Sample records for dna double-strand break

  1. Quantitative measurement and modeling of the DNA damage signaling network : DNA double-strand breaks

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2009-01-01T23:59:59.000Z

    DNA double-strand breaks (DSB) are one of the major mediators of chemotherapy-induced cytotoxicity in tumors. Cells that experience DNA damage can initiate a DNA damage-mediated cell-cycle arrest, attempt to repair the ...

  2. Induction of linear tracks of DNA double-strand breaks by -particle irradiation of

    E-Print Network [OSTI]

    Cai, Long

    Induction of linear tracks of DNA double- strand breaks by -particle irradiation of cells Jan Stap1,4, Przemek M Krawczyk1,4, Carel H Van Oven1, Gerrit W Barendsen2, Jeroen Essers3, Roland Kanaar3 & Jacob describe a procedure for induction of easily recognizable linear arrays of DSBs in nuclei of adherent

  3. A MICROBEAM STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS

    E-Print Network [OSTI]

    stained with different dyes. Directly irradiated cells have exhibited the expected early and linear dose by assessing DNA double-strand break (DSB) formation in situ with the rapid and sensitive c-H2AX focus formation assay. Utilising the Columbia University single-cell microbeam system to deliver 2 or 20

  4. Processing of 3'-Phosphoglycolate-Terminated DNA Double-StrandBreaks by Artemis Nuclease

    SciTech Connect (OSTI)

    Povrik, Lawrence F.; Zhou, Tong; Zhou, Ruizhe; Cowan, Morton J.; Yannone, Steven M.

    2005-10-01T23:59:59.000Z

    The Artemis nuclease is required for V(D)J recombination and for repair of an as yet undefined subset of radiation-induced DNA double-strand breaks. To assess the possibility that Artemis functions on oxidatively modified double-strand break termini, its activity toward model DNA substrates, bearing either 3{prime}-hydroxyl or 3{prime}-phosphoglycolate moieties, was examined. A 3{prime}-phosphoglycolate had little effect on Artemis-mediated trimming of long 3{prime} overhangs (>9 nucleotides), which were efficiently trimmed to 4-5 nucleotides. However, 3{prime}-phosphoglycolates on overhangs of 4-5 bases promoted selective Artemis-mediated trimming of a single 3{prime}-terminal nucleotide, while at least 2 nucleotides were trimmed from identical hydroxyl-terminated substrates. Artemis also efficiently removed a single nucleotide from a phosphoglycolate-terminated 3-base 3{prime} overhang, while leaving an analogous hydroxyl-terminated overhang largely intact. Such removal was dependent upon Ku, DNA-dependent protein kinase, and ATP. Together, these data suggest that Artemis-mediated cleavage of 3{prime} overhangs requires a minimum of 2 nucleotides, or a nucleotide plus a phosphoglycolate, 3{prime} to the cleavage site. Shorter 3{prime}-phosphoglycolate-terminated overhangs and blunt ends were also processed by Artemis, but much less efficiently. Consistent with the in vitro substrate specificity of Artemis, human cells lacking Artemis exhibited hypersensitivity to X-rays, bleomycin and neocarzinostatin, which all induce 3{prime}-phosphoglycolate-terminated double-strand breaks. Collectively, these results suggest that 3{prime}-phosphoglycolate termini and/or specific classes of DNA ends that arise from such blocked termini are relevant Artemis substrates in vivo.

  5. 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. [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Iwaki, Takafumi [Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103 (Japan); Mori, Toshiaki [Radiation Research Center, Osaka Prefecture University, Sakai 599-8570 (Japan); Yoshikawa, Kenichi [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394 (Japan)

    2013-05-07T23:59:59.000Z

    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.

  6. Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

    SciTech Connect (OSTI)

    Povirk, Lawrence; Yannone, Steven M.; Khan, Imran S.; Zhou, Rui-Zhe; Zhou, Tong; Valerie, Kristoffer; F., Lawrence

    2008-02-18T23:59:59.000Z

    Previous work showed that, in the presence of DNA-PK, Artemis slowly trims 3'-phosphoglycolate-terminated blunt ends. To examine the trimming reaction in more detail, long internally labeled DNA substrates were treated with Artemis. In the absence of DNA-PK, Artemis catalyzed extensive 5' {yields} 3' exonucleolytic resection of double-stranded DNA. This resection required a 5'-phosphate but did not require ATP, and was accompanied by endonucleolytic cleavage of the resulting 3' overhang. In the presence of DNA-PK, Artemis-mediated trimming was more limited, was ATP-dependent, and did not require a 5'-phosphate. For a blunt end with either a 3'-phosphoglycolate or 3'-hydroxyl terminus, endonucleolytic trimming of 2-4 nucleotides from the 3'-terminal strand was accompanied by trimming of 6 nucleotides from the 5'-terminal strand. The results suggest that autophosphorylated DNA-PK suppresses the exonuclease activity of Artemis toward blunt-ended DNA, and promotes slow and limited endonucleolytic trimming of the 5'-terminal strand, resulting in short 3' overhangs that are trimmed endonucleolytically. Thus, Artemis and DNA-PK can convert terminally blocked DNA ends of diverse geometry and chemical structure to a form suitable for polymerase mediated patching and ligation, with minimal loss of terminal sequence. Such processing could account for the very small deletions often found at DNA double-strand break repair sites.

  7. Crystal Structure of E. coli RecE Protein Reveals a Toroidal Tetramer for Processing Double-Stranded DNA Breaks

    SciTech Connect (OSTI)

    Zhang, Jinjin; Xing, Xu; Herr, Andrew B.; Bell, Charles E.; (OSU); (UCIN)

    2009-07-21T23:59:59.000Z

    Escherichia coli RecE protein is part of the classical RecET recombination system that has recently been used in powerful new methods for genetic engineering. RecE binds to free double-stranded DNA (dsDNA) ends and processively digests the 5{prime}-ended strand to form 5{prime}-mononucleotides and a 3{prime}-overhang that is a substrate for single strand annealing promoted by RecT. Here, we report the crystal structure of the C-terminal nuclease domain of RecE at 2.8 {angstrom} resolution. RecE forms a toroidal tetramer with a central tapered channel that is wide enough to bind dsDNA at one end, but is partially plugged at the other end by the C-terminal segment of the protein. Four narrow tunnels, one within each subunit of the tetramer, lead from the central channel to the four active sites, which lie about 15 {angstrom} from the channel. The structure, combined with mutational studies, suggests a mechanism in which dsDNA enters through the open end of the central channel, the 5{prime}-ended strand passes through a tunnel to access one of the four active sites, and the 3{prime}-ended strand passes through the plugged end of the channel at the back of the tetramer.

