEMO-3 Collaboration

    2013-12-30

    The double beta decay experiment NEMO-3 has taken data from February 2003 to January 2011. The two-neutrino decay half lives were measured for seven different isotopes ({sup 100}Mo, {sup 82}Se, {sup 116}Cd, {sup 150}Nd, {sup 96}Zr, {sup 48}Ca and {sup 130}Te). No evidence for neutrinoless double beta decay is observed. The 0??? half-life limits are found to be T{sub 1/2}{sup 0?}({sup 100}Mo)>1.010{sup 24}yr(90%C.L.) and T{sub 1/2}{sup 0?}({sup 82}Se)>3.210{sup 23}yr(90%C.L.)

  2. Extra dimensions and neutrinoless double beta decay experiments

    SciTech Connect (OSTI)

    Gozdz, Marek; Kaminski, Wieslaw A.; Faessler, Amand [Theoretical Physics Department, Maria Curie-Sklodowska University, Lublin (Poland); Institute fuer Theoretische Physik, Universitaet Tuebingen, Auf der Morgenstelle 14, D-72076 Tuebingen (Germany)

    2005-05-01

    The neutrinoless double beta decay is one of the few phenomena, belonging to the nonstandard physics, which is extensively being sought for in experiments. In the present paper the link between the half-life of the neutrinoless double beta decay and theories with large extra dimensions is explored. The use of the sensitivities of currently planned 0{nu}2{beta} experiments: DAMA, CANDLES, COBRA, DCBA, CAMEO, GENIUS, GEM, MAJORANA, MOON, CUORE, EXO, and XMASS, gives the possibility for a nondirect 'experimental' verification of various extra dimensional scenarios. We discuss also the results of the Heidelberg-Moscow Collaboration. The calculations are based on the Majorana neutrino mass generation mechanism in the Arkani-Hamed-Dimopoulos-Dvali model.

  3. Origin of superstructures in (double) perovskite thin films

    SciTech Connect (OSTI)

    Shabadi, V. Major, M.; Komissinskiy, P.; Vafaee, M.; Radetinac, A.; Baghaie Yazdi, M.; Donner, W.; Alff, L.

    2014-09-21

    We have investigated the origin of superstructure peaks as observed by X-ray diffraction of multiferroic Bi(Fe{sub 0.5}Cr{sub 0.5})O{sub 3} thin films grown by pulsed laser deposition on single crystal SrTiO{sub 3} substrates. The photon energy dependence of the contrast between the atomic scattering factors of Fe and Cr is used to rule out a chemically ordered double perovskite Bi{sub 2}FeCrO{sub 6} (BFCO). Structural calculations suggest that the experimentally observed superstructure occurs due to unequal cation displacements along the pseudo-cubic [111] direction that mimic the unit cell of the chemically ordered compound. This result helps to clarify discrepancies in the correlations of structural and magnetic order reported for Bi{sub 2}FeCrO{sub 6}. The observation of a superstructure in itself is not a sufficient proof of chemical order in double perovskites.

  4. Electrical-assisted double side incremental forming and processes thereof

    SciTech Connect (OSTI)

    Roth, John; Cao, Jian

    2014-06-03

    A process for forming a sheet metal component using an electric current passing through the component is provided. The process can include providing a double side incremental forming machine, the machine operable to perform a plurality of double side incremental deformations on the sheet metal component and also apply an electric direct current to the sheet metal component during at least part of the forming. The direct current can be applied before or after the forming has started and/or be terminated before or after the forming has stopped. The direct current can be applied to any portion of the sheet metal. The electrical assistance can reduce the magnitude of force required to produce a given amount of deformation, increase the amount of deformation exhibited before failure and/or reduce any springback typically exhibited by the sheet metal component.

  5. Oligonucleotide and Long Polymeric DNA Encoding

    SciTech Connect (OSTI)

    Miller, E; Mariella Jr., R P; Christian, A T; Gardner, S N; Williams, J M

    2003-11-24

    This report summarizes the work done at Lawrence Livermore National Laboratory for the Oligonucleotide and Long Polymeric DNA Encoding project, part of the Microelectronic Bioprocesses Program at DARPA. The goal of the project was to develop a process by which long (circa 10,000 base-pair) synthetic DNA molecules could be synthesized in a timely and economic manner. During construction of the long molecule, errors in DNA sequence occur during hybridization and/or the subsequent enzymatic process. The work done on this project has resulted in a novel synthesis scheme that we call the parallel pyramid synthesis protocol, the development of a suit of computational tools to minimize and quantify errors in the synthesized DNA sequence, and experimental proof of this technique. The modeling consists of three interrelated modules: the bioinformatics code which determines the specifics of parallel pyramid synthesis for a given chain of long DNA, the thermodynamics code which tracks the products of DNA hybridization and polymerase extension during the later steps in the process, and the kinetics model which examines the temporal and spatial processes during one thermocycle. Most importantly, we conducted the first successful syntheses of a gene using small starting oligomers (tetramers). The synthesized sequence, 813 base pairs long, contained a 725 base pair gene, modified green fluorescent protein (mGFP), which has been shown to be a functional gene by cloning into cells and observing its green fluorescent product.

  6. Double sided circuit board and a method for its manufacture

    DOE Patents [OSTI]

    Lindenmeyer, Carl W. (St. Charles, IL)

    1989-01-01

    Conductance between the sides of a large double sided printed circuit board is provided using a method which eliminates the need for chemical immersion or photographic exposure of the entire large board. A plurality of through-holes are drilled or punched in a substratum according to the desired pattern, conductive laminae are made to adhere to both sides of the substratum covering the holes and the laminae are pressed together and permanently joined within the holes, providing conductive paths.

  7. Double-clad nuclear-fuel safety rod

    DOE Patents [OSTI]

    McCarthy, W.H.; Atcheson, D.B.

    1981-12-30

    A device for shutting down a nuclear reactor during an undercooling or overpower event, whether or not the reactor's scram system operates properly. This is accomplished by double-clad fuel safety rods positioned at various locations throughout the reactor core, wherein melting of a secondary internal cladding of the rod allows the fuel column therein to shift from the reactor core to place the reactor in a subcritical condition.

  8. 241-SY Double Shell Tanks (DST) Integrity Assessment Report

    SciTech Connect (OSTI)

    JENSEN, C.E.

    1999-09-21

    This report presents the results of the integrity assessment of the 241-SY double-shell tank farm facility located in the 200 West Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations, are made to ensure the continued safe operation of the tanks.

  9. Double sided circuit board and a method for its manufacture

    DOE Patents [OSTI]

    Lindenmeyer, C.W.

    1988-04-14

    Conductance between the sides of a large double sided printed circuit board is provided using a method which eliminates the need for chemical immersion or photographic exposure of the entire large board. A plurality of through-holes are drilled or punched in a substratum according to the desired pattern, conductive laminae are made to adhere to both sides of the substratum covering the holes and the laminae are pressed together and permanently joined within the holes, providing conductive paths. 4 figs.

  10. Tritium emissions from 200 East Area Double-Shell Tanks

    SciTech Connect (OSTI)

    Bachand, D.D.

    1994-11-28

    This document evaluates the need for tritium sampling of the emissions from the 200 East Area Double Shell Tanks based on the requirements of {open_quotes}National Emission Standards for Hazardous Air Pollutants{close_quotes} (NESHAP). The NESHAP requirements are specified in 40 Code of Federal Regulation (CFR), Part 61, Subpart H; {open_quotes}National Emission Standards for Emissions of Radionuclides Other than Radon from Department of Energy Facilities{close_quotes}.

  11. 241-AN Double Shell Tanks (DST) Integrity Assessment Report

    SciTech Connect (OSTI)

    JENSEN, C.E.

    1999-09-21

    This report presents the results of the integrity assessment of the 241-AN double-shell tank farm facility located in the 200 East Area of the Hanford Site. The assessment included the design evaluation and integrity examinations of the tanks and concluded that the facility is adequately designed, is compatible with the waste, and is fit for use. Recommendations including subsequent examinations, are made to ensure the continued safe operation of the tanks.

  12. The Search for Neutrinoless Double Beta Decay with 130Te with CUORE-0

    SciTech Connect (OSTI)

    Ouellet, Jonathan, L

    2015-06-02

    This thesis describes the design, operation and results of an experimental search for neutrinoless double beta decay (0$\

  13. Monitoring of Double-Stud Wall Moisture Conditions in the Northeast

    SciTech Connect (OSTI)

    Ueno, K.

    2015-03-01

    Double-stud walls insulated with cellulose or low-density spray foam can have R-values of 40 or higher. However, double-stud walls have a higher risk of interior-sourced condensation moisture damage when compared with high-R approaches using exterior insulating sheathing. Moisture conditions in double-stud walls were monitored in Zone 5A (Massachusetts); three double-stud assemblies were compared.

  14. What can we learn from neutrinoless double beta decay experiments? (Journal

    Office of Scientific and Technical Information (OSTI)

    Article) | SciTech Connect What can we learn from neutrinoless double beta decay experiments? Citation Details In-Document Search Title: What can we learn from neutrinoless double beta decay experiments? We assess how well next generation neutrinoless double beta decay and normal neutrino beta decay experiments can answer four fundamental questions. 1) If neutrinoless double beta decay searches do not detect a signal, and if the spectrum is known to be inverted hierarchy, can we conclude

  15. Exact nonlinear excitations in double-degenerate plasmas

    SciTech Connect (OSTI)

    Akbari-Moghanjoughi, M.

    2012-06-15

    In this work, we use the conventional hydrodynamics formalism and incorporate the Chew-Goldberger-Low double-adiabatic theory to evaluate the nonlinear electrostatic ion excitations in double-degenerate (electron spin-orbit degenerate) magnetized quantum plasmas. Based on the Sagdeev pseudopotential method, an exact general pseudopotential is calculated which leads to the allowed Mach-number range criteria for such localized density structures in an anisotropic magnetized plasma. We employ the criteria on the Mach-number range for diverse magnetized quantum plasma with different equations of state. It is remarked that various plasma fractional parameters such as the system dimensionality, ion-temperature, relativistic-degeneracy, Zeeman-energy, and plasma composition are involved in the stability of an obliquely propagating nonlinear ion-acoustic wave in a double-degenerate quantum plasma. Current study is most appropriate for nonlinear wave analysis in dense astrophysical magnetized plasma environments such as white-dwarfs and neutron-star crusts where the strong magnetic fields can be present.

  16. DOE Tour of Zero Floorplans: Double ZeroHouse 3.0 by KB Home | Department

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    of Energy Double ZeroHouse 3.0 by KB Home DOE Tour of Zero Floorplans: Double ZeroHouse 3.0 by KB Home DOE Tour of Zero Floorplans: Double ZeroHouse 3.0 by KB Home

  17. Investigation of structure and properties of the Nb rods manufactured by different deformation and heat treatment regimes in mass production conditions for the Nb{sub 3}Sn strands

    SciTech Connect (OSTI)

    Abdyukhanov, I. M.; Vorobieva, A. E.; Alekseev, M. V.; Mareev, K. A.; Dergunova, E. A.; Peredkova, T. N. [JSC Bochvar High-Technology Research Institute of Inorganic Materials, 5a Rogova St., Moscow, 123060 (Russian Federation); Shikov, A. K. [NRC Kurchatov Institute, 1 Akademika Kurchatova Sq., Moscow, 123182 (Russian Federation); Utkin, K. V.; Vorobieva, A. V.; Kharkovsky, D. N. [JSC Chepetsky Mechanical Plant, 7 Belova St., Glazov, 427620 (Russian Federation)

    2014-01-27

    From 2009 the mass production of the Nb{sub 3}Sn strands for ITER with the yield of several tens of tons per year operates at JSC Chepetsky Mechanical Plant (Glazov, Russia). In order to enhance the stability of output characteristics of the produced Nb{sub 3}Sn strands, to increase the Nb filaments dimensional homogeneity the manufacture regimes improvement of the used semiproducts such as Nb rods intended for the superconducting filaments formation in the finished strands has been carried out. In the work the investigations of the Nb rheological behavior, the influence of heat treatment in the wide temperature range from 700 to 1300 C on the predeformed Nb rods structure and mechanical properties have been performed. Different production routes of the Nb rods, including such operations like forging, extrusion and drawing combined with the recrystallization annealings, were used. Composite Nb{sub 3}Sn strands have been produced and their electrophysical properties have been tested. For the first time influence of the niobium rods manufacture regimes on the current carrying capacity of the industrial Nb{sub 3}Sn strands has been investigated.

  18. Optical selection and collection of DNA fragments

    DOE Patents [OSTI]

    Roslaniec, Mary C. (Los Alamos, NM); Martin, John C. (Los Alamos, NM); Jett, James H. (Los Alamos, NM); Cram, L. Scott (Los Alamos, NM)

    1998-01-01

    Optical selection and collection of DNA fragments. The present invention includes the optical selection and collection of large (>.mu.g) quantities of clonable, chromosome-specific DNA from a sample of chromosomes. Chromosome selection is based on selective, irreversible photoinactivation of unwanted chromosomal DNA. Although more general procedures may be envisioned, the invention is demonstrated by processing chromosomes in a conventional flow cytometry apparatus, but where no droplets are generated. All chromosomes in the sample are first stained with at least one fluorescent analytic dye and bonded to a photochemically active species which can render chromosomal DNA unclonable if activated. After passing through analyzing light beam(s), unwanted chromosomes are irradiated using light which is absorbed by the photochemically active species, thereby causing photoinactivation. As desired chromosomes pass this photoinactivation point, the inactivating light source is deflected by an optical modulator; hence, desired chromosomes are not photoinactivated and remain clonable. The selection and photoinactivation processes take place on a microsecond timescale. By eliminating droplet formation, chromosome selection rates 50 times greater than those possible with conventional chromosome sorters may be obtained. Thus, usable quantities of clonable DNA from any source thereof may be collected.