  8. 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

    2010-06-29T23:59:59.000Z

    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.

  9. The Impact of Individual In Vivo Repair of DNA Double-Strand Breaks on Oral Mucositis in Adjuvant Radiotherapy of Head-and-Neck Cancer

    SciTech Connect (OSTI)

    Fleckenstein, Jochen, E-mail: rajfle@uks.eu [Department of Radiotherapy and Radiation Oncology, Saarland University Medical School, Homburg (Germany); Kuehne, Martin; Seegmueller, Katharina; Derschang, Sarah; Melchior, Patrick [Department of Radiotherapy and Radiation Oncology, Saarland University Medical School, Homburg (Germany); Graeber, Stefan [Institute for Medical Biometry, Epidemiology und Medical Informatics (IMBEI), Saarland University Medical School, Homburg (Germany); Fricke, Andreas; Ruebe, Claudia E.; Ruebe, Christian [Department of Radiotherapy and Radiation Oncology, Saarland University Medical School, Homburg (Germany)

    2011-12-01T23:59:59.000Z

    Purpose: To evaluate the impact of individual in vivo DNA double-strand break (DSB) repair capacity on the incidence of severe oral mucositis in patients with head-and-neck cancer undergoing adjuvant radiotherapy (RT) or radiochemotherapy (RCT). Patients and Methods: Thirty-one patients with resected head-and-neck cancer undergoing adjuvant RT or RCT were examined. Patients underwent RT of the primary tumor site and locoregional lymph nodes with a total dose of 60-66 Gy (single dose 2 Gy, five fractions per week). Chemotherapy consisted of two cycles of cisplatin and 5-fluorouracil. To assess DSB repair, {gamma}-H2AX foci in blood lymphocytes were quantified before and 0.5 h, 2.5 h, 5 h, and 24 h after in vivo radiation exposure (the first fraction of RT). World Health Organization scores for oral mucositis were documented weekly and correlated with DSB repair. Results: Sixteen patients received RT alone; 15 patients received RCT. In patients who developed Grade {>=} 3 mucositis (n = 18) the amount of unrepaired DSBs 24 h after radiation exposure and DSB repair half-times did not differ significantly from patients with Grade {<=}2 mucositis (n = 13). Patients with a proportion of unrepaired DSBs after 24 h higher than the mean value + one standard deviation had an increased incidence of severe oral mucositis. Conclusions: Evaluation of in vivo DSB repair by determination of {gamma}-H2AX foci loss is feasible in clinical practice and allows identification of patients with impaired DSB repair. The incidence of oral mucositis is not closely correlated with DSB repair under the evaluated conditions.

  10. Creating Directed Double-strand Breaks with the Ref Protein A NOVEL RecA-DEPENDENT NUCLEASE FROM BACTERIOPHAGE P1*S

    E-Print Network [OSTI]

    Cox, Michael M.

    tar- geted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required

  11. auger electron-induced double-strand: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  12. Site-Selective Binding of Nanoparticles to Double-Stranded DNA via Peptide Nucleic Acid "Invasion"

    SciTech Connect (OSTI)

    Stadler, A.L.; van der Lelie, D.; Sun, D.; Maye, M. M.; Gang, O.

    2011-04-01T23:59:59.000Z

    We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

  13. A novel high-throughput in-cell Western assay for the quantitative measurement of signaling dynamics in DNA damage signaling networks : cell decision processes in response to DNA double strand breaks

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2006-01-01T23:59:59.000Z

    Following exposure to DNA damage, cells initiate a stress response involving multiple protein kinase signaling cascades. The DNA damage response results in one of several possible cell-fate decisions, or cellular responses: ...

  14. Sequence-Enabled Reassembly of -Lactamase (SEER-LAC): A Sensitive Method for the Detection of Double-Stranded DNA

    E-Print Network [OSTI]

    Ghosh, Indraneel

    Sequence-Enabled Reassembly of -Lactamase (SEER-LAC): A Sensitive Method for the Detection the development of a new methodology for the detection of specific double- stranded DNA sequences. We previously of a predefined DNA sequence. This system, designated sequence-enabled reassembly (SEER), was demonstrated

  15. Mechanistic studies of bleomycin-mediated double-stranded DNA cleavage and structural studies of DNA containing normal and 4'-oxidized abasic sites

    E-Print Network [OSTI]

    Chen, Jingyang, Ph. D. Massachusetts Institute of Technology

    2006-01-01T23:59:59.000Z

    In order to examine the role of partial intercalation in double-stranded (ds) DNA cleavage mediated by a single bleomycin (BLM), a bulky group ([-cyclodextrin) was chemically attached to the polyamine tail of BLM A5 to ...

  16. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23T23:59:59.000Z

    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.

  17. Local compression properties of double-stranded DNA based on a dynamic simulation

    E-Print Network [OSTI]

    Xiaoling Lei; Wenpeng Qi; Haiping Fang

    2013-03-13T23:59:59.000Z

    The local mechanical properties of DNA are believed to play an important role in their biological functions and DNA-based nanomechanical devices. Using a simple sphere-tip compression system, the local radial mechanical properties of DNA are systematically studied by changing the tip size. The compression simulation results for the 16 nm diameter sphere tip are well consistent with the experimental results. With the diameter of the tip decreasing, the radial compressive elastic properties under external loads become sensitive to the tip size and the local DNA conformation. There appears a suddenly force break in the compression-force curve when the sphere size is less than or equal to 12 nm diameter. The analysis of the hydrogen bonds and base stacking interaction shows there is a local unwinding process occurs. During the local unwinding process, first the hydrogen bonds between complement base pairs are broken. With the compression aggregating, the local backbones in the compression center are unwound from the double helix conformation to a kind of parallel conformation. This local unwinding behavior deducing by external loads is helpful to understand the biological process, and important to DNA-based nanomechanical devices.