  19. Container lid gasket protective strip for double door transfer system

    DOE Patents [OSTI]

    Allen, Jr., Burgess M

    2013-02-19

    An apparatus and a process for forming a protective barrier seal along a "ring of concern" of a transfer container used with double door systems is provided. A protective substrate is supplied between a "ring of concern" and a safety cover in which an adhesive layer of the substrate engages the "ring of concern". A compressive foam strip along an opposite side of the substrate engages a safety cover such that a compressive force is maintained between the "ring of concern" and the adhesive layer of the substrate.

  20. High-performance double-filter soft x-ray

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    performance double-filter soft x-ray diagnostic for measurement of electron temperature structure and dynamics M. B. McGarry, P. Franz, D. J. Den Hartog, J. A. Goetz, M. A. Thomas et al. Citation: Rev. Sci. Instrum. 83, 10E129 (2012); doi: 10.1063/1.4740274 View online: http://dx.doi.org/10.1063/1.4740274 View Table of Contents: http://rsi.aip.org/resource/1/RSINAK/v83/i10 Published by the American Institute of Physics. Additional information on Rev. Sci. Instrum. Journal Homepage:

  1. Efficient double beta decay nuclear matrix elements computations

    SciTech Connect (OSTI)

    Neacsu, Andrei [Horia Hulubei Foundation (FHH) 407 Atomistilor, Horia Hulubei National Institute for Physics and Nuclear Engineering (IFIN-HH) 30 Reactorului, Magurele-Bucharest 077125 (Romania)

    2012-11-20

    We have developed a shell model code for the accurate computation of the two-body matrix elements of the transition operators involved in the neutrinoless double beta decay. This code features coupled cluster method short-range correlations with Jastrow-like functions, finite nucleon size effect and higher order nucleon current corrections. We present the results obtained for {sup 48}Ca and {sup 82}Se, then we compare them with other results in the literature. In the case of {sup 48}Ca, we also study the contributions of the included effects and find good agreement with other published results.

  2. The nuclear matrix elements for neutrinoless double beta decay

    SciTech Connect (OSTI)

    Simkovic, Fedor [Department of Nuclear Physics and Biophysics, Comenius University, Mlynska dolina, SK-84248 Bratislava (Slovakia)

    2007-10-12

    The status of calculation of the neutrinoless double beta decay (0{nu}{beta}{beta}-decay) nuclear matrix elements (NME's) is reviewed. The spread of published values of NME's is discussed. The main attention is paid to the recent progress achieved in the evaluation of the 0{nu}{beta}{beta}-decay NME's in the framework of the quasiparticle random phase approximation (QRPA). The obtained results are compared with those of the nuclear shell model. The problem of reliable determination of the 0{nu}{beta}{beta}-decay NME's is addressed. The uncertainty in NME's are analyzed and further progress in calculation of the 0{nu}{beta}{beta}-decay NME's is outlined.

  3. The GERDA Neutrinoless Double Beta-Decay Experiment

    SciTech Connect (OSTI)

    Majorovits, Bela A. [Max Planck Institut fuer Physik, Foehringer Ring 6, 80805 Munich (Germany)

    2007-10-12

    Neutrinoless double beta (0{nu}{beta}{beta})-decay is the key process to gain understanding of the nature of neutrinos. The GErmanium Detector Array (GERDA) is designed to search for 0{nu}{beta}{beta}-decay of the isotope {sup 76}Ge. Germanium crystals enriched in {sup 76}Ge, acting as source and detector simultaneously, will be submerged directly into an ultra pure cooling medium that also serves as a radiation shield. This concept will allow for a reduction of the background by up to two orders of magnitudes with respect to earlier experiments.

  4. Neutrinoless double beta decay and nuclear matrix elements

    SciTech Connect (OSTI)

    Simkovic, Fedor [BLTP, JINR Dubna, 141980 Dubna, Moscow region (Russian Federation); Comenius University, Mlynska dolina, Bratislava (Slovakia)

    2011-11-23

    The fundamental importance of searching for neutrinoless double-beta decay (0{nu}{beta}{beta}-decay) is widely recognized. Observation of the decay would tell us that the total lepton number is not conserved and that, consequently, neutrinos are massive Majorana fermions. The 0{nu}{beta}{beta}-decay is discussed in context of neutrino oscillation data. The perspectives of the experimental 0{nu}{beta}{beta}-decay searches are analyzed. The importance of reliable determination of the 0{nu}{beta}{beta}-decay nuclear matrix elements is pointed out.

  5. WATER-LITHIUM BROMIDE DOUBLE-EFFECT ABSORPTION COOLING ANALYSIS

    Office of Scientific and Technical Information (OSTI)

    WATER-LITHIUM BROMIDE DOUBLE-EFFECT ABSORPTION COOLING ANALYSIS Gary C . V l i e t , Michael B . Lawson, and Rudolf0 A . Lithgow Center f o r Energy Studies The University of Texas a t Austin December 1980 Final Report f o r Contract: DE AC03-79SF10540 (Mu1 tiple-Effect Absorption Cycle Solar Cooling) with the U.S. Department of Energy DISCLAIMER This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any

  6. Physics constraints on double-pulse LIA engineering

    SciTech Connect (OSTI)

    Ekdahl, Carl August Jr.

    2015-05-20

    The options for advanced-radiography double-pulse linear induction accelerators (LIA) under consideration naturally fall into three categories that differ by the number of cells required. Since the two major physics issues, beam breakup (BBU) and corkscrew, are also dependent on the number of cells, it may be useful for the decision process to review the engineering consequences of beam physics constraints for each class. The LIAs can be categorized three different ways, and this report compares the different categories based upon the physics of their beams.

  7. Computational modeling of electrophotonics nanomaterials: Tunneling in double quantum dots

    SciTech Connect (OSTI)

    Vlahovic, Branislav Filikhin, Igor

    2014-10-06

    Single electron localization and tunneling in double quantum dots (DQD) and rings (DQR) and in particular the localized-delocalized states and their spectral distributions are considered in dependence on the geometry of the DQDs (DQRs). The effect of violation of symmetry of DQDs geometry on the tunneling is studied in details. The cases of regular and chaotic geometries are considered. It will be shown that a small violation of symmetry drastically affects localization of electron and that anti-crossing of the levels is the mechanism of tunneling between the localized and delocalized states in DQRs.

  8. Npn double heterostructure bipolar transistor with ingaasn base region

    DOE Patents [OSTI]

    Chang, Ping-Chih; Baca, Albert G.; Li, Nein-Yi; Hou, Hong Q.; Ashby, Carol I. H.

    2004-07-20

    An NPN double heterostructure bipolar transistor (DHBT) is disclosed with a base region comprising a layer of p-type-doped indium gallium arsenide nitride (InGaAsN) sandwiched between n-type-doped collector and emitter regions. The use of InGaAsN for the base region lowers the transistor turn-on voltage, V.sub.on, thereby reducing power dissipation within the device. The NPN transistor, which has applications for forming low-power electronic circuitry, is formed on a gallium arsenide (GaAs) substrate and can be fabricated at commercial GaAs foundries. Methods for fabricating the NPN transistor are also disclosed.

  9. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Intriguing DNA Editor Has a Structural Trigger Print Wednesday, 30 July 2014 00:00 A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9

  10. Method for promoting specific alignment of short oligonucleotides on nucleic acids

    DOE Patents [OSTI]

    Studier, F. William (Stony Brook, NY); Kieleczawa, Jan (Coram, NY); Dunn, John J. (Bellport, NY)

    1996-01-01

    Disclosed is a method for promoting specific alignment of short oligonucleotides on a nucleic acid polymer. The nucleic acid polymer is incubated in a solution containing a single-stranded DNA-binding protein and a plurality of oligonucleotides which are perfectly complementary to distinct but adjacent regions of a predetermined contiguous nucleotide sequence in the nucleic acid polymer. The plurality of oligonucleotides anneal to the nucleic acid polymer to form a contiguous region of double stranded nucleic acid. Specific application of the methods disclosed include priming DNA synthesis and template-directed ligation.

  11. Sequential addition of short DNA oligos in DNA-polymerase-based synthesis reactions

    DOE Patents [OSTI]

    Gardner, Shea N. (San Leandro, CA); Mariella, Jr., Raymond P. (Danville, CA); Christian, Allen T. (Tracy, CA); Young, Jennifer A. (Berkeley, CA); Clague, David S. (Livermore, CA)

    2011-01-18

    A method of fabricating a DNA molecule of user-defined sequence. The method comprises the steps of preselecting a multiplicity of DNA sequence segments that will comprise the DNA molecule of user-defined sequence, separating the DNA sequence segments temporally, and combining the multiplicity of DNA sequence segments with at least one polymerase enzyme wherein the multiplicity of DNA sequence segments join to produce the DNA molecule of user-defined sequence. Sequence segments may be of length n, where n is an even or odd integer. In one embodiment the length of desired hybridizing overlap is specified by the user and the sequences and the protocol for combining them are guided by computational (bioinformatics) predictions. In one embodiment sequence segments are combined from multiple reading frames to span the same region of a sequence, so that multiple desired hybridizations may occur with different overlap lengths. In one embodiment starting sequence fragments are of different lengths, n, n+1, n+2, etc.

  12. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1986-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as bromodeoxyuridine (BrdU) is used as a probe for the measurement of BrdU uptake by the cells as a measure of DNA synthesis.

  13. Neutrinoless double beta decay and future neutrino oscillation precision experiments

    SciTech Connect (OSTI)

    Choubey, Sandhya [Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP (United Kingdom); Rodejohann, Werner [Physik-Department, Technische Universitaet Muenchen, James-Franck-Strasse, D-85748 Garching (Germany)

    2005-08-01

    We discuss to what extent future precision measurements of neutrino mixing observables will influence the information we can draw from a measurement of (or an improved limit on) neutrinoless double beta decay. Whereas the {delta}m{sup 2} corresponding to solar and atmospheric neutrino oscillations are expected to be known with good precision, the parameter {theta}{sub 12} will govern a large part of the uncertainty. We focus, in particular, on the possibility of distinguishing the neutrino mass hierarchies and on setting a limit on the neutrino mass. We give the largest allowed values of the neutrino masses which allow to distinguish the normal from the inverted hierarchy. All aspects are discussed as a function of the uncertainty stemming from the involved nuclear matrix elements. The implications of a vanishing, or extremely small, effective mass are also investigated. By giving a large list of possible neutrino mass matrices and their predictions for the observables, we finally explore how a measurement of (or an improved limit on) neutrinoless double beta decay can help to identify the neutrino mass matrix if more precise values of the relevant parameters are known.

  14. DOUBLE TRACKS Test Site interim corrective action plan

    SciTech Connect (OSTI)

    1996-06-01

    The DOUBLE TRACKS site is located on Range 71 north of the Nellis Air Force Range, northwest of the Nevada Test Site (NTS). DOUBLE TRACKS was the first of four experiments that constituted Operation ROLLER COASTER. On May 15, 1963, weapons-grade plutonium and depleted uranium were dispersed using 54 kilograms of trinitrotoluene (TNT) explosive. The explosion occurred in the open, 0.3 m above the steel plate. No fission yield was detected from the test, and the total amount of plutonium deposited on the ground surface was estimated to be between 980 and 1,600 grams. The test device was composed primarily of uranium-238 and plutonium-239. The mass ratio of uranium to plutonium was 4.35. The objective of the corrective action is to reduce the potential risk to human health and the environment and to demonstrate technically viable and cost-effective excavation, transportation, and disposal. To achieve these objectives, Bechtel Nevada (BN) will remove soil with a total transuranic activity greater then 200 pCI/g, containerize the soil in ``supersacks,`` transport the filled ``supersacks`` to the NTS, and dispose of them in the Area 3 Radioactive Waste Management Site. During this interim corrective action, BN will also conduct a limited demonstration of an alternative method for excavation of radioactive near-surface soil contamination.

  15. Structures of Clamp-Loader Complexes Are Key to DNA Replication

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    are also crucial components of various other cellular pathways, such as DNA repair, cell cycle control, and chromatin structure. Sliding DNA clamps are loaded onto DNA by...

  16. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V.

    2000-10-03

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.

  17. Synthesis of DNA (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    Synthesis of DNA Citation Details In-Document Search Title: Synthesis of DNA You are accessing a document from the Department of Energy's (DOE) SciTech Connect. This site is a...

  18. Encapsulation of Gold Nanoparticles in a DNA Origami Cage

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Encapsulation of Gold Nanoparticles in a DNA Origami Cage Authors: Zhao, Z., Jacovetty, E. L., Liu, Y., and Yan, H. Title: Encapsulation of Gold Nanoparticles in a DNA Origami Cage...

  19. DNA Gridiron Nanostructures Based on Four-Arm Junctions

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA Gridiron Nanostructures Based on Four-Arm Junctions Authors: Han, D., Pal, S., Yang, Y., Jiang, S., Nangreave, J., Liu, Y., and Yan, H. Title: DNA Gridiron Nanostructures Based...

  20. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, F.A.; Gray, J.W.