  18. Intense photoluminescence from dried double-stranded DNA and single-walled carbon nanotube hybrid

    SciTech Connect (OSTI)

    Ito, M.; Kobayashi, T.; Ito, Y.; Hayashida, T.; Nii, D.; Umemura, K.; Homma, Y. [Department of Physics, Tokyo University of Science, Tokyo 162-8601 (Japan)

    2014-01-27T23:59:59.000Z

    Semiconducting single-walled carbon nanotubes (SWNTs) show near-infrared photoluminescence (PL) when they are individually isolated. This was an obstacle to use photonic properties of SWNTs on a solid surface. We show that SWNTs wrapped with DNA maintain intense PL under the dry conditions. SWNTs are well isolated individually by DNA even when the DNA-SWNT hybrids are agglomerated. This finding opens up application of SWNTs to photonic devices.

  19. adducts strand breaks: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  20. ancient human dna: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  1. ancient dna studies: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  2. DNA Repair Decline During Mouse Spermiogenesis Results in the Accumulation of Heritable DNA Damage

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    van Buul, D.G. de Rooij, DNA double-strand breaks and gamma-for the transition proteins in DNA strand break repair, FEBSBoissonneault, Stimulation of DNA repair by the spermatidal

  3. DNA repair decline during mouse spermiogenesis results in the accumulation of heritable DNA damage

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    van Buul, D.G. de Rooij, DNA double-strand breaks and gamma-for the transition proteins in DNA strand break repair, FEBSBoissonneault, Stimulation of DNA repair by the spermatidal

  4. ORIGINAL PAPER Ionizing radiation induces DNA double-strand breaks in bystander primary

    E-Print Network [OSTI]

    fibroblasts Mykyta V Sokolov1,2 , Lubomir B Smilenov3 , Eric J Hall3 , Igor G Panyutin1 , William M Bonner*,4

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

    DOE Patents [OSTI]

    Cantor, Charles R. (Boston, MA); Ito, Takashi (Chiba, JP); Smith, Cassandra L. (Boston, MA)

    1996-01-01T23:59:59.000Z

    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. DNA Double-Strand Breaks Form in Bystander Cells after Microbeam Irradiation of Three-dimensional Human Tissue Models

    E-Print Network [OSTI]

    Brenner, David Jonathan

    Research Accelerator Facility, Center for Radiological Research, College of Physicians and Surgeons Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada; and 3 Radiological implications for cancer radiother- apy and diagnostic radiology as well as for human health in general

  7. PAXX, a paralog of XRCC4 and XLF, interacts with Ku to promote DNA double-strand break repair

    E-Print Network [OSTI]

    Ochi, Takashi; Blackford, Andrew N.; Coates, Julia; Jhujh, Satpal; Mehmood, Shahid; Tamura, Naoka; Travers, Jon; Wu, Qian; Draviam, Viji M.; Robinson, Carol V.; Blundell, Tom L.; Jackson, Stephen P.

    2015-01-09T23:59:59.000Z

    ) for 2 hours with end-to-end mixing at 4 °C. Beads were washed five times in IP buffer before resuspension in 2x SDS loading buffer. 5% input lysate was loaded alongside unless otherwise stated. Surface plasmon resonance SPR experiments were performed...

  8. Polymorphisms in genes involved in DNA double-strand break repair pathway and susceptibility to benzene-induced hematotoxicity

    E-Print Network [OSTI]

    California at Berkeley, University of

    to benzene-induced hematotoxicity Min Shen1,Ă, Qing Lan1 , Luoping Zhang2 , Stephen Chanock1,3 , Guilan Li4; Email: shenmi@mail.nih.gov Benzene is a recognized hematotoxicant and carcinogen that produces genotoxic and indirectly by benzene metabolites. DSB may lead to chromosome aberrations, apoptosis and hematopoietic

  9. DNA end resection by Dna2Sgs1RPA and its stimulation by Top3Rmi1 and Mre11Rad50Xrs2

    E-Print Network [OSTI]

    Kowalczykowski, Stephen C.

    LETTERS DNA end resection by Dna2­Sgs1­RPA and its stimulation by Top3­Rmi1 and Mre11­Rad50­Xrs2. Campbell3 & Stephen C. Kowalczykowski1,2 The repair of DNA double-strand breaks (DSBs) by homologous to generate a 39-single- stranded DNA (ssDNA) overhang, which becomes a substrate forthe

  10. Synthesis of DNA

    DOE Patents [OSTI]

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

    2008-11-18T23:59:59.000Z

    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.

  11. DNA damage responses in the context of the cell division cycle

    E-Print Network [OSTI]

    Giunta, Simona

    2010-11-16T23:59:59.000Z

    During my PhD, I have investigated aspects of the DNA damage response (DDR) in the context of three different cellular scenarios: DNA damage signalling in response to double-strand breaks during mitosis, coordination of DNA replication with DNA...

  12. Identification, Exploitation and Manipulation of BRCA1-Dependent DNA Double-Strand Break and Interstrand Crosslink Repair in Breast and Ovarian Cancer Therapy

    E-Print Network [OSTI]

    Stecklein, Shane Richard

    2012-05-12T23:59:59.000Z

    required by my academic journey. Your encouragement, support and love will always be the greatest treasures of my life. vi Acknowledgements To my mentor, Dr. Roy Jensen, I can never fully express my gratitude... hope to continue working in this discipline for the rest of my life. To my co-mentor, Dr. Fariba Behbod, I thank you for your unwavering support and enthusiasm throughout my graduate career. Your decision to come to KUMC has truly been a blessing...

  13. Dose-dependent misrejoining of radiation-induced DNA double-strand breaks in human fibroblasts: Experimental and theoretical study for high and low LET radiation

    E-Print Network [OSTI]

    Rydberg, Bjorn; Cooper, Brian; Cooper, Priscilla K.; Holley, William; Chatterjee, Aloke

    2004-01-01T23:59:59.000Z

    S. Kim, and R. M. Myers. Radiation hybrid mapping: a somaticformulation of dual radiation action. Radiat. Res. 75: 471-High-Linear Energy Transfer Radiation in Human Fibroblasts.

  14. The DNA Single-Strand Break Repair Machinery Facilitates CAF-1-Mediated Histone Deposition at Oxidative DNA Strand Breaks

    E-Print Network [OSTI]

    Arman Nabatiyan; Zhihong Zeng; Keith W. Caldecott

    2012-02-01T23:59:59.000Z

    Oxidative DNA single strand breaks arise continuously in cells and defects in their repair have been implicated in neurological disease. While much progress has been made in understanding how chromosomal single strand breaks are repaired little is known about the changes chromatin structure that accompany this process. Here, we show that nascent recombinant histone H3.1 protein accumulates and is deposited into chromatin at sites of DNA strand breakage in quiescent human cells following oxidative stress, and that core components of the single-strand break repair machinery are required for this process. We show that the SSBR sensor and scaffold proteins poly (ADP-ribose) polymerase and XRCC1 facilitate accumulation of chromatin assembly factor-1 (CAF-1) at sites of oxidative DNA strand breakage, which in turn mediates the deposition of Histone H3.1. We also demonstrate that depletion of CAF-1 slows global rates of DNA strand break repair in quiescent cells following oxidative stress, demonstrating that single-strand break repair and histone deposition are tightly coordinated processes. These data describe a novel role for the DNA singlestrand break repair machinery and implicate histone turnover as a core component of the cellular response of quiescent cells to oxidative damage.

  15. DNA Repair Alterations in Children With Pediatric Malignancies: Novel Opportunities to Identify Patients at Risk for High-Grade Toxicities

    SciTech Connect (OSTI)

    Ruebe, Claudia E., E-mail: claudia.ruebe@uks.e [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Fricke, Andreas; Schneider, Ruth; Simon, Karin; Kuehne, Martin; Fleckenstein, Jochen [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany); Graeber, Stefan [Institute of Medical Biometrics, Epidemiology and Medical Informatics, Saarland University, Homburg/Saar (Germany); Graf, Norbert [Department of Pediatric Hematology and Oncology, Saarland University, Homburg/Saar (Germany); Ruebe, Christian [Department of Radiation Oncology, Saarland University, Homburg/Saar (Germany)

    2010-10-01T23:59:59.000Z

    Purpose: To evaluate, in a pilot study, the phosphorylated H2AX ({gamma}H2AX) foci approach for identifying patients with double-strand break (DSB) repair deficiencies, who may overreact to DNA-damaging cancer therapy. Methods and Materials: The DSB repair capacity of children with solid cancers was analyzed compared with that of age-matched control children and correlated with treatment-related normal-tissue responses (n = 47). Double-strand break repair was investigated by counting {gamma}H2AX foci in blood lymphocytes at defined time points after irradiation of blood samples. Results: Whereas all healthy control children exhibited proficient DSB repair, 3 children with tumors revealed clearly impaired DSB repair capacities, and 2 of these repair-deficient children developed life-threatening or even lethal normal-tissue toxicities. The underlying mutations affecting regulatory factors involved in DNA repair pathways were identified. Moreover, significant differences in mean DSB repair capacity were observed between children with tumors and control children, suggesting that childhood cancer is based on genetic alterations affecting DSB repair function. Conclusions: Double-strand break repair alteration in children may predispose to cancer formation and may affect children's susceptibility to normal-tissue toxicities. Phosphorylated H2AX analysis of blood samples allows one to detect DSB repair deficiencies and thus enables identification of children at risk for high-grade toxicities.

  16. Asymmetric quantum transport in a double-stranded Kronig-Penney model

    E-Print Network [OSTI]

    Taksu Cheon; Sergey S. Poghosyan

    2015-03-03T23:59:59.000Z

    We introduce a double-stranded Kronig-Penney model and analyze its transport properties. The asymmetric fluxes between two strands with suddenly alternating localization patterns are found as the energy is varied. The zero-size limit of the internal lines connecting two strands is examined using quantum graph vertices with four edges. We also consider a two-dimensional Kronig-Penney lattice with two types of alternating layers with $\\delta$ and $\\delta'$ connections, and show that the existence of energy bands in which the quantum flux can flow only in selected directions.

  17. CtIP tetramer assembly is required for DNA-end resection and repair

    E-Print Network [OSTI]

    Davies, Owen R.; Forment, Josep V.; Sun, Meidai; Belotserkovskaya, Rimma; Coates, Julia; Galanty, Yaron; Demir, Mukerrem; Morton, Christopher; Rzechorzek, Neil; Jackson, Stephen P.; Pellegrini, Luca

    2015-01-05T23:59:59.000Z

    1     CtIP tetramer assembly is required for DNA-end resection and repair Owen R. Davies1,4*, Josep V. Forment1,2,3*, Meidai Sun1, Rimma Belotserkovskaya1,2, Julia Coates1,2, Yaron Galanty1,2, Mukerrem Demir1,2, Christopher Morton1... that a CtIP tetramer architecture is essential for effective DSB repair by homologous recombination. Keywords CtIP/RBBP8, double-strand DNA break repair, DNA-end resection, gene conversion, homologous recombination. 3...

  18. Structural basis of double-stranded RNA recognition by the RIG-I like receptor MDA5

    E-Print Network [OSTI]

    Strong, Roland K.

    Structural basis of double-stranded RNA recognition by the RIG-I like receptor MDA5 Xiaojun Li online 14 June 2009 Keywords: Innate immunity Nucleic acid receptor MDA5 CTD Crystal structure a b s t r a c t RIG-I, MDA5 and LGP2 are cytosolic pattern recognition receptors detecting single

  19. Mitigating security issues in the evolving DNA synthesis industry

    E-Print Network [OSTI]

    Turlington, Ralph Donald, III

    2013-01-01T23:59:59.000Z

    DNA synthesis technologies are advancing at exponential rates, with production of ever longer, more complex, and less expensive sequences of double stranded DNA. This has fostered development of industrial scale design, ...

  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.

    2011-06-01T23:59:59.000Z

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

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What's PossibleRadiationImplementingnpitcheResearchPhysics LabwildfiresScott Taylor,

  2. Electrochemical DNA Hybridization Detection Using DNA Dohyoung Kwon,a

    E-Print Network [OSTI]

    Kwak, Juhyoun

    Full Paper Electrochemical DNA Hybridization Detection Using DNA Cleavage Dohyoung Kwon,a Kyuwon method for detection of DNA hybridization using enzymatic cleavage. The strategy is based on that S1 nuclease is able to specifically cleave only single strand DNA, but not double strand DNA. The capture

  3. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07T23:59:59.000Z

    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.

  4. aluminum strand coating: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov by assessing DNA double-strand break (DSB) formation in situ with the rapid and...

  5. 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)

    2014-01-17T23:59:59.000Z

    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.