    1983-10-18

    A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)

  1. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  2. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  3. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  4. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  5. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  6. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked to a DNA's nucleic acid segment through its active site tyrosine, cleaving the DNA. Details of this

  7. Foreign DNA Capture during CRISPR-CAS Adaptive Immunity

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Foreign DNA Capture during CRISPR-CAS Adaptive Immunity Print Thursday, 21 January 2016 16:45 While we humans view bacteria as the enemy, bacteria have enemies too, for example, viruses. To protect themselves, bacteria have developed an adaptive-type immune system that revolves around a unit of DNA known as CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats. A CRISPR unit of DNA is made up of

  8. DNA origami with Complex Curvatures in 3D

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    with Complex Curvatures in 3D 15 Apr 2011 Center researchers have developed a new DNA origami design strategy for engineering complex, arbitrarily shaped 3D DNA nanostructures that have substantial intrinsic curvatures. This strategy has been presented in a paper by Professors Hao Yan, Yan Liu and coworkers that was featured on the cover of Science for April 15, 2011. Use of DNA as a structural material is in the basis of the DNA nanotechnology searching for ways to assemble nanoscale structures

  9. Kinetic model for an auroral double layer that spans many gravitational

    Office of Scientific and Technical Information (OSTI)

    scale heights (Journal Article) | SciTech Connect Kinetic model for an auroral double layer that spans many gravitational scale heights Citation Details In-Document Search Title: Kinetic model for an auroral double layer that spans many gravitational scale heights The electrostatic potential profile and the particle densities of a simplified auroral double layer are found using a relaxation method to solve Poisson's equation in one dimension. The electron and ion distribution functions for

  10. Double beta decay versus cosmology: Majorana CP phases and nuclear matrix elements

    SciTech Connect (OSTI)

    Deppisch, Frank; Paes, Heinrich [Institut fuer Theoretische Physik und Astrophysik, Universitaet Wuerzburg, D-97074 Wuerzburg (Germany); Suhonen, Jouni [Department of Physics, University of Jyvaeskylae, P.O.B. 35, FIN-40014, Jyvaeskylae (Finland)

    2005-08-01

    We discuss the relation between the absolute neutrino mass scale, the effective mass measured in neutrinoless double beta decay, and the Majorana CP phases. Emphasis is placed on estimating the upper bound on the nuclear matrix element entering calculations of the double beta decay half-life. Combining the claimed evidence for neutrinoless double beta decay with the neutrino mass bound from cosmology, one of the Majorana CP phases can be constrained.

  11. Shell model nuclear matrix elements for competing mechanisms contributing to double beta decay

    SciTech Connect (OSTI)

    Horoi, Mihai

    2013-12-30

    Recent progress in the shell model approach to the nuclear matrix elements for the double beta decay process are presented. This includes nuclear matrix elements for competing mechanisms to neutrionless double beta decay, a comparison between closure and non-closure approximation for {sup 48}Ca, and an updated shell model analysis of nuclear matrix elements for the double beta decay of {sup 136}Xe.

  12. High School Academic Competition - Double Elimination | U.S. DOE Office of

    Office of Science (SC) Website

    Science (SC) Double Elimination National Science Bowl® (NSB) NSB Home About High School Middle School Attending National Event Volunteers 2015 Competition Results Middle School Round Robin Middle School Double Elimination Middle School Electric Car High School Round Robin High School Double Elimination Top Teams for 2015 News Media WDTS Home Contact Information National Science Bowl® U.S. Department of Energy SC-27/ Forrestal Building 1000 Independence Ave., SW Washington, DC 20585 P:

  13. The MAJORANA DEMONSTRATOR: A Search for Neutrinoless Double-beta Decay of

    Office of Scientific and Technical Information (OSTI)

    Germanium-76 (Conference) | SciTech Connect MAJORANA DEMONSTRATOR: A Search for Neutrinoless Double-beta Decay of Germanium-76 Citation Details In-Document Search Title: The MAJORANA DEMONSTRATOR: A Search for Neutrinoless Double-beta Decay of Germanium-76 The observation of neutrinoless double-beta decay would determine whether the neutrino is a Majorana particle and provide information on the absolute scale of neutrino mass. The MAJORANA Collaboration is constructing the DEMONSTRATOR, an

  14. Methods to alter levels of a DNA repair protein

    DOE Patents [OSTI]

    Petrini, John H.; Morgan, William Francis; Maser, Richard Scott; Carney, James Patrick

    2006-10-17

    An isolated and purified DNA molecule encoding a DNA repair protein, p95, is provided, as is isolated and purified p95. Also provided are methods of detecting p95 and DNA encoding p95. The invention further provides p95 knock-out mice.

  15. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect (OSTI)

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  16. RKKY interaction in a chirally coupled double quantum dot system

    SciTech Connect (OSTI)

    Heine, A. W.; Tutuc, D.; Haug, R. J.; Zwicknagl, G.; Schuh, D.; Wegscheider, W.

    2013-12-04

    The competition between the Kondo effect and the Ruderman-Kittel-Kasuya-Yoshida (RKKY) interaction is investigated in a double quantum dots system, coupled via a central open conducting region. A perpendicular magnetic field induces the formation of Landau Levels which in turn give rise to the so-called Kondo chessboard pattern in the transport through the quantum dots. The two quantum dots become therefore chirally coupled via the edge channels formed in the open conducting area. In regions where both quantum dots exhibit Kondo transport the presence of the RKKY exchange interaction is probed by an analysis of the temperature dependence. The thus obtained Kondo temperature of one dot shows an abrupt increase at the onset of Kondo transport in the other, independent of the magnetic field polarity, i.e. edge state chirality in the central region.

  17. Out-of-Equilibrium Kondo Effect in Double Quantum Dots

    SciTech Connect (OSTI)

    Aguado, Ramon; Langreth, David C.

    2000-08-28

    The out-of-equilibrium transport properties of a double quantum dot system in the Kondo regime are studied theoretically by means of a two-impurity Anderson Hamiltonian with interimpurity hopping. The Hamiltonian is solved by means of a nonequilibrium generalization of the slave-boson mean-field theory. It is demonstrated that measurements of the differential conductance dI/dV , for appropriate values of voltages and tunneling couplings, can give a direct observation of the coherent superposition between the many-body Kondo states of each dot. For large voltages and arbitrarily large interdot tunneling, there is a critical voltage above which the physical behavior of the system again resembles that of two decoupled quantum dots. (c) 2000 The American Physical Society.

  18. Ultrasonic probe for inspecting double-wall tube

    DOE Patents [OSTI]

    Cook, Kenneth V. (Clinton, TN); Cunningham, Jr., Robert A. (Powell, TN); Murrin, Horace T. (Alcoa, TN)

    1983-01-01

    An ultrasonic probe for inspecting the interface between the walls of a double-wall tube comprises a cylindrical body member having two cavities axially spaced apart thereon. The probe is placed in the tube and ultrasonic energy is transmitted from a transducer in its body member to a reflector in one of its cavities and thence into the inner wall of the tube. A second transducer in the probe body member communicates with the second cavity through a collimation passage in the body member, and the amount of ultrasonic energy reflected from the interface between the walls of the tube to a second reflector through the collimation passage to the second transducer depends upon the characteristics of said interface.

  19. Ultrasonic probe for inspecting double-wall tube. [Patent application

    DOE Patents [OSTI]

    Cook, K.V.; Cunningham, R.A. Jr.; Murrin, H.T.

    1981-05-29

    An ultrasonic probe for inspecting the interface between the walls of a double-wall tube comprises a cylindrical body member having two cavities axially spaced apart thereon. The probe is placed in the tube and ultrasonic energy is transmitted from a transducer in its body member to a reflector in one of its cavities and thence into the inner wall of the tube. A second transducer in the probe body member communicates with the second cavity through a collimation passage in the body member, and the amount of ultrasonic energy reflected from the interface between the walls of the tube to a second reflector through the collimation passage to the second transducer depends upon the characteristics of said interface.

  20. Quantum chaos and the double-slit experiment

    SciTech Connect (OSTI)

    Casati, Giulio [Center for Nonlinear and Complex Systems, Universita' degli Studi dell'Insubria, Como (Italy); Istituto Nazionale per la Fisica della Materia, unita' di Como, Como (Italy); Istituto Nazionale di Fisica Nucleare, sezione di Milano, Milan (Italy); Department of Physics, National University of Singapore (Singapore); Prosen, Tomaz [Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana (Slovenia); Department of Physics, National University of Singapore (Singapore)

    2005-09-15

    We report on the numerical simulation of the double-slit experiment, where the initial wave packet is bounded inside a billiard domain with perfectly reflecting walls. If the shape of the billiard is such that the classical ray dynamics is regular, we obtain interference fringes whose visibility can be controlled by changing the parameters of the initial state. However, if we modify the shape of the billiard thus rendering classical (ray) dynamics fully chaotic, the interference fringes disappear and the intensity on the screen becomes the (classical) sum of intensities for the two corresponding one-slit experiments. Thus we show a clear and fundamental example in which transition to chaotic motion in a deterministic classical system, in absence of any external noise, leads to a profound modification in the quantum behavior.

  1. A Double Scattering Analytical Model For Elastic Recoil Detection Analysis

    SciTech Connect (OSTI)

    Barradas, N. P.; Lorenz, K.; Alves, E.; Darakchieva, V.

    2011-06-01

    We present an analytical model for calculation of double scattering in elastic recoil detection measurements. Only events involving the beam particle and the recoil are considered, i.e. 1) an ion scatters off a target element and then produces a recoil, and 2) an ion produces a recoil which then scatters off a target element. Events involving intermediate recoils are not considered, i.e. when the primary ion produces a recoil which then produces a second recoil. If the recoil element is also present in the stopping foil, recoil events in the stopping foil are also calculated. We included the model in the standard code for IBA data analysis NDF, and applied it to the measurement of hydrogen in Si.

  2. Low Radioactivity Crystals for Neutrinoless Double Beta Decay Detectors

    SciTech Connect (OSTI)

    Dafinei, Ioan [Sezione INFN di Roma, P-le Aldo Moro 2, Roma I-00185 (Italy)

    2011-04-27

    The production of crystals needed for rare events physics represent a relatively new, exciting challenge in the field of materials science and engineering. Extremely low concentration of radioactive impurities and very high crystal perfection is required for the crystals to be used in experiments in which the main concerns are the reduction of the background and the use of high sensitivity detectors. A further complication is the fact that for an experiment with a significant discovery potential, relatively large quantities of crystals are needed. The present work makes a review of the general problems related to the production of crystals for rare events physics and gives details related to the production of the TeO{sub 2} crystals needed for the major experiment in this field using bolometric technique, namely the CUORE experiment. The potential use of crystals for future double beta decay experiments is also discussed.

  3. Radiopurity control in the NEXT-100 double beta decay experiment

    SciTech Connect (OSTI)

    lvarez, V.; Crcel, S.; Cervera, A.; Daz, J.; Ferrario, P.; Gil, A.; Gmez-Cadenas, J. J.; Laing, A.; Liubarsky, I.; Lorca, D.; Martn-Albo, J.; Martnez, A.; Monrabal, F.; Muoz Vidal, J.; Nebot-Guinot, M.; Rodrguez, J.; Serra, L.; Simn, A.; Sofka, C.; Sorel, M. [Instituto de Fsica Corpuscular (IFIC), CSIC and Universitat de Valncia, 46980 Paterna, Valencia (Spain)] [Instituto de Fsica Corpuscular (IFIC), CSIC and Universitat de Valncia, 46980 Paterna, Valencia (Spain); and others

    2013-08-08

    An extensive material screening and selection process is underway in the construction of the 'Neutrino Experiment with a Xenon TPC' (NEXT), intended to investigate neutrinoless double beta decay using a high-pressure xenon gas TPC filled with 100 kg of Xe enriched in {sup 136}Xe. Determination of the radiopurity levels of the materials is based on gamma-ray spectroscopy using ultra-low background germanium detectors at the Laboratorio Subterrneo de Canfranc (Spain) and also on Glow Discharge Mass Spectrometry. Materials to be used in the shielding, pressure vessel, electroluminescence and high voltage components and energy and tracking readout planes have been already taken into consideration. The measurements carried out are presented, describing the techniques and equipment used, and the results obtained are shown, discussing their implications for the NEXT experiment.

  4. Chiral Two-body Currents and Neutrinoless Double Beta Decay

    SciTech Connect (OSTI)

    Menendez, Javier [Institut fuer Kernphysik, Technische Universitaet Darmstadt, 64289 Darmstadt (Germany); ExtreMe Matter Institute EMMI, GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, 64291 Darmstadt (Germany)

    2011-12-16

    The nuclear matrix elements (NMEs) of neutrinoless double-beta (0{nu}{beta}{beta}) decay are studied using weak currents derived in the framework of chiral effective field theory. Apart from the standard one-body (1b) currents, it is shown that two-body (2b) currents contribute to weak processes. The normal-ordered 1b part of 2b currents modifies the Gamow-Teller (GT){sigma}{tau}{sup -} part of the 1b current, contributing to the well-known quenching of GT single-{beta} decays. The momentum-transfer dependence of the quenching due to 2b currents is also predicted. Therefore, including 2b currents allows to address, microscopically, the problem of the axial weak coupling (g{sub A}) value, which is the biggest uncertainty in the 0{nu}{beta}{beta} decay NME calculations for all available methods.

  5. Ferroelectric modulation on resonant tunneling through perovskite double-barriers

    SciTech Connect (OSTI)

    Du, Ruifang; Qiu, Xiangbiao; Li, Aidong; Wu, Di

    2014-04-07

    The negative differential resistance (NDR) due to resonance tunneling is achieved at room temperature in perovskite double-barrier heterostructures composed of a 10 unit-cell-thick SrTiO{sub 3} quantum well sandwiched in two 10 unit-cell-thick LaAlO{sub 3} barriers. The NDR occurs at 1.2?V and does not change with voltage cycling. When the paraelectric SrTiO{sub 3} quantum well is replaced by a ferroelectric BaTiO{sub 3}, the onset of the NDR can be modulated by polarization switching in the ultrathin BaTiO{sub 3}. A polarization pointing to the collector lowers the NDR voltage but a polarization pointing to the emitter increases it. The shift of the NDR voltage is ascribed to reversal of the extra electric field in the quantum well due to the polarization switching.

  6. The MAJORANA DEMONSTRATOR Neutrinoless Double-Beta Decay Experiment

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Abgrall, N.; Aguayo, E.; Avignone, F. T.; Barabash, A. S.; Bertrand, F. E.; Boswell, M.; Brudanin, V.; Busch, M.; Caldwell, A. S.; Chan, Y.-D.; et al

    2014-01-01

    Tmore » he M ajorana D emonstrator will search for the neutrinoless double-beta ( β β 0 ν ) decay of the isotope Ge with a mixed array of enriched and natural germanium detectors. The observation of this rare decay would indicate that the neutrino is its own antiparticle, demonstrate that lepton number is not conserved, and provide information on the absolute mass scale of the neutrino. The D emonstrator is being assembled at the 4850-foot level of the Sanford Underground Research Facility in Lead, South Dakota. The array will be situated in a low-background environment and surrounded by passive and active shielding. Here we describe the science goals of the D emonstrator and the details of its design. « less

  7. Double-ended ceramic helical-rotor expander

    DOE Patents [OSTI]

    Mohr, P.B.; Myers, W.B.

    1995-02-28

    A ceramic helical rotor expander is disclosed using a double-ended or tandem herringbone type rotor arrangement with bearing and seal assemblies remote from the hot gas inlets and especially capable of operating at an inlet temperature of above 1,100 C. The rotors are solid or hollow and bonded to hollow metal shafts, and mounted in a composite or simple prismatic casing. The rotors, casing and shafts are constructed from low expansivity materials. In the preferred embodiment the rotors are constructed of silicon nitride and the shafts constructed of an molybdenum alloy, with the metal shafts being supported in bearings and secured to synchronizing gears. The rotors and casing may be provided with coolant channels therein, and are constructed to eliminate the problem of end leakages at inlet temperature and pressure, and the need for high temperature bearings and seals. 3 figs.

  8. Double-ended ceramic helical-rotor expander

    DOE Patents [OSTI]

    Mohr, Peter B. (Livermore, CA); Myers, Wendell B. (Livermore, CA)

    1995-01-01

    A ceramic helical rotor expander using a double-ended or tandem herringbone type rotor arrangement with bearing and seal assemblies remote from the hot gas inlets and especially capable of operating at an inlet temperature of above 1100.degree. C. The rotors are solid or hollow and bonded to hollow metal shafts, and mounted in a composite or simple prismatic casing. The rotors, casing and shafts are constructed from low expansivity materials. In the preferred embodiment the rotors are constructed of silicon nitride and the shafts constructed of an molybdenum alloy, with the metal shafts being supported in bearings and secured to synchronizing gears. The rotors and casing may be provided with coolant channels therein, and are constructed to eliminate the problem of end leakages at inlet temperature and pressure, and the need for high temperature bearings and seals.

  9. Nonlinear Dynamics in the SPEAR 3 Double-Waist Chicane

    SciTech Connect (OSTI)

    Safranek, J.A.; Huang, X.; Terebilo, A.; /SLAC

    2007-08-08

    One of the two 7.6 m long straight sections in SPEAR3 has been divided into two short straights to provide places for two new small-gap insertion devices (IDs). A chicane generates an angular separation of 10 mrad between the two straights. A quadrupole triplet has been added in the center of the 7.6 m long chicane to create a 'double-waist chicane' optics with {beta}{sub {gamma}}=1.6 m at the center of each of two future IDs. The new optics also reduces {beta}{sub {gamma}}to 2.5 m in the four 4.8 m straight sections. In this paper, the authors discuss nonlinear dynamic studies associated with design and implementation of the new optics. They present tracking results generated during the design stage and compare them to nonlinear dynamics measurements made with the quadrupole triplet installed in SPEAR3.

  10. Double rotation NMR studies of zeolites and aluminophosphate molecular sieves

    SciTech Connect (OSTI)

    Jelinek, R. |

    1993-07-01

    Goal is to study the organization and structures of guest atoms and molecules and their reactions on internal surfaces within pores of zeolites and aluminophosphate molecular sieves. {sup 27}Al and {sup 23}Na double rotation NMR (DOR) is used since it removes the anisotropic broadening in NMR spectra of quadrupolar nuclei, thus increasing resolution. This work concentrates on probing aluminum framework atoms in aluminophosphate molecular sieves and sodium extra framework cations in porous aluminosilicates. In aluminophosphates, ordering and electronic environments of the framework {sup 27}Al nuclei are modified upon adsorption of water molecules within the channels; a relation is sought between the sieve channel topology and the organization of adsorbed water, as well as the interaction between the Al nuclei and the water molecules. Extra framework Na{sup +} cations are directly involved in adsorption processes and reactions in zeolite cavities.

  11. Double dumbbell shaped AgNi alloy by pulsed electrodeposition

    SciTech Connect (OSTI)

    Dhanapal, K.; Vasumathi, M.; Santhi, Kalavathy; Narayanan, V. Stephen, A.

    2014-01-28

    Silver-Nickel is the well-known thermally immiscible system that makes them quite complex for the formation of alloy. This kind of alloy can be attained from electrodeposition method. In the present work, AgNi alloy was synthesized by pulsed electrodeposition in a single bath two electrode system with the use of anodic alumina membrane. The prepared AgNi alloy and pure Ag were characterized with X-ray Diffraction (XRD) for structural confirmation, Scanning Electron Microscopy (SEM) for morphological, and magnetic properties by Vibrating Sample Magnetometer, respectively. The X-ray Diffraction study shows the formation of cubic structure for pure Ag. SEM analysis reveals the double dumbbell morphology for AgNi alloy and spherically agglomeration for pure silver. Hysteresis behaviour from VSM measurement indicates that the AgNi alloy have good ferro-magnetic properties.

  12. Secretary Moniz Unveils Roadmap to Double U.S. Energy Productivity by 2030

    Broader source: Energy.gov [DOE]

    Secretary Moniz unveiled a strategic plan laying out a roadmap to achieve the President’s goal to double U.S. energy productivity by 2030.

  13. Large Hadron Collider Probe of Supersymmetric Neutrinoless Double-Beta-Decay Mechanism

    SciTech Connect (OSTI)

    Allanach, B. C.; Kom, C. H.; Paes, H. [DAMTP, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA (United Kingdom); Cavendish Laboratory, J. J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Fakultaet fuer Physik, Technische Universitaet Dortmund, D-44221, Dortmund (Germany)

    2009-08-28

    In the minimal supersymmetric extension to the standard model, a nonzero lepton number violating coupling {lambda}{sub 111}{sup '} predicts both neutrinoless double-beta-decay and resonant single slepton production at the LHC. We show that, in this case, if neutrinoless double beta decay is discovered in the next generation of experiments, there exist good prospects to observe single slepton production at the LHC. Neutrinoless double beta decay could otherwise result from a different source (such as a nonzero Majorana neutrino mass). Resonant single slepton production at the LHC can therefore discriminate between the {lambda}{sub 111}{sup '} neutrinoless double-beta-decay mechanism and others.

  14. DOE Zero Energy Ready Home Case Study: Sterling Brook Custom Homes, Double

    Energy Savers [EERE]

    Oak, TX | Department of Energy Sterling Brook Custom Homes, Double Oak, TX DOE Zero Energy Ready Home Case Study: Sterling Brook Custom Homes, Double Oak, TX DOE Zero Energy Ready Home Case Study: Sterling Brook Custom Homes, Double Oak, TX Case study of a DOE Zero Energy Ready home in Double Oak, TX, north of Dallas, that scored a HERS 44 without PV. The 3,752-ft2 two-story home served as an energy-efficient model home for the custom home builder: 1,300 visitors toured the home, thousands

  15. Observation of Two-Neutrino Double-Beta Decay in Xe-136 with...

    Office of Scientific and Technical Information (OSTI)

    the more interesting neutrinoless double-beta decay, the most sensitive probe for the existence of Majorana particles and the measurement of the neutrino mass scale. Authors:...

  16. Structural and mechanistic insights into Mcm2-7 double-hexamer...

    Office of Scientific and Technical Information (OSTI)

    and mechanistic insights into Mcm2-7 double-hexamer assembly and function Sun, Jingchuan Brookhaven National Laboratory (BNL), Upton, NY (United States); Li, Huilin Brookhaven...

  17. Phase one contamination migration testing of the double-lid bagless posting system

    SciTech Connect (OSTI)

    Smith, J.A.

    1994-09-01

    This document describes leak rate tests on a double lid radioactive waste storage container, developed during the Microwave Solidification Project at Rocky Flats Plant.

  18. Study of a double bubbler for material balance in liquids

    SciTech Connect (OSTI)

    Hugues Lambert

    2013-09-01

    The objective of this project was to determine the potential of a double bubbler to measure density and fluid level of the molten salt contained in an electrorefiner. Such in-situ real-time measurements can provide key information for material balances in the pyroprocessing of the nuclear spent fuel. This theoretical study showed this technique has a lot of promise. Four different experiments were designed and performed. The first three experiments studied the influence of a variety of factors such as depth difference between the two tubes, gas flow rate, the radius of the tubes and determining the best operating conditions. The last experiment purpose was to determine the precision and accuracy of the apparatus during specific conditions. The elected operating conditions for the characterization of the system were a difference of depth of 25 cm and a flow rate of 55 ml/min in each tube. The measured densities were between 1,000 g/l and 1,400g/l and the level between 34cm and 40 cm. The depth difference between the tubes is critical, the larger, the better. The experiments showed that the flow rate should be the same in each tube. The concordances with theoretical predictions were very good. The density precision was very satisfying (spread<0.1%) and the accuracy was about 1%. For the level determination, the precision was also very satisfying (spread<0.1%), but the accuracy was about 3%. However, those two biases could be corrected with calibration curves. In addition to the aqueous systems studied in the present work, future work will focus on examining the behavior of the double bubbler instrumentation in molten salt systems. The two main challenges which were identified in this work are the effect of the temperature and the variation of the superficial tension.

  19. Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches (474th Brookhaven Lecture)

    SciTech Connect (OSTI)

    Gang, Oleg

    2012-01-18

    In the field of nanoscience, if you can control how nanoparticles self-assemble in particular structures joining each other, for example, as molecules can form, atom-by-atom you can design new materials that have unique properties that industry needs. Nature already uses the DNA genetic code to instruct the building of specific proteins and whole organisms in both plants and people. Taking a cue from nature, scientists at BNL devised a way of using strands of synthetic DNA attached to the surface of nanoparticles to instruct them to self-assemble into specific nanoscale structures, clusters, and three-dimensional organizations. Novel materials designed and fabricated this way promise use in photovoltaics, energy storage, catalysis, cell-targeted systems for more effective medical treatments, and biomolecular sensing for environmental monitoring and medical applications. To find out more about the rapid evolution of this nanoassembly method and its applications, join Physicist Oleg Gang of the Center for Functional Nanomaterials (CFN) as he gives the 474th Brookhaven Lecture, titled Self-Assembly by Instruction: Designing Nanoscale Systems Using DNA-Based Approaches." Gang, who has led this work at the CFN, will explain the rapid evolution of this nanoassembly method, and discuss its present and future applications in highly specific biosensors, optically active nano-materials, and new ways to fabricate complex architectures in a rational manner via self-assembly. Gang and his colleagues used the CFN and the National Synchrotron Light Source (NSLS) facilities to perform their groundbreaking research. At the CFN, the scientists used electron microscopes and optical methods to visualize the clusters that they fabricated. At the NSLS, they applied x-rays to study a particles-assembly process in solution, DNAs natural environment. Gang earned a Ph.D. in soft matter physics from Bar-Ilan University in 2000, and he was a Rothschild Fellow at Harvard University from 1999 to 2002. After joining BNL as a Goldhaber Fellow in 2002, he became an assistant scientist at the CFN in 2004. He became the CFNs leader for Soft and Biological Nanomaterials Theme Group in 2006, and earned the title of scientist in 2009. Gang has received numerous honors and recognitions, including the 2010 Gordon Battelle Prize for Scientific Discovery.

  20. DOI-BLM-NM-L000-2012-0200-DNA | Open Energy Information

    Open Energy Info (EERE)

    00-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0200-DNA DNA at Lightning Dock Geothermal Area for GeothermalWell Field, DNA for Injection...

  1. DOI-BLM-NV-C010-2012--044-DNA | Open Energy Information

    Open Energy Info (EERE)

    DOI-BLM-NV-C010-2012--044-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012--044-DNA DNA for GeothermalPower Plant, DNA for Ormatt Nevada Sundry...

  2. DOI-BLM-NV-C010-2013-0037-DNA | Open Energy Information

    Open Energy Info (EERE)

    37-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0037-DNA DNA at Gabbs Valley Geothermal Area for GeothermalWell Field, DNA for Wild Rose Unit...

  3. DOI-BLM-NV-C010-2010-0006-DNA | Open Energy Information

    Open Energy Info (EERE)

    DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2010-0006-DNA DNA at Gabbs Valley Geothermal Area for GeothermalExploration, DNA for Thermal Gradient...

  4. DOI-BLM-NM-L000-2012-0111-DNA | Open Energy Information

    Open Energy Info (EERE)

    111-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0111-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration, DNA for Three...

  5. DOI-BLM-NV-C010-2012-0005-DNA | Open Energy Information

    Open Energy Info (EERE)

    05-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2012-0005-DNA DNA at McCoy Geothermal Area for GeothermalWell Field DNA for Observation Wells 62-8...

  6. DOI-BLM-NV-C010-2011-0517-DNA | Open Energy Information

    Open Energy Info (EERE)

    7-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2011-0517-DNA DNA at Dead Horse Wells Geothermal Area for GeothermalExploration DNA at Dead Horse...

  7. DOI-BLM-NM-L000-2012-0042-DNA | Open Energy Information

    Open Energy Info (EERE)

    2-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NM-L000-2012-0042-DNA DNA at Lightning Dock Geothermal Area for GeothermalExploration DNA for Well 55-7 at...

  8. DOI-BLM-NV-B020-2008-0071-DNA | Open Energy Information

    Open Energy Info (EERE)

    0071-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-B020-2008-0071-DNA DNA at Reese River Geothermal Area for GeothermalExploration DNA at Reese River...