  6. Mutations Abrogating VP35 Interaction with Double-Stranded RNA Render Ebola Virus Avirulent in Guinea Pigs

    SciTech Connect (OSTI)

    Prins, Kathleen C.; Delpeut, Sebastien; Leung, Daisy W.; Reynard, Olivier; Volchkova, Valentina A.; Reid, St. Patrick; Ramanan, Parameshwaran; Cárdenas, Washington B.; Amarasinghe, Gaya K.; Volchkov, Viktor E.; Basler, Christopher F. (CNRS-INSERM); (Mount Sinai Hospital); (LB-Ecuador); (Iowa State)

    2010-10-11T23:59:59.000Z

    Ebola virus (EBOV) protein VP35 is a double-stranded RNA (dsRNA) binding inhibitor of host interferon (IFN)-{alpha}/{beta} responses that also functions as a viral polymerase cofactor. Recent structural studies identified key features, including a central basic patch, required for VP35 dsRNA binding activity. To address the functional significance of these VP35 structural features for EBOV replication and pathogenesis, two point mutations, K319A/R322A, that abrogate VP35 dsRNA binding activity and severely impair its suppression of IFN-{alpha}/{beta} production were identified. Solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography reveal minimal structural perturbations in the K319A/R322A VP35 double mutant and suggest that loss of basic charge leads to altered function. Recombinant EBOVs encoding the mutant VP35 exhibit, relative to wild-type VP35 viruses, minimal growth attenuation in IFN-defective Vero cells but severe impairment in IFN-competent cells. In guinea pigs, the VP35 mutant virus revealed a complete loss of virulence. Strikingly, the VP35 mutant virus effectively immunized animals against subsequent wild-type EBOV challenge. These in vivo studies, using recombinant EBOV viruses, combined with the accompanying biochemical and structural analyses directly correlate VP35 dsRNA binding and IFN inhibition functions with viral pathogenesis. Moreover, these studies provide a framework for the development of antivirals targeting this critical EBOV virulence factor.

  7. Double-strand DNA-templated formation of copper nanoparticles as fluorescent probe for label free nuclease enzyme detection

    E-Print Network [OSTI]

    Tan, Weihong

    cleavage activity. Thus, a label-free strategy for sensitive detection of nuclease has been developed B.V. All rights reserved. 1. Introduction As promising substitutes for organic dyes and quantum dots epithelial cervical cancer cells (HeLa cells) using fluorescent gold nanoparticles which emitted a stable

  8. ExpandplusCrystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA

    SciTech Connect (OSTI)

    M Langelier; J Planck; S Roy; J Pascal

    2011-12-31T23:59:59.000Z

    Poly(ADP-ribose) polymerase-1 (PARP-1) has two homologous zinc finger domains, Zn1 and Zn2, that bind to a variety of DNA structures to stimulate poly(ADP-ribose) synthesis activity and to mediate PARP-1 interaction with chromatin. The structural basis for interaction with DNA is unknown, which limits our understanding of PARP-1 regulation and involvement in DNA repair and transcription. Here, we have determined crystal structures for the individual Zn1 and Zn2 domains in complex with a DNA double strand break, providing the first views of PARP-1 zinc fingers bound to DNA. The Zn1-DNA and Zn2-DNA structures establish a novel, bipartite mode of sequence-independent DNA interaction that engages a continuous region of the phosphodiester backbone and the hydrophobic faces of exposed nucleotide bases. Biochemical and cell biological analysis indicate that the Zn1 and Zn2 domains perform distinct functions. The Zn2 domain exhibits high binding affinity to DNA compared with the Zn1 domain. However, the Zn1 domain is essential for DNA-dependent PARP-1 activity in vitro and in vivo, whereas the Zn2 domain is not strictly required. Structural differences between the Zn1-DNA and Zn2-DNA complexes, combined with mutational and structural analysis, indicate that a specialized region of the Zn1 domain is re-configured through the hydrophobic interaction with exposed nucleotide bases to initiate PARP-1 activation.

  9. DNA cleavage and opening reactions of human topoisomerase II are regulated via Mg2-

    E-Print Network [OSTI]

    Hohng, Sung Chul

    DNA cleavage and opening reactions of human topoisomerase II are regulated via Mg2ţ- mediated dynamic bending of gate-DNA Sanghwa Leea,b,1 , Seung-Ryoung Junga,b,1 , Kang Heoa,b , Jo Ann W. Bylc intrinsic topological problems of double- stranded DNA. As part of its essential cellular functions, the en

  10. ageing human fibroblasts: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  11. ataxia telangiectasia fibroblasts: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  12. acidic fibroblast growth: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  13. adult-onset primary open-angle: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  14. angiogenic gene-modified fibroblasts: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  15. acid-induced fibroblast cell: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  16. asymptomatic primary hyperparathyroidism: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  17. aliphatic primary diamines: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  18. autologous fibroblast metabolism: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  19. acid induces human: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  20. arthritis synovial fibroblasts: Topics by E-print Network

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

    STUDY OF DNA DOUBLE-STRAND BREAKS IN BYSTANDER PRIMARY HUMAN FIBROBLASTS L. B. Smilenov-or-nothing manner(7) . Bystander cells exhibit a variety of characteristics of...

  1. Detailed Architecture of a DNA Translocating Machine: The High-resolution Structure of the Bacteriophage

    E-Print Network [OSTI]

    Rossmann, Michael G.

    . The structure suggests a translocation mechanism in which the longitudinal displacement of the DNA along its of the best known. f29 is a small double- stranded DNA bacteriophage that infects Bacillus subtilis cells from its distal part. Electron microscopy studies, based on two- dimensional projections and three

  2. 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)

    2006-08-15T23:59:59.000Z

    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.

  3. 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

    2009-09-07T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

    Hingerty, B.E.

    1992-07-01T23:59:59.000Z

    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.

  5. Collection, focusing, and metering of DNA in microchannels using addressable electrode arrays for portable low-power bioanalysis

    E-Print Network [OSTI]

    Shaikh, Faisal

    2008-10-10T23:59:59.000Z

    the funding for this work. vii NOMENCLATURE DNA Deoxyribonucleic Acid dsDNA Double Stranded DNA ssDNA Single Stranded DNA EDTA Ethylene Diamine Tetracetic Acid TBE Tris-Borate EDTA BME Beta Mercapto Ethanol PCB Printed Circuit Board DI Deionized... through a USB cable using a Personal Computer........................................................................................ 66 Figure 27 Top level block diagram of the FPGA based portable analysis device showing flow of information...