  9. DOI-BLM-NV-C010-2013-0026-DNA | Open Energy Information

    Open Energy Info (EERE)

    6-DNA Jump to: navigation, search NEPA Document Collection for: DOI-BLM-NV-C010-2013-0026-DNA DNA at Dixie Valley Geothermal Area for GeothermalWell Field, DNA for Production...

  10. US ITER | About

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    includes: 9 active double-pancake lengths (about 765 m each), with 2 using Oxford Superconductor Technology (OST) strand and 7 using Luvata strand; 1 dummy length of...

  11. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 510 minutes.

  12. Stepped electrophoresis for movement and concentration of DNA

    DOE Patents [OSTI]

    Miles, Robin R.; Wang, Amy Wei-Yun; Mariella, Jr., Raymond P.

    2005-03-15

    A fluidic channel patterned with a series of thin-film electrodes makes it possible to move and concentrate DNA in a fluid passing through the fluidic channel. The DNA has an inherent negative charge and by applying a voltage between adjacent electrodes the DNA is caused to move. By using a series of electrodes, when one electrode voltage or charge is made negative with respect to adjacent electrodes, the DNA is repelled away from this electrode and attached to a positive charged electrode of the series. By sequentially making the next electrode of the series negative, the DNA can be moved to and concentrated over the remaining positive electrodes.

  13. DNA-Guided Crystallization of Colloidal Nanoparticles

    SciTech Connect (OSTI)

    Nykypanchuk,D.; Maye, M.; van der Lelie, D.; Gang, O.

    2008-01-01

    Many nanometre-sized building blocks will readily assemble into macroscopic structures. If the process is accompanied by effective control over the interactions between the blocks and all entropic effects, then the resultant structures will be ordered with a precision hard to achieve with other fabrication methods. But it remains challenging to use self-assembly to design systems comprised of different types of building blocks--to realize novel magnetic, plasmonic and photonic metamaterials for example. A conceptually simple idea for overcoming this problem is the use of 'encodable' interactions between building blocks; this can in principle be straightforwardly implemented using biomolecules6, 7, 8, 9, 10. Strategies that use DNA programmability to control the placement of nanoparticles in one and two dimensions have indeed been demonstrated. However, our theoretical understanding of how to extend this approach to three dimensions is limited14, 15, and most experiments have yielded amorphous aggregates and only occasionally crystallites of close-packed micrometre-sized particles. Here, we report the formation of three-dimensional crystalline assemblies of gold nanoparticles mediated by interactions between complementary DNA molecules attached to the nanoparticles' surface. We find that the nanoparticle crystals form reversibly during heating and cooling cycles. Moreover, the body-centred-cubic lattice structure is temperature-tuneable and structurally open, with particles occupying only {approx}4% of the unit cell volume. We expect that our DNA-mediated crystallization approach, and the insight into DNA design requirements it has provided, will facilitate both the creation of new classes of ordered multicomponent metamaterials and the exploration of the phase behaviour of hybrid systems with addressable interactions.

  14. Allosteric Modulation of DNA by Small Molecules

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Allosteric Modulation of DNA by Small Molecules Signals originating at the cell surface are conveyed by a complex system of interconnected signaling pathways to the nucleus. They converge at transcription factors, which in turn regulate the transcription of sets of genes that result in the gene expression. Many human diseases are caused by dysregulated gene expression and the oversupply of transcription factors may be required for the growth and metastatic behavior of human cancers. Cell

  15. Method for in vitro recombination

    DOE Patents [OSTI]

    Gibson, Daniel Glenn; Smith, Hamilton O

    2013-05-07

    The present invention relates to an in vitro method, using isolated protein reagents, for joining two double-stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest.

  16. Repair of radiation-induced heat-labile sites is independent of DNA-PKcs, XRCC1 or PARP

    SciTech Connect (OSTI)

    Stenerlw, Bo; Karlsson, Karin H.; Radulescu, Irina; Rydberg, Bjorn; Stenerlow, Bo

    2008-04-29

    Ionizing radiation induces a variety of different DNA lesions: in addition to the most critical DNA damage, the DSB, numerous base alterations, SSBs and other modifications of the DNA double-helix are formed. When several non-DSB lesions are clustered within a short distance along DNA, or close to a DSB, they may interfere with the repair of DSBs and affect the measurement of DSB induction and repair. We have previously shown that a substantial fraction of DSBs measured by pulsed-field gel electrophoresis (PFGE) are in fact due to heat-labile sites (HLS) within clustered lesions, thus reflecting an artifact of preparation of genomic DNA at elevated temperature. To further characterize the influence of HLS on DSB induction and repair, four human cell lines (GM5758, GM7166, M059K, U-1810) with apparently normal DSB rejoining were tested for bi-phasic rejoining after gamma irradiation. When heat-released DSBs were excluded from the measurements the fraction of fast rejoining decreased to less than 50% of the total. However, neither the half-times of the fast (t{sub 1/2} = 7-8 min) or slow (t{sub 1/2} = 2.5 h) DSB rejoining were changed significantly. At t=0 the heat-released DSBs accounted for almost 40% of the DSBs, corresponding to 10 extra DSB/cell/Gy in the initial DSB yield. These heat-released DSBs were repaired within 60-90 min in all tested cells, including M059K cells treated with wortmannin or DNA-PKcs defect M059J cells. Furthermore, cells lacking XRCC1 or Poly(ADP-ribose) polymerase-1 (PARP-1) rejoined both total DSBs and heat-released DSBs similar to normal cells. In summary, the presence of heat-labile sites have a substantial impact on DSB induction yields and DSB rejoining rates measured by pulsed-field gel electrophoresis, and HLS repair is independent of DNA-PKcs, XRCC1 and PARP.

  17. Overlapping double etch technique for evaluation of metallic alloys to stress corrosion cracking

    DOE Patents [OSTI]

    Not Available

    1980-05-28

    A double overlapping etch zone technique for evaluation of the resistance of metallic alloys to stress corrosion cracking is described. The technique involves evaluating the metallic alloy along the line of demarcation between an overlapping double etch zone and single etch zone formed on the metallic alloy surface.

  18. HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT SUMMARY OF COMBINED THERMAL & OPERATING LOADS

    SciTech Connect (OSTI)

    MACKEY, T.C.

    2006-03-17

    This report summarizes the results of the Double-Shell Tank Thermal and Operating Loads Analysis (TOLA) combined with the Seismic Analysis. This combined analysis provides a thorough, defensible, and documented analysis that will become a part of the overall analysis of record for the Hanford double-shell tanks (DSTs).

  19. Overlapping double etch technique for evaluation of metallic alloys to stress corrosion cracking

    DOE Patents [OSTI]

    Steeves, Arthur F.; Stewart, James C.

    1981-01-01

    A double overlapping etch zone technique for evaluation of the resistance of metallic alloys to stress corrosion cracking. The technique involves evaluating the metallic alloy along the line of demarcation between an overlapping double etch zone and single etch zone formed on the metallic alloy surface.

  20. Changes in the Zero-Point Energy of the Protons as the Source of the Binding Energy of Water to A-Phase DNA

    SciTech Connect (OSTI)

    Reiter, G. F.; Senesi, R.; Mayers, J.

    2010-10-01

    The measured changes in the zero-point kinetic energy of the protons are entirely responsible for the binding energy of water molecules to A phase DNA at the concentration of 6 water molecules/base pair. The changes in kinetic energy can be expected to be a significant contribution to the energy balance in intracellular biological processes and the properties of nano-confined water. The shape of the momentum distribution in the dehydrated A phase is consistent with coherent delocalization of some of the protons in a double well potential, with a separation of the wells of 0.2 Angst .

  1. Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Kowalski, Karol; Valiev, Marat

    2007-01-01

    High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

  2. Life cycle inventory analysis of regenerative thermal oxidation of air emissions from oriented strand board facilities in Minnesota - a perspective of global climate change

    SciTech Connect (OSTI)

    Nicholson, W.J.

    1997-12-31

    Life cycle inventory analysis has been applied to the prospective operation of regenerative thermal oxidation (RTO) technology at oriented strand board plants at Bemidji (Line 1) and Cook, Minnesota. The net system destruction of VOC`s and carbon monoxide, and at Cook a small quantity of particulate, has a very high environmental price in terms of energy and water use, global warming potential, sulfur and nitrogen oxide emissions, solids discharged to water, and solid waste deposited in landfills. The benefit of VOC destruction is identified as minor in terms of ground level ozone at best and possibly slightly detrimental. Recognition of environmental tradeoffs associated with proposed system changes is critical to sound decision-making. There are more conventional ways to address carbon monoxide emissions than combustion in RTO`s. In an environment in which global warming is a concern, fuel supplemental combustion for environmental control does not appear warranted. Consideration of non-combustion approaches to address air emission issues at the two operations is recommended. 1 ref., 5 tabs.

  3. Analysis of Strand-Specific RNA-Seq Data Using Machine Learning Reveals the Structures of Transcription Units in Clostridium thermocellum

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Chou, Wen-Chi; Ma, Qin; Yang, Shihui; Cao, Sha; Klingeman, Dawn M.; Brown, Steven D.; Xu, Ying

    2015-03-12

    The identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. A total of 2590 distinct TUs are predicted based on the four RNA-seq datasets.more » Moreover, among the predicted TUs, 44% have multiple genes. We assessed our prediction method on an independent set of RNA-seq data with longer reads. The evaluation confirmed the high quality of the predicted TUs. Functional enrichment analyses on a selected subset of the predicted TUs revealed interesting biology. To demonstrate the generality of the prediction method, we have also applied the method to RNA-seq data collected on Escherichia coli and achieved high prediction accuracies. The TU prediction program named SeqTU is publicly available athttps://code.google.com/p/seqtu/. We expect that the predicted TUs can serve as the baseline information for studying transcriptional and post-transcriptional regulation in C. thermocellum and other bacteria.« less

  4. DNA repair decline during mouse spermiogenesis results in the accumulation of heritable DNA damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Marchetti, Francesco; Wryobek, Andrew J

    2008-02-21

    The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7- 1 dbf). Analysis of chromosomalaberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

  5. DNA Repair Decline During Mouse Spermiogenesis Results in the Accumulation of Heritable DNA Damage

    SciTech Connect (OSTI)

    Marchetti, Francesco; Marchetti, Francesco; Wyrobek, Andrew J.

    2007-12-01

    The post-meiotic phase of mouse spermatogenesis (spermiogenesis) is very sensitive to the genomic effects of environmental mutagens because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. We hypothesized that repeated exposures to mutagens during this repair-deficient phase result in the accumulation of heritable genomic damage in mouse sperm that leads to chromosomal aberrations in zygotes after fertilization. We used a combination of single or fractionated exposures to diepoxybutane (DEB), a component of tobacco smoke, to investigate how differential DNA repair efficiencies during the three weeks of spermiogenesis affected the accumulation of DEB-induced heritable damage in early spermatids (21-15 days before fertilization, dbf), late spermatids (14-8 dbf) and sperm (7-1 dbf). Analysis of chromosomal aberrations in zygotic metaphases using PAINT/DAPI showed that late spermatids and sperm are unable to repair DEB-induced DNA damage as demonstrated by significant increases (P<0.001) in the frequencies of zygotes with chromosomal aberrations. Comparisons between single and fractionated exposures suggested that the DNA repair-deficient window during late spermiogenesis may be less than two weeks in the mouse and that during this repair-deficient window there is accumulation of DNA damage in sperm. Finally, the dose-response study in sperm indicated a linear response for both single and repeated exposures. These findings show that the differential DNA repair capacity of post-meioitic male germ cells has a major impact on the risk of paternally transmitted heritable damage and suggest that chronic exposures that may occur in the weeks prior to fertilization because of occupational or lifestyle factors (i.e, smoking) can lead to an accumulation of genetic damage in sperm and result in heritable chromosomal aberrations of paternal origin.

  6. Intermittent bursts induced by double tearing mode reconnection

    SciTech Connect (OSTI)

    Wei, Lai; Wang, Zheng-Xiong, E-mail: zxwang@dlut.edu.cn [Key Laboratory of Materials Modification by Beams of the Ministry of Education, School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China)

    2014-06-15

    Reversed magnetic shear (RMS) configuration is assumed to be the steady-state operation scenario for the future advanced tokamaks like International Thermonuclear Experimental Reactor. In this work, we numerically discover a phenomenon of violent intermittent bursts induced by self-organized double tearing mode (DTM) reconnection in the RMS configuration during the very long evolution, which may continuously lead to annular sawtooth crashes and thus badly impact the desired steady-state operation of the future advanced RMS tokamaks. The key process of the intermittent bursts in the off-axis region is similar to that of the typical sawtooth relaxation oscillation in the positive magnetic shear configuration. It is interestingly found that in the decay phase of the DTM reconnection, the zonal field significantly counteracts equilibrium field to make the magnetic shear between the two rational surfaces so weak that the residual self-generated vortices of the previous DTM burst are able to trigger a reverse DTM reconnection by curling the field lines.

  7. 137 Ba Double Gamma Decay Measurement with GAMMASPHERE

    SciTech Connect (OSTI)

    Merchn, E.; Moran, K.; Lister, C. J.; Chowdhury, P.; McCutchan, E. A.; Greene, J. P.; Zhu, S.; Lauritsen, T.; Carpenter, M. P.; Shearman, R.

    2015-05-28

    The study of the electromagnetic moments (EM), and decay probability, provides detailed information about nuclear wave functions. The well-know properties of EM interactions are good for extracting information about the motion of nucleons. Higher order EM processes always occur, but are usually too weak to be measured. In the case of a 0+ ? 0+ transitions, where a single gamma transition is forbidden, the simultaneous emission of two ?-rays has been studied. An interesting opportunity to further investigate 2-photon emission phenomena is by using a standard 137Cs source populating, via ?-decay, the J? = 11/2- isomeric state at 662 keV in 137Ba. In this case, two photon process can have contributions from quadrupole-quadrupole or dipole-octupole multipolarities in direct competition with the high multipolarity M4 decay. Since the yield of the double gamma decay is around six orders of magnitude less than the first order transition, very good statistics are needed in order to observe the phenomena and great care must be taken to suppress the first-order decay. The Gammasphere array is ideal since its configuration allows a good coverage of the angular distribution and the Compton events can be suppressed. Nevertheless the process to understand and eliminate the Compton background is a challenge. Geant4 simulations were carried out to help understand and correct for those factors.

  8. Purification of lanthanides for double beta decay experiments

    SciTech Connect (OSTI)

    Polischuk, O. G.; Barabash, A. S.; Belli, P.; Bernabei, R.; Boiko, R. S.; Danevich, F. A.; Mokina, V. M.; Poda, D. V.; Tretyak, V. I.; Cappella, F.; Incicchitti, A.; Cerulli, R.; Laubenstein, M.; Nisi, S.

    2013-08-08

    There are several potentially double beta active isotopes among the lanthanide elements. However, even high purity grade lanthanide compounds contain {sup 238}U, {sup 226}Ra and {sup 232,228}Th typically on the level of ? (0.1 - 1) Bq/kg. The liquid-liquid extraction technique was used to remove traces of U, Ra and Th from CeO{sub 2}, Nd{sub 2}O{sub 3} and Gd{sub 2}O{sub 3}. The radioactive contamination of the samples before and after the purification was tested by using ultra-low-background HPGe ? spectrometry at the underground Gran Sasso National Laboratories of the INFN (Italy). After the purification the radioactive contamination of gadolinium oxide by Ra and Th was decreased at least one order of magnitude. The efficiency of the approach to purify cerium oxide from Ra was on same level, while the radioactive contamination of neodymium sample before and after the purification is below the sensitivity of analytical methods. The purification method is much less efficient for chemically very similar radioactive elements like lanthanum, lutetium and actinium. R and D of the methods to remove the pollutions with improved efficiency is in progress.

  9. 137 Ba Double Gamma Decay Measurement with GAMMASPHERE

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Merchán, E.; Moran, K.; Lister, C. J.; Chowdhury, P.; McCutchan, E. A.; Greene, J. P.; Zhu, S.; Lauritsen, T.; Carpenter, M. P.; Shearman, R.

    2015-05-28

    The study of the electromagnetic moments (EM), and decay probability, provides detailed information about nuclear wave functions. The well-know properties of EM interactions are good for extracting information about the motion of nucleons. Higher order EM processes always occur, but are usually too weak to be measured. In the case of a 0+ → 0+ transitions, where a single gamma transition is forbidden, the simultaneous emission of two γ-rays has been studied. An interesting opportunity to further investigate 2-photon emission phenomena is by using a standard 137Cs source populating, via β-decay, the Jπ = 11/2- isomeric state at 662 keVmore » in 137Ba. In this case, two photon process can have contributions from quadrupole-quadrupole or dipole-octupole multipolarities in direct competition with the high multipolarity M4 decay. Since the yield of the double gamma decay is around six orders of magnitude less than the first order transition, very good statistics are needed in order to observe the phenomena and great care must be taken to suppress the first-order decay. The Gammasphere array is ideal since its configuration allows a good coverage of the angular distribution and the Compton events can be suppressed. Nevertheless the process to understand and eliminate the Compton background is a challenge. Geant4 simulations were carried out to help understand and correct for those factors.« less

  10. Analysis of Residential Demand Response and Double-Auction Markets

    SciTech Connect (OSTI)

    Fuller, Jason C.; Schneider, Kevin P.; Chassin, David P.

    2011-10-10

    Demand response and dynamic pricing programs are expected to play increasing roles in the modern Smart Grid environment. While direct load control of end-use loads has existed for decades, price driven response programs are only beginning to be explored at the distribution level. These programs utilize a price signal as a means to control demand. Active markets allow customers to respond to fluctuations in wholesale electrical costs, but may not allow the utility to control demand. Transactive markets, utilizing distributed controllers and a centralized auction can be used to create an interactive system which can limit demand at key times on a distribution system, decreasing congestion. With the current proliferation of computing and communication resources, the ability now exists to create transactive demand response programs at the residential level. With the combination of automated bidding and response strategies coupled with education programs and customer response, emerging demand response programs have the ability to reduce utility demand and congestion in a more controlled manner. This paper will explore the effects of a residential double-auction market, utilizing transactive controllers, on the operation of an electric power distribution system.

  11. Plasmons in spatially separated double-layer graphene nanoribbons

    SciTech Connect (OSTI)

    Bagheri, Mehran, E-mail: mh-bagheri@sbu.ac.ir [Laser and Plasma Research Institute, Shahid Beheshti University, G. C., Evin, Tehran 19835-63113 (Iran, Islamic Republic of); Bahrami, Mousa [ICFO-Institut de Ciencies Fotoniques, Parc Mediterrani de la Tecnologia, 08860 Castelldefels (Barcelona) (Spain)

    2014-05-07

    Motivated by innovative progresses in designing multi-layer graphene nanostructured materials in the laboratory, we theoretically investigate the Dirac plasmon modes of a spatially separated double-layer graphene nanoribbon system, made up of a vertically offset armchair and metallic graphene nanoribbon pair. We find striking features of the collective excitations in this novel Coulomb correlated system, where both nanoribbons are supposed to be either intrinsic (undoped/ungated) or extrinsic (doped/gated). In the former, it is shown the low-energy acoustical and the high-energy optical plasmon modes are tunable only by the inter-ribbon charge separation. In the later, the aforementioned plasmon branches are modified by the added doping factor. As a result, our model could be useful to examine the existence of a linear Landau-undamped low-energy acoustical plasmon mode tuned via the inter-ribbon charge separation as well as doping. This study might also be utilized for devising novel quantum optical waveguides based on the Coulomb coupled graphene nanoribbons.

  12. MAJORANA Neutrinoless Double-Beta Decay DUSEL R&D

    SciTech Connect (OSTI)

    Wilkerson, John F.

    2009-09-04

    The Majorana research and development is addressing key issues and risks related to the collaboration's goal of undertaking a search for neutrinoless double-beta decay (0{nu}{beta}{beta}) in {sup 76}Ge using an array of hyper-pure Ge-diodes (HPGe). The observation of this decay would provide critical insight into our understanding of neutrinos, yielding definitive evidence that neutrinos are Majorana particles and providing information on the absolute mass of neutrinos. Achieving sensitivities to 0{nu}{beta}{beta} decay half-lives on the order of 10{sup 26} years requires ultra-low backgrounds in the 2039 keV region where a 0{nu}{beta}{beta} decay peak would be observed. The goal of our R&D program has been to demonstrate the feasibility of all components of Majorana and to provide an integrated evaluation framework, allowing for optimization of these components in terms of background, background suppression, and signal detection efficiency and acceptance. This report covers work carried out by Majorana collaboration members at the University of Washington as part of the overall Majorana collaboration activities. Specifically the Majorana group at the University of Washington was involved in moving forward on demonstrating technology for clean large-scale cryostats and mounting the HPGe crystals in low-mass holders. The UW activities included assistance in the procurement and assembly of an electroforming system for large size cryostats, and design and fabrication of prototype crystal mounting hardware.

  13. Tribimaximal neutrino mixing and neutrinoless double beta decay

    SciTech Connect (OSTI)

    Hirsch, M.; Morisi, S.; Valle, J. W. F. [AHEP Group, Institut de Fisica Corpuscular-- C.S.I.C./Universitat de Valencia, Edificio Institutos de Paterna, Apt 22085, E-46071 Valencia (Spain)

    2008-11-01

    We present a tribimaximal lepton mixing scheme where the neutrinoless double beta decay rate has a lower bound which correlates with the ratio {alpha}{identical_to}{delta}m{sub sol}{sup 2}/{delta}m{sub atm}{sup 2} well determined by current data, as well as with the unknown Majorana CP phase {phi}{sub 12} characterizing the solar neutrino subsystem. For the special value {phi}{sub 12}=({pi}/2) (opposite CP-sign neutrinos) the {beta}{beta}{sub 0{nu}} rate vanishes at tree level when {delta}m{sub sol}{sup 2}/{delta}m{sub atm}{sup 2}=3/80, only allowed at 3{sigma}. For all other cases the rate is nonzero, and lies within current and projected experimental sensitivities close to {phi}{sub 12}=0. We suggest two model realizations of this scheme in terms of A{sub 4}xZ{sub 2} and A{sub 4}xZ{sub 4} flavor symmetries.

  14. Search for Neutrinoless Double Beta Decay with the CUORE experiment

    SciTech Connect (OSTI)

    Gorla, P. [Laboratori Nazionali del Gran Sasso-INFN, S.S. 17 bis, km 18-910 67010 Assergi (Italy)

    2009-12-17

    CUORE is a next generation experiment aimed at the detection of neutrinoless Double Beta Decay of the nuclide {sup 130}Te. The experiment, which will take place in the Gran Sasso National Laboratory (Italy), will look for this rare decay using the macrobolometric technique with a prospected array of 988 detectors. Each bolometer will be constituted by a 5x5x5 cm{sup 3} TeO{sub 2} crystal, for a total mass of about 200 kg of {sup 130}Te, and will be maintained at a temperature of 10 mK. CUORE will probe the effective mass of the neutrino with a sensitivity of a few tens of meV. If an excess of counts are observed above background at the 2.5 MeV corresponding to the Q-value of the decay, CUORE will answer several questions that are still open in the field of neutrino physics, such as the determination of the particle's Majorana nature and of the absolute mass scale. A prototype for CUORE in Gran Sasso, named CUORICINO, has just closed after five years proving its importance as a stand-alone experiment.

  15. Single Helix to Double Gyroid in Chiral Block Copolymers

    SciTech Connect (OSTI)

    C Chen; H Hsueh; Y Chiang; R Ho; S Akasaka; H Hasegawa

    2011-12-31

    An order-order phase transition of chiral block copolymers (BCPs*) from single helix to double gyroid (H* {yields} G) through a nucleation and growth process was demonstrated. The H* and G phases can be obtained by solution casting from fast and slow solvent evaporation, respectively, suggesting that the H* phase is a metastable phase. Consequently, the coexistence of H* and G phases can be found in the solution-cast samples from intermediate solvent evaporation. To truly examine the transition mechanism of the H* {yields} G, electron tomography was carried out to directly visualize the morphological evolution in real space, in particular, the transition zone at interface. Unlike the mechanisms for the transitions of block copolymers (BCPs) by considering the interdomain spacing matching, a significant mismatch in the lattices for the H* {yields} G was found. Consequently, the transition may require an adjustment on the geometric dimensions to justify corresponding lattice mismatch. As a result, the morphological observations from electron tomography offer new insights into BCP phase transitions.

  16. Flame and flow characteristics of double concentric jets

    SciTech Connect (OSTI)

    Huang, R.F.; Yang, J.T.; Lee, P.C.

    1997-01-01

    The characteristic flame and flow modes of a double concentric type of combustor possessing a central air jet and an annular propane gas are experimentally studied. Subject to the effects of the gravitational, inertial, and pressure forces, the cold flow is classified into three primary patterns: annular fountain, unstable fountain, and recirculation bubble flows. Using direct and schlieren photography techniques, the flames in the velocity domain of annulus and central jets are systematically classified into several characteristic modes. At low central jet velocity, a central flame enclosed in a annular diffusion flame might exist. At high central jet velocity, only the annular flames exist. The existence of the central flame dominates the flame and flow behaviors at low central jet velocity. The interaction between the central jet and the recirculation bubble in the near wake region dominates the flame characteristics at high central jet velocity. The interaction between the flame behavior and the flow patterns in each characteristic mode is comprehensively discussed. The temperature profiles are probed by a fine-wire thermocouple. The radial temperature profiles for each characteristic flame mode at various levels are presented to show the thermal structures.

  17. Interstellar scintillation of the double pulsar J07373039

    SciTech Connect (OSTI)

    Rickett, B. J.; Coles, W. A.; Nava, C. F.; McLaughlin, M. A.; Ransom, S. M.; Camilo, F.; Ferdman, R. D.; Kramer, M.; Lyne, A. G.; Freire, P. C. C.; Stairs, I. H.

    2014-06-01

    We report a series of observations of the interstellar scintillation (ISS) of the double pulsar J07373039 over the course of 18 months. As in earlier work, the basic phenomenon is the variation in the ISS caused by the changing transverse velocities of each pulsar, the ionized interstellar medium (IISM), and the Earth. The transverse velocity of the binary system can be determined both by very long baseline interferometry and timing observations. The orbital velocity and inclination is almost completely determined from timing observations, but the direction of the orbital angular momentum is not known. Since the Earth's velocity is known, and can be compared with the orbital velocity by its effect on the timescale of the ISS, we can determine the orientation ? of the pulsar orbit with respect to equatorial coordinates (? = 65 2). We also resolve the ambiguity (i = 88.7 or 91.3) in the inclination of the orbit deduced from the measured Shapiro delay by our estimate i = 88.1 0.5. This relies on the analysis of the ISS over both frequency and time, and provides a model for the location, anisotropy, turbulence level, and transverse phase gradient of the IISM. We find that the IISM can be well-modeled during each observation, typically of a few orbital periods, but its turbulence level and mean velocity vary significantly over the 18 months.

  18. Heavy-fermion instability in double-degenerate plasmas

    SciTech Connect (OSTI)

    Akbari-Moghanjoughi, M.