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

    DOE Patents [OSTI]

    Karger, Barry L. (Newton, MA); Thilly, William G. (Winchester, MA); Foret, Frantisek (Malden, MA); Khrapko, Konstaintin (Brookline, MA); Koehavong, Phouthone (Pittsburgh, PA); Cohen, Aharon S. (Newton, MA); Giese, Roger W. (Quincy, MA)

    1997-01-01T23:59:59.000Z

    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.

  7. 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.

    1997-05-27T23:59:59.000Z

    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.

  8. DNA . DNA

    E-Print Network [OSTI]

    1. DNA . , . , . . DNA DNA . , DNA . DNA . DNA . DNA DNA DNA . DNA [6, 7, 8]. DNA . DNA NACST/Sim DNA/DNA

  9. Effects of Sequence Disorder on DNA Looping and Cyclization

    E-Print Network [OSTI]

    Yuri O. Popov; Alexei V. Tkachenko

    2007-06-08T23:59:59.000Z

    Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of cyclization probabilities. For short DNA segments, the range of the distribution reaches several orders of magnitude for even completely random sequences. The ensemble averaged values of the cyclization probability are also calculated, and the connection to the recent experiments is discussed.

  10. C-terminal region of DNA ligase IV drives XRCC4/DNA ligase IV complex to chromatin

    SciTech Connect (OSTI)

    Liu, Sicheng; Liu, Xunyue; Kamdar, Radhika Pankaj; Wanotayan, Rujira; Sharma, Mukesh Kumar [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)] [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan); Adachi, Noritaka [Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027 (Japan)] [Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027 (Japan); Matsumoto, Yoshihisa, E-mail: yoshim@nr.titech.ac.jp [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)] [Research Laboratory for Nuclear Reactors and Department of Nuclear Engineering, Graduate School of Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550 (Japan)

    2013-09-20T23:59:59.000Z

    Highlights: •Chromatin binding of XRCC4 is dependent on the presence of DNA ligase IV. •C-terminal region of DNA ligase IV alone can recruit itself and XRCC4 to chromatin. •Two BRCT domains of DNA ligase IV are essential for the chromatin binding of XRCC4. -- Abstract: DNA ligase IV (LIG4) and XRCC4 form a complex to ligate two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). It is not fully understood how these proteins are recruited to DSBs. We recently demonstrated radiation-induced chromatin binding of XRCC4 by biochemical fractionation using detergent Nonidet P-40. In the present study, we examined the role of LIG4 in the recruitment of XRCC4/LIG4 complex to chromatin. The chromatin binding of XRCC4 was dependent on the presence of LIG4. The mutations in two BRCT domains (W725R and W893R, respectively) of LIG4 reduced the chromatin binding of LIG4 and XRCC4. The C-terminal fragment of LIG4 (LIG4-CT) without N-terminal catalytic domains could bind to chromatin with XRCC4. LIG4-CT with W725R or W893R mutation could bind to chromatin but could not support the chromatin binding of XRCC4. The ability of C-terminal region of LIG4 to interact with chromatin might provide us with an insight into the mechanisms of DSB repair through NHEJ.

  11. ESI/TOF Measurements of a Noncovalent Complex between Lactose Repressor Protein (LacI) and Double-Stranded DNA Containing its Specific Operator Sequence

    E-Print Network [OSTI]

    Ens, Werner

    M buffer solution. Initial attempts to observe the protein tetramer were unsuccessful (as in the case rather broad peaks for both dimer and tetramer. The tetramer appears in two separate envelopes, suggesting that the the charge states 20 to 22 between m/z 7000 and 8000 represent the native tetramer

  12. DNA adsorption at liquid/solid interfaces

    E-Print Network [OSTI]

    Carine Douarche; Robert Cortčs; Steven J. Roser; Jean-Louis Sikorav; Alan Braslau

    2008-09-26T23:59:59.000Z

    DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through chemical grafting of a homogeneous organicmonomolecular layer of N-(2-aminoethyl) dodecanamide on an oxide-free monocrystalline Si(111) wafer. The adsorbed dsDNA is found to embed into the soft monolayer which is deformed in the process. The surface coverage is very high and this adsorbed layer is expected to display 2D nematic ordering.

  13. Shear Unzipping of DNA

    E-Print Network [OSTI]

    Buddhapriya Chakrabarti; David R. Nelson

    2009-04-09T23:59:59.000Z

    We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder model of shear unzipping proposed earlier by deGennes [deGennes P. G. C. R. Acad. Sci., Ser. IV; Phys., Astrophys. 2001, 1505]. Using this model and a combination of analytical and numerical methods, we study the DNA "unzipping" transition when the shearing force exceeds a critical threshold at zero temperature. We also explore the effects of sequence heterogeneity and finite temperature and discuss possible applications to determine the strength of colloidal nanoparticle assemblies functionalized by DNA.

  14. DNA DNA DNA (d)DNA DNA DNA

    E-Print Network [OSTI]

    Hagiya, Masami

    DNA DNA DNA DNA DNA DNA DNA DNA [ 2008] (d)DNA DNA DNA DNA 2 3 DNA DNA DNA DNA DNA DNA DNA (a) (c) (b) (d) #12;DNA DNA DNA DNA DNA DNA DNA DNA (b) DNA [Tanaka et al.2008] DNA DNA DNA DNA DNA DNA DNA #12;iGEM MIT MIT

  15. Dynamic change of histone H2AX phosphorylation independent of ATM and DNA-PK in mouse skin in situ

    SciTech Connect (OSTI)

    Koike, Manabu [DNA Repair Gene Research, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)], E-mail: m_koike@nirs.go.jp; Mashino, Minako; Sugasawa, Jun; Koike, Aki [DNA Repair Gene Research, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)

    2007-11-30T23:59:59.000Z

    Histone H2AX undergoes phosphorylation on Ser 139 ({gamma}-H2AX) rapidly in response to DNA double-strand breaks induced by exogenous stimuli, such as ionizing radiation. However, the endogenous phosphorylation pattern and modifier of H2AX remain unclear. Here we show that H2AX is regulated physically at the level of phosphorylation at Ser139 during a hair cycle in the mouse skin. In anagen hair follicles, {gamma}-H2AX-positive cells were observed in the outer root sheath (ORS) and hair bulb in a cycling inferior region but not in a permanent superficial region. In telogen hair follicles, {gamma}-H2AX-positive cells were only detected around the germ cell cap. In contrast, following X-irradiation, {gamma}-H2AX was observed in various cell types including the ORS cells in the permanent superficial region. Furthermore, {gamma}-H2AX-positive cells were detected in the skin of mice lacking either ATM or DNA-PK, suggesting that these kinases are not essential for phosphorylation in vivo.

  16. 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)

    1997-01-01T23:59:59.000Z

    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.

  17. Analysis of cell cycle surveillance mechanisms in meiosis

    E-Print Network [OSTI]

    Hochwagen, Andreas

    2006-01-01T23:59:59.000Z

    Numerous DNA double-strand breaks (DSBs) are introduced into the genome in the course of meiotic recombination. This poses a significant hazard to the genomic integrity of the cell. Studies in a number of organisms have ...

  18. The impact of age, exposure and genetics on homologous recombination at the engineered repeat sequence in mice

    E-Print Network [OSTI]

    Wiktor-Brown, Dominika M

    2007-01-01T23:59:59.000Z

    Mitotic homologous recombination is a critical pathway for the repair of DNA double-strand breaks and broken replication forks. Although homologous recombination is generally error-free, recombination between misaligned ...

  19. DNA DNA . DNA

    E-Print Network [OSTI]

    1. DNA DNA , . . DNA ( ) DNA "exhaustive " . Boolean , 40 2 40 10 12 pico mole . DNA . 20 3-SAT DNA NP-complete [1]. [2, 3]. DNA

  20. 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)

    1998-01-01T23:59:59.000Z

    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.

  1. 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

    1998-12-08T23:59:59.000Z

    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.

  2. In vivo evidence of alternative loop geometries in DNA-protein complexes

    E-Print Network [OSTI]

    Leonor Saiz; Jose M. G. Vilar

    2006-02-10T23:59:59.000Z

    The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an oscillatory component of about half the helical period and oscillates asymmetrically with an amplitude significantly smaller than predicted by current theories. Here, we show that the in vivo behavior is accurately accounted for by the simultaneous presence of two distinct conformations of looped DNA. Our analysis reveals that these two conformations have different optimal free energies and phases and that they behave distinctly in the presence of key architectural proteins.

  3. A model for melting of confined DNA

    E-Print Network [OSTI]

    Werner, E; Ambjörnsson, T; Mehlig, B

    2015-01-01T23:59:59.000Z

    When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.

  4. WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN

    SciTech Connect (OSTI)

    Rangaraj, K.; Cooper, P.K.; Trego, K.S.

    2009-01-01T23:59:59.000Z

    The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 3’–5’ DNA-dependent helicase, 3’–5’ exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

  5. RADIATION SENSITIVITY & PROCESSING OF DNA DAMAGE FOLLOWING LOW DOSES OF GAMMA-RAY ALPHA PARTICLES & HZE IRRADIATION OF NORMAL DSB REPAIR DEFICIENT CELLS

    SciTech Connect (OSTI)

    O'Neil, Peter

    2009-05-15T23:59:59.000Z

    Non-homologous end joining (NHEJ) predominates in the repair of DNA double strand breaks (DSB) over homologous recombination (HR). NHEJ occurs throughout the cell cycle whereas HR occurs in late S/G2 due to the requirement of a sister chromatid (Rothkamm et al, Mol Cell Biol 23 5706-15 [2003]). To date evidence obtained with DSB repair deficient cells using pulsed-field gel electrophoresis has revealed the major pathway throughout all phases of the cell cycle for processing high dose induced DSBs is NHEJ (Wang et al, Oncogene 20 2212-24 (2001); Pluth et al, Cancer Res. 61 2649-55 [2001]). These findings however were obtained at high doses when on average >> 20-30 DSBs are formed per cell. The contribution of the repair pathways (NHEJ and HR) induced in response to DNA damage during the various phases of the cell cycle may depend upon the dose (the level of initial DSBs) especially since low levels of DSBs are induced at low dose. To date, low dose studies using NHEJ and HR deficient mutants have not been carried out to address this important question with radiations of different quality. The work presented here leads us to suggest that HR plays a relatively minor role in the repair of radiation-induced prompt DSBs. SSBs lead to the induction of DSBs which are associated specifically with S-phase cells consistent with the idea that they are formed at stalled replication forks in which HR plays a major role in repair. That DNA-PKcs is in some way involved in the repair of the precursors to replication-induced DSB remains an open question. Persistent non-DSB oxidative damage also leads to an increase in RAD51 positive DSBs. Both simple and complex non-DSB DNA damage may therefore contribute to indirect DSBs induced by ionising radiation at replication forks.

  6. DNA -DNA--

    E-Print Network [OSTI]

    Glykos, Nikolaos

    #12;#12;#12;8.1 DNA - . DNA- - (DNA-binding domains) ( 100 ). - DNA- - -, DNA. - -- - DNA. 173 8 DNA : -- 8.1 8.2 8.3 Cro - 8.4 Cro 8.5 DNA- - 8.6 Cro DN 8

  7. GENETIC AND MOLECULAR ANALYSIS OF DNA DAMAGE REPAIR AND TOLERANCE PATHWAYS.

    SciTech Connect (OSTI)

    SUTHERLAND, B.M.

    2001-07-26T23:59:59.000Z

    Radiation can damage cellular components, including DNA. Organisms have developed a panoply of means of dealing with DNA damage. Some repair paths have rather narrow substrate specificity (e.g. photolyases), which act on specific pyrimidine photoproducts in a specific type (e.g., DNA) and conformation (double-stranded B conformation) of nucleic acid. Others, for example, nucleotide excision repair, deal with larger classes of damages, in this case bulky adducts in DNA. A detailed discussion of DNA repair mechanisms is beyond the scope of this article, but one can be found in the excellent book of Friedberg et al. [1] for further detail. However, some DNA damages and paths for repair of those damages important for photobiology will be outlined below as a basis for the specific examples of genetic and molecular analysis that will be presented below.