    2012-07-15

    In this work, we study the propagations of normal frequency modes for quantum hydrodynamic waves in the linear limit and introduce a new kind of instability in a double-degenerate plasma. Three different regimes, namely, low, intermediate, and high magnetic field strengths are considered which span the applicability of the work to a wide variety of environments. Distinct behavior is observed for different regimes, for instance, in the laboratory-scale field regime no frequency-mode instability occurs unlike those of intermediate and high magnetic-field strength regimes. It is also found that the instability of this kind is due to the heavy-fermions which appear below a critical effective-mass parameter ({mu}{sub cr}={radical}(3)) and that the responses of the two (lower and upper frequency) modes to fractional effective-mass change in different effective-mass parameter ranges (below and above the critical value) are quite opposite to each other. It is shown that the heavy-fermion instability due to extremely high magnetic field such as that encountered for a neutron-star crust can lead to confinement of stable propagations in both lower and upper frequency modes to the magnetic poles. Current study can have important implications for linear wave dynamics in both laboratory and astrophysical environments possessing high magnetic fields.

  19. A compact double-pass Raman backscattering amplifier/compressor

    SciTech Connect (OSTI)

    Ren, J.; Li, S.; Morozov, A.; Suckewer, S.; Yampolsky, N. A.; Malkin, V. M.; Fisch, N. J.

    2008-05-15

    The enhancement of stimulated Raman backscattering (SRBS) amplification was demonstrated by introducing a plasma density gradient along the pump and the seed interaction path and by a novel double-pass design. The energy transfer efficiency was significantly improved to a level of 6.4%. The seed pulse was amplified by a factor of more than 20 000 from the input in a 2 mm long plasma, which also exceeded the intensity of the pump pulse by 2 orders of magnitude. This was accompanied by very effective pulse compression, from 500 fs to 90 fs in the first pass measurements and in the second pass down to approximately 50 fs, as it is indicated by the energy-pulse duration relation. Further improvements to the energy transfer efficiency and the SRBS performance by extending the region of resonance is also discussed where a uniform {approx}4 mm long plasma channel for SRBS was generated by using two subsequent laser pulses in an ethane gas jet.

  20. Double helix boron-10 powder thermal neutron detector

    DOE Patents [OSTI]

    Wang, Zhehui; Morris, Christopher L.; Bacon, Jeffrey D.

    2015-06-02

    A double-helix Boron-10 powder detector having intrinsic thermal neutron detection efficiency comparable to 36'' long, 2-in diameter, 2-bar Helium-3 detectors, and which can be used to replace such detectors for use in portal monitoring, is described. An embodiment of the detector includes a metallic plate coated with Boron-10 powder for generating alpha and Lithium-7 particles responsive to neutrons impinging thereon supported by insulators affixed to at least two opposing edges; a grounded first wire wound in a helical manner around two opposing insulators; and a second wire having a smaller diameter than that of the first wire, wound in a helical manner around the same insulators and spaced apart from the first wire, the second wire being positively biased. A gas, disposed within a gas-tight container enclosing the plate, insulators and wires, and capable of stopping alpha and Lithium-7 particles and generating electrons produces a signal on the second wire which is detected and subsequently related to the number of neutrons impinging on the plate.

  1. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  2. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  3. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  4. Intriguing DNA Editor Has a Structural Trigger

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Intriguing DNA Editor Has a Structural Trigger Print A powerful new tool for genome editing and gene regulation has emerged in the form of a family of enzymes known as Cas9. Cas9 could become an even more valuable tool with the creation of the first detailed picture of its three-dimensional shape. An international collaboration used x-ray crystallography to produce high-resolution structures of two major types of Cas9 enzymes. Combined with electron microscopy, the results point the way to the

  5. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, Frank A. (Livermore, CA); Gray, Joe W. (Livermore, CA)

    1988-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide or Hoechst 33258 is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as halodeoxy-uridine (HdU), more specifically bromodeoxyuridine (BrdU) is used as a probe for the measurement of HdU or BrdU uptake by the cells as a measure of DNA synthesis.

  6. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect (OSTI)

    Greulich-Bode, Karin M.; Wang, Mei; Rhein, Andreas P.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-12-04

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  7. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    SciTech Connect (OSTI)

    Greulich-Bode, Karin; Wang, Mei; Rhein, Andreas; Weier, Jingly; Weier, Heinz-Ulli

    2008-12-16

    Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-?B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation and characterization, the assembly of physical maps for model organisms or in studies on gene rearrangements.

  8. Photocatalytic probing of DNA sequence by using TiO{sub 2}/dopamine-DNA triads.

    SciTech Connect (OSTI)

    Liu, J.; de la Garza, L.; Zhang, L.; Dimitrijevic, N. M.; Zuo, X.; Tiede, D. M.; Rajh, T.

    2007-10-15

    A method to control charge transfer reaction in DNA using hybrid nanometer-sized TiO{sub 2} nanoparticles was developed. In this system extended charge separation reflects the sequence of DNA and was measured using metallic silver deposition or by photocurrent response. Light-induced extended charge separation in these systems was found to be dependent on the DNA-bridge length and sequence. The yield of photocatalytic deposition of silver was studied in systems having GG accepting sites imbedded in AT runs at varying distances from the TiO{sub 2} nanoparticle surface. Weak distance dependence of charge separation indicative of a hole hopping through mediating adenine (A) sites was found. The quantum yield of silver deposition in the system having a GG accepting site placed 8.5 {angstrom} from the nanoparticle surface was found to be {Phi} = 0.70 (70%) and {Phi} = 0.56 (56%) for (A){sub n} and (AT){sub n/2} bridge, respectively. Hole injection to GG trapping sites as far as 70 {angstrom} from a nanoparticle surface in the absence of G hopping sites was measured. Introduction of G hopping sites increased the efficiency of hole injection. The efficiency of photocatalytic deposition of metallic silver was found to be sensitive to the presence of a single nucleobase mismatch in the DNA sequence.

  9. DISCOVERY OF GIANT RELIC RADIO LOBES STRADDLING THE CLASSICAL DOUBLE RADIO GALAXY 3C452

    SciTech Connect (OSTI)

    Sirothia, S. K.; Gopal-Krishna; Wiita, Paul J. E-mail: krishna@ncra.tifr.res.in

    2013-03-01

    We report the discovery of a pair of megaparsec size radio lobes of extremely steep spectrum straddling the well-known classical double radio source 3C452. The existence of such fossil lobes was unexpected since for the past several decades this powerful radio galaxy has been regarded as a textbook example of an edge-brightened double radio source of Fanaroff-Riley type II (FR II), which we now show to be a bona fide ''double-double'' radio galaxy (DDRG). Thus, 3C452 presents a uniquely robust example of recurrent nuclear activity in which the restarted jets are expanding non-relativistically within the relic synchrotron plasma from an earlier active phase and hence the inner double fed by them has evolved into a perfectly normal FR II radio source. This situation contrasts markedly with the strikingly narrow inner doubles observed in a few other DDRGs that have been interpreted in terms of compression of the synchrotron plasma of the relic outer lobes at the relativistic bow-shocks driven by the near ballistic propagation of the two inner jets through the relic plasma. A key ramification of this finding is that it cautions against the currently widespread use of FR II classical double radio sources for testing cosmological models and unification schemes for active galactic nuclei.

  10. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism Print Wednesday, 26 January 2011 00:00 Type II topoisomerases are molecular machines that regulate DNA supercoiling and separate interlocked chromosomes. These enzymes are also exploited clinically as targets of antibiotics and anticancer therapeutics. Researchers at ALS Beamline 8.3.1 imaged type II topoisomerase's ordinarily short-lived state in which it is linked

  11. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Protein Bridges DNA Base and Nucleotide Excision Repair Pathways Print Wednesday, 28 October 2009 00:00 Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition of alkyl groups (alkylation). Alkyltransferase-like proteins (ATLs) can do the same, but they lack the reactive cysteine residue that allows the alkyltransferase function, and the mechanism for cell protection has

  12. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine

    Office of Scientific and Technical Information (OSTI)

    lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition (Journal Article) | SciTech Connect Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition Citation Details In-Document Search Title: Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition DNA arranges into rectangular columnar superlattices between

  13. DNA release from lipoplexes by anionic lipids: correlation with lipid

    Office of Scientific and Technical Information (OSTI)

    mesomorphism, interfacial curvature, and membrane fusion (Journal Article) | SciTech Connect DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion Citation Details In-Document Search Title: DNA release from lipoplexes by anionic lipids: correlation with lipid mesomorphism, interfacial curvature, and membrane fusion DNA release from lipoplexes is an essential step during lipofection and is probably a result of charge

  14. DNA-Binding Mechanism in Prokaryotic Partition Complex Formation

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of

  15. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, C.M.; Berg, D.E.; Wang, G.

    1997-07-08

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed. 4 figs.

  16. Transposon-containing DNA cloning vector and uses thereof

    DOE Patents [OSTI]

    Berg, Claire M. (W. Willington, CT); Berg, Douglas E. (St. Louis, MO); Wang, Gan (Storrs, CT)

    1997-01-01

    The present invention discloses a rapid method of restriction mapping, sequencing or localizing genetic features in a segment of deoxyribonucleic acid (DNA) that is up to 42 kb in size. The method in part comprises cloning of the DNA segment in a specialized cloning vector and then isolating nested deletions in either direction in vivo by intramolecular transposition into the cloned DNA. A plasmid has been prepared and disclosed.

  17. Sense and sensitivity of double beta decay experiments

    SciTech Connect (OSTI)

    Gmez-Cadenas, J.J.; Martn-Albo, J.; Sorel, M.; Ferrario, P.; Monrabal, F.; Muoz, J. [Instituto de Fsica Corpuscular (IFIC), CSIC and Universidad de Valencia, Calle Catedrtico Jos Beltrn 2, 46071 Valencia (Spain); Novella, P. [Centro de Investigaciones Energticas, Medioambientales y Tecnolgicas (CIEMAT), Avda. Complutense 22, 28040 Madrid (Spain); Poves, A., E-mail: gomez@mail.cern.ch, E-mail: justo.martin-albo@ific.uv.es, E-mail: sorel@ific.uv.es, E-mail: paola.ferrario@ific.uv.es, E-mail: francesc.monrabal@ific.uv.es, E-mail: jmunoz@ific.uv.es, E-mail: pau.novella@ciemat.es, E-mail: alfredo.poves@uam.es [Dpto. de de Fsica Terica and IFT-UAM/CSIC, Universidad Autnoma de Madrid, Calle Nicols Cabrera 13-15, 28049 Madrid (Spain)

    2011-06-01

    The search for neutrinoless double beta decay is a very active field in which the number of proposals for next-generation experiments has proliferated. In this paper we attempt to address both the sense and the sensitivity of such proposals. Sensitivity comes first, by means of proposing a simple and unambiguous statistical recipe to derive the sensitivity to a putative Majorana neutrino mass, m{sub ??}. In order to make sense of how the different experimental approaches compare, we apply this recipe to a selection of proposals, comparing the resulting sensitivities. We also propose a ''physics-motivated range'' (PMR) of the nuclear matrix elements as a unifying criterium between the different nuclear models. The expected performance of the proposals is parametrized in terms of only four numbers: energy resolution, background rate (per unit time, isotope mass and energy), detection efficiency, and ?? isotope mass. For each proposal, both a reference and an optimistic scenario for the experimental performance are studied. In the reference scenario we find that all the proposals will be able to partially explore the degenerate spectrum, without fully covering it, although four of them (KamLAND-Zen, CUORE, NEXT and EXO) will approach the 50 meV boundary. In the optimistic scenario, we find that CUORE and the xenon-based proposals (KamLAND-Zen, EXO and NEXT) will explore a significant fraction of the inverse hierarchy, with NEXT covering it almost fully. For the long term future, we argue that {sup 136}Xe-based experiments may provide the best case for a 1-ton scale experiment, given the potentially very low backgrounds achievable and the expected scalability to large isotope masses.

  18. Axisymmetric oscillation modes of a double droplet system

    SciTech Connect (OSTI)

    Ramalingam, Santhosh K.; Basaran, Osman A.

    2010-11-15

    A double droplet system (DDS) consists of a sessile and a pendant drop that are coupled through a liquid filled cylindrical hole in a plate of thickness d. For a small hole radius R, equilibrium shapes of both drops are sections of spheres. While DDSs have a number of applications in microfluidics, a DDS oscillating about its equilibrium state can be used as a fast focusing liquid lens. Here, a DDS consisting of an isothermal, incompressible Newtonian fluid of constant density p and constant viscosity u that is surrounded by a gas is excited by oscillating in time (a) the pressure in the gas surrounding either drop (pressure excitation), (b) the plate perpendicular to its plane (axial excitation), and (c) the hole radius (radial excitation). In contrast to previous works that assumed transient drop shapes are spherical, they are determined here by simulation and used to identify the natural modes of axisymmetric oscillations from resonances observed during frequency sweeps with DDSs for which the combined volume V of the two drops is less than (4/3)?R3. Pressure and axial excitations are found to have identical responses but axial and radial excitations are shown to excite different modes. These modes are compared to those exhibited by single pendant (sessile) drop systems. In particular, while a single pendant (sessile) drop has one additional oscillation mode compared to a free drop, a DDS is found to exhibit roughly twice as many oscillation modes as a pendant (sessile) drop. The effects of dimensionless volume V/R3, dimensionless plate thickness d/R, and Ohnesorge number Oh =?/??R? , where ? is the surface tension of the DDS-gas interface, on the resonance frequencies are also investigated.

  19. Axisymmetric oscillation modes of a double droplet system

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Ramalingam, Santhosh K.; Basaran, Osman A.

    2010-11-15

    A double droplet system (DDS) consists of a sessile and a pendant drop that are coupled through a liquid filled cylindrical hole in a plate of thickness d. For a small hole radius R, equilibrium shapes of both drops are sections of spheres. While DDSs have a number of applications in microfluidics, a DDS oscillating about its equilibrium state can be used as a fast focusing liquid lens. Here, a DDS consisting of an isothermal, incompressible Newtonian fluid of constant density p and constant viscosity u that is surrounded by a gas is excited by oscillating in time (a) themore » pressure in the gas surrounding either drop (pressure excitation), (b) the plate perpendicular to its plane (axial excitation), and (c) the hole radius (radial excitation). In contrast to previous works that assumed transient drop shapes are spherical, they are determined here by simulation and used to identify the natural modes of axisymmetric oscillations from resonances observed during frequency sweeps with DDSs for which the combined volume V of the two drops is less than (4/3)πR3. Pressure and axial excitations are found to have identical responses but axial and radial excitations are shown to excite different modes. These modes are compared to those exhibited by single pendant (sessile) drop systems. Specifically, while a single pendant (sessile) drop has one additional oscillation mode compared to a free drop, a DDS is found to exhibit roughly twice as many oscillation modes as a pendant (sessile) drop. The effects of dimensionless volume V/R3, dimensionless plate thickness d/R, and Ohnesorge number Oh =μ/√ρRσ , where σ is the surface tension of the DDS-gas interface, on the resonance frequencies are also investigated.« less

  20. DETAILED MOLECULAR OBSERVATIONS TOWARD THE DOUBLE HELIX NEBULA

    SciTech Connect (OSTI)

    Torii, K.; Enokiya, R.; Hasegawa, K.; Kudo, N.; Fukui, Y.; Morris, M. R.

    2014-07-01

    The Double Helix Nebula (DHN), located 100 pc above Sgr A* in the Galactic center (GC), is a unique structure whose morphology suggests it is a magnetic feature. Recent molecular observations toward the DHN revealed two candidate molecular counterparts of the DHN at radial velocities of 35 km s{sup 1} and 0 km s{sup 1} and discussed the model in which the DHN has its origin at the circumnuclear disk in the GC. In this paper, new CO observations toward the DHN using the Caltech Submillimeter Observatory and Mopra telescopes are presented. The higher-resolution observations of ?1 pc scale reveal the detailed distributions and kinematics of the two CO counterparts (the 0 km s{sup 1} and 35 km s{sup 1} features) and provide new information on their physical conditions. As a result, we find that the 0 km s{sup 1} feature with a mass of 3.3 10{sup 4} M {sub ?} coincides with the infrared emission of the DHN, indicating clear association with the DHN. The association of the 35 km s{sup 1} feature, with a mass of 0.8 10{sup 4} M {sub ?}, is less clear compared with the 0 km s{sup 1} feature, but the complementary distribution between the molecular gas and the DHN and velocity variation along the DHN support its association with the DHN. The two molecular features are highly excited, as shown by the relatively high CO J = 2-1/J = 1-0 intensity ratios of ?1.0, and have kinetic temperatures of ?30 K, consistent with the typical molecular clouds in the GC.

  1. QCAD simulation and optimization of semiconductor double quantum dots

    SciTech Connect (OSTI)

    Nielsen, Erik; Gao, Xujiao; Kalashnikova, Irina; Muller, Richard Partain; Salinger, Andrew Gerhard; Young, Ralph Watson

    2013-12-01

    We present the Quantum Computer Aided Design (QCAD) simulator that targets modeling quantum devices, particularly silicon double quantum dots (DQDs) developed for quantum qubits. The simulator has three di erentiating features: (i) its core contains nonlinear Poisson, e ective mass Schrodinger, and Con guration Interaction solvers that have massively parallel capability for high simulation throughput, and can be run individually or combined self-consistently for 1D/2D/3D quantum devices; (ii) the core solvers show superior convergence even at near-zero-Kelvin temperatures, which is critical for modeling quantum computing devices; (iii) it couples with an optimization engine Dakota that enables optimization of gate voltages in DQDs for multiple desired targets. The Poisson solver includes Maxwell- Boltzmann and Fermi-Dirac statistics, supports Dirichlet, Neumann, interface charge, and Robin boundary conditions, and includes the e ect of dopant incomplete ionization. The solver has shown robust nonlinear convergence even in the milli-Kelvin temperature range, and has been extensively used to quickly obtain the semiclassical electrostatic potential in DQD devices. The self-consistent Schrodinger-Poisson solver has achieved robust and monotonic convergence behavior for 1D/2D/3D quantum devices at very low temperatures by using a predictor-correct iteration scheme. The QCAD simulator enables the calculation of dot-to-gate capacitances, and comparison with experiment and between solvers. It is observed that computed capacitances are in the right ballpark when compared to experiment, and quantum con nement increases capacitance when the number of electrons is xed in a quantum dot. In addition, the coupling of QCAD with Dakota allows to rapidly identify which device layouts are more likely leading to few-electron quantum dots. Very efficient QCAD simulations on a large number of fabricated and proposed Si DQDs have made it possible to provide fast feedback for design comparison and optimization.

  2. Structural and mechanistic insights into Mcm2-7 double-hexamer...

    Office of Scientific and Technical Information (OSTI)

    Laboratory (BNL), Upton, NY (United States); Stony Brook Univ., Stony Brook, NY (United States) Imperial College Faculty of Medicine, London (United Kingdom). DNA ...

  3. DNA-Based Optomechanical Molecular Motor

    SciTech Connect (OSTI)

    McCullagh, Martin; Franco, Ignacio; Ratner, Mark A.; Schatz, George C.

    2011-03-16

    An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol-1 of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.

  4. Three-Dimensional Modeling and Simulation of DNA Hybridization...

    Office of Scientific and Technical Information (OSTI)

    Three-Dimensional Modeling and Simulation of DNA Hybridization Kinetics and Mass Transport as Functions of Temperature in a Microfluidic Channel. Citation Details In-Document...

  5. Nanoscale topographical replication of graphene architecture by artificial DNA nanostructures

    SciTech Connect (OSTI)

    Moon, Y.; Seo, S.; Park, J.; Park, T.; Ahn, J. R., E-mail: jrahn@skku.edu [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Shin, J.; Dugasani, S. R. [Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Woo, S. H. [College of Pharmacy, Chungnam National University, Daejeon 305-764 (Korea, Republic of); Park, S. H., E-mail: sunghapark@skku.edu [Department of Physics, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-06-09

    Despite many studies on how geometry can be used to control the electronic properties of graphene, certain limitations to fabrication of designed graphene nanostructures exist. Here, we demonstrate controlled topographical replication of graphene by artificial deoxyribonucleic acid (DNA) nanostructures. Owing to the high degree of geometrical freedom of DNA nanostructures, we controlled the nanoscale topography of graphene. The topography of graphene replicated from DNA nanostructures showed enhanced thermal stability and revealed an interesting negative temperature coefficient of sheet resistivity when underlying DNA nanostructures were denatured at high temperatures.

  6. DNA-NV-030-09-03 | Open Energy Information

    Open Energy Info (EERE)

    Info Energy Sector Geothermal energy Environmental Analysis Type DNA Applicant Dusty Miller LLC Geothermal Area Gabbs Valley Geothermal Area Project Location Nevada Project Phase...

  7. When DNA Needs to Stand Up and Be Counted

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    biomolecules must be properly oriented to perform their biological function. In other words, the DNA literally must stand up to be counted. Understanding both the attachment...

  8. Ionic switch controls the DNA state in phage λ

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Li, Dong; Liu, Ting; Zuo, Xiaobing; Li, Tao; Qiu, Xiangyun; Evilevitch, Alex

    2015-06-19

    We have recently found that DNA packaged in phage λ undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious λ particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated λ-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid bymore » changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ‘switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37°C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. The results suggest a remarkable adaptation of phage λ to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.« less

  9. Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine...

    Office of Scientific and Technical Information (OSTI)

    Columnar DNA superlattices in lamellar O-ethylphosphatidylcholine lipoplexes. Mechanism of the gel-liquid crystalline lipid phase transition Citation Details In-Document Search ...

  10. Evolutionary theory, web-search technology combine for DNA analysis

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sequedex: bioinformatics breakthrough Evolutionary theory, web-search technology combine ... Evolutionary theory, web-search technology combine for DNA analysis Bioinformatics ...

  11. Fleet DNA Project - Data Dictionary for Public Download Files

    SciTech Connect (OSTI)

    Duran, A.; Burton, E.; Kelly, K.; Walkowicz, K.

    2014-09-01

    Reference document for the Fleet DNA results data shared on the NREL public website. The document includes variable definitions and descriptions to assist users in understanding data.

  12. DNA release from lipoplexes by anionic lipids: correlation with...

    Office of Scientific and Technical Information (OSTI)

    Research Org: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL ... Subject: 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; CAPACITY; DNA; ENERGY ...

  13. TWC Committee: Draft Advice re: Double-Shell Tank AY-102, v.4

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    5/15/2013 TWC Committee: Draft Advice re: Double-Shell Tank AY-102, v.4 Dunning, Panesko, Holland, Cimon, Larsen Page 1 of 2 Draft Advice re: Double-Shell Tank AY-102 and Leaking Single-Shell Tanks Background: The U.S. Department of Energy - Office of River Protection (DOE-ORP) announced at the Tank Waste Committee meeting on April 10, 2013 that the cause of the leak in the bottom of double- shell tank AY-102 was due to corrosive materials on the tank floor. This waste has now leaked into the

  14. The H2 Double-Slit Experiment: Where Quantum and Classical Physics Meet

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    The H2 Double-Slit Experiment: Where Quantum and Classical Physics Meet The H2 Double-Slit Experiment: Where Quantum and Classical Physics Meet Print Wednesday, 27 February 2008 00:00 For the first time, an international research team carried out a double-slit experiment in H2, the smallest and simplest molecule. Thomas Young's original experiment in 1803 passed light through two slits cut in a solid thin plate. In the groundbreaking experiment performed at ALS Beamlines 4.0 and 11.0.1, the

  15. Pinning Down the Mechanism of Neutrinoless Double {beta} Decay with Measurements in Different Nuclei

    SciTech Connect (OSTI)

    Deppisch, Frank [Deutsches Elektronen-Synchrotron (DESY), D-22603 Hamburg (Germany); Paes, Heinrich [Department of Physics and Astronomy, University of Alabama, Tuscaloosa, Alabama 35487 (United States)

    2007-06-08

    A measurement of neutrinoless double beta decay in one isotope does not allow us to determine the underlying physics mechanism. We discuss the discrimination of mechanisms for neutrinoless double beta decay by comparing ratios of half-life measurements for different isotopes. Six prominent examples for specific new physics contributions to neutrinoless double beta decay are analyzed. We find that the change in corresponding ratios of half lives varies from 60% for supersymmetric models up to a factor of 5-20 for extra-dimensional and left-right-symmetric mechanisms.

  16. Searching for neutrinoless double-beta decay of {sup 130}Te with CUORE

    Office of Scientific and Technical Information (OSTI)

    (Journal Article) | SciTech Connect Searching for neutrinoless double-beta decay of {sup 130}Te with CUORE Citation Details In-Document Search Title: Searching for neutrinoless double-beta decay of {sup 130}Te with CUORE Neutrinoless double-beta (0#23;{nu}{beta}{beta}#12;#12;) decay is a hypothesized lepton-number-violating process that offers the only known means of asserting the possible Majorana nature of neutrino mass. The Cryogenic Underground Observatory for Rare Events (CUORE) is an

  17. Microporous SiO{sub 2} with huge electric-double-layer capacitance for

    Office of Scientific and Technical Information (OSTI)

    low-voltage indium tin oxide thin-film transistors (Journal Article) | SciTech Connect SciTech Connect Search Results Journal Article: Microporous SiO{sub 2} with huge electric-double-layer capacitance for low-voltage indium tin oxide thin-film transistors Citation Details In-Document Search Title: Microporous SiO{sub 2} with huge electric-double-layer capacitance for low-voltage indium tin oxide thin-film transistors Electric-double-layer (EDL) effect is observed in microporous SiO{sub 2}

  18. HANFORD DOUBLE SHELL TANK (DST) THERMAL & SEISMIC PROJECT BUCKLING EVALUATION METHODS & RESULTS FOR THE PRIMARY TANKS

    SciTech Connect (OSTI)

    MACKEY, T.C.

    2006-03-17

    This report documents a detailed buckling evaluation of the primary tanks in the Hanford double shell waste tanks. The analysis is part of a comprehensive structural review for the Double-Shell Tank Integrity Project. This work also provides information on tank integrity that specifically responds to concerns raise by the Office of Environment, Safety, and Health (ES&H) Oversight (EH-22) during a review (in April and May 2001) of work being performed on the double-shell tank farms, and the operation of the aging waste facility (AWF) primary tank ventilation system.

  19. The nature of fluctuations in a double arc argon-nitrogen plasma jet

    SciTech Connect (OSTI)

    Tu Xin; Yan Jianhua; Yu Liang; Cen, Kefa; Cheron, Bruno

    2007-09-24

    The dynamic behavior of the double arc argon-nitrogen plasma jet is investigated by combined means of the fast Fourier transform, correlation function, and Wigner distribution. The restrike mode is identified as the fluctuation behavior in an argon-nitrogen plasma jet. The Fourier spectra exhibit two characteristic frequencies of 150 Hz and 4.1 kHz, which indicates that the nature of fluctuations in the double arc argon-nitrogen plasma can be ascribed to the power supply undulation and both arc roots motion on the anode channels. It is further found that the double anode torch could inhibit and reduce the restrike phenomenon.

  20. EERE Success Story-Nebraska: Company More than Doubles Annual Sales and

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Employees | Department of Energy Nebraska: Company More than Doubles Annual Sales and Employees EERE Success Story-Nebraska: Company More than Doubles Annual Sales and Employees August 21, 2013 - 12:38pm Addthis Hexagon Lincoln, of Lincoln, Nebraska, has more than doubled its workforce and added a fourth shift for 24-hour/7-days-a-week operation to accommodate growing demand for its carbon fiber composite tanks. With EERE support, Hexagon developed a new trailer that uses high-strength