  8. Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor

    SciTech Connect (OSTI)

    Jin, Tengchuan; Perry, Andrew; Jiang, Jiansheng; Smith, Patrick; Curry, James A.; Unterholzner, Leonie; Jiang, Zhaozhao; Horvath, Gabor; Rathinam, Vijay A.; Johnstone, Ricky W.; Hornung, Veit; Latz, Eicke; Bowie, Andrew G.; Fitzgerald, Katherine A.; Xiao, T. Sam (UMASS, MED); (Bonn); (Trinity); (PMCI-A); (NIH)

    2012-05-21T23:59:59.000Z

    Recognition of DNA by the innate immune system is central to antiviral and antibacterial defenses, as well as an important contributor to autoimmune diseases involving self DNA. AIM2 (absent in melanoma 2) and IFI16 (interferon-inducible protein 16) have been identified as DNA receptors that induce inflammasome formation and interferon production, respectively. Here we present the crystal structures of their HIN domains in complex with double-stranded (ds) DNA. Non-sequence-specific DNA recognition is accomplished through electrostatic attraction between the positively charged HIN domain residues and the dsDNA sugar-phosphate backbone. An intramolecular complex of the AIM2 Pyrin and HIN domains in an autoinhibited state is liberated by DNA binding, which may facilitate the assembly of inflammasomes along the DNA staircase. These findings provide mechanistic insights into dsDNA as the activation trigger and oligomerization platform for the assembly of large innate signaling complexes such as the inflammasomes.

  9. DNA heats up : Energetics of genome ejection from phage revealed by isothermal titration calorimetry

    E-Print Network [OSTI]

    Meerim Jeembaeva; B. Jönsson; Martin Castelnovo; Alex Evilevitch

    2010-01-06T23:59:59.000Z

    Most bacteriophages are known to inject their double-stranded DNA into bacteria upon receptor binding in an essentially spontaneous way. This downhill thermodynamic process from the intact virion toward the empty viral capsid plus released DNA is made possible by the energy stored during active packaging of the genome into the capsid. Only indirect measurements of this energy have been available until now using either single-molecule or osmotic suppression techniques. In this paper, we describe for the first time the use of isothermal titration calorimetry to directly measure the heat released (or equivalently the enthalpy) during DNA ejection from phage lambda, triggered in solution by a solubilized receptor. Quantitative analyses of the results lead to the identification of thermodynamic determinants associated with DNA ejection. The values obtained were found to be consistent with those previously predicted by analytical models and numerical simulations. Moreover, the results confirm the role of DNA hydration in the energetics of genome confinement in viral capsids.

  10. Theory of DNA translocation through narrow ion channels and nanopores with charged walls

    E-Print Network [OSTI]

    Tao Hu; B. I. Shklovskii

    2008-06-20T23:59:59.000Z

    Translocation of a single stranded DNA through genetically engineered $\\alpha$-hemolysin channels with positively charged walls is studied. It is predicted that transport properties of such channels are dramatically different from neutral wild type $\\alpha$-hemolysin channel. We assume that the wall charges compensate the fraction $x$ of the bare charge $q_{b}$ of the DNA piece residing in the channel. Our prediction are as follows (i) At small concentration of salt the blocked ion current decreases with $x$. (ii) The effective charge $q$ of DNA piece, which is very small at $x = 0$ (neutral channel) grows with $x$ and at $x=1$ reaches $q_{b}$. (iii) The rate of DNA capture by the channel exponentially grows with $x$. Our theory is also applicable to translocation of a double stranded DNA in narrow solid state nanopores with positively charged walls.

  11. DNA repair decline during mouse spermiogenesis results in the accumulation of heritable DNA damage

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    male germ cells handle DNA damage? Toxicol. Appl. Pharmacol.strand breaks and DNA base damage at different cellularrelationship to genetic damage, Mutat. Res. 216 (1989) 221-

  12. DNA Repair Decline During Mouse Spermiogenesis Results in the Accumulation of Heritable DNA Damage

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

    male germ cells handle DNA damage? Toxicol. Appl. Pharmacol.strand breaks and DNA base damage at different cellularrelationship to genetic damage, Mutat. Res. 216 (1989) 221-

  13. Binary electrokinetic separation of target DNA from background DNA primers.

    SciTech Connect (OSTI)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01T23:59:59.000Z

    This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.

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

    SciTech Connect (OSTI)

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

    2009-06-08T23:59:59.000Z

    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.

  15. RADIATION RESEARCH 169, 17 (2008) 0033-7587/08 $15.00

    E-Print Network [OSTI]

    2008-01-01T23:59:59.000Z

    1 RADIATION RESEARCH 169, 1­7 (2008) 0033-7587/08 $15.00 2008 by Radiation Research Society. All and Double-Strand Breaks ­ All's Well that ``Ends'' Well. . . . Radiat. Res. 169, 1­7 (2008). Sometimes one--they protected the physical ends of chromosomes from interaction with broken DNA ends created by ionizing radi

  16. . DNA, RNA, Protein

    E-Print Network [OSTI]

    Yoo, SukIn

    1. , . DNA, RNA, Protein [1-4]. DNA . DNA A, T, G, C . DNA , DNA DNA . , DNA DNA . DNA DNA . , PCR , , DNA [5]. DNA DNA , DNA

  17. Dietary fish oil and butyrate increase apoptosis and decrease aberrant crypt foci in colon cancer by enhancing histone acetylation and p21waf1/cip1 expression

    E-Print Network [OSTI]

    Covert, Kristy Lynn

    2006-08-16T23:59:59.000Z

    shrinkage, mitochondrial membrane blebbing, nuclear degradation, and DNA fragmentation (Shanmugathasan and Jothy, 2000). As the DNA fragments, the remaining double-strand breaks can be identified by gel electrophoresis, producing a specific pattern..., the nuclear chromatin condenses and DNA is degraded. Cellular remnants are packaged into apoptotic bodies, which are then phagocytized or sloughed into the passing lumenal contents (Vaux and Strasser, 1996). p21Waf1/Cip1 One of the earliest events...

  18. DNA Twist Elasticity: Mechanics and Thermal Fluctuations

    E-Print Network [OSTI]

    Supurna Sinha; Joseph Samuel

    2010-11-30T23:59:59.000Z

    The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that thermal fluctuations play an important role in determining molecular elastic properties, but a full theoretical treatment of the problem of twist elasticity of fluctuating ribbons using the simplest worm like chain model (WLC) remains elusive. In this paper, we approach this problem by taking first a mechanical approach and then incorporating thermal effects in a quadratic approximation applying the Gelfand-Yaglom (GY) method for computing fluctuation determinants. Our study interpolates between mechanics and statistical mechanics in a controlled way and shows how profoundly thermal fluctuations affect the elasticity of semiflexible polymers. The new results contained here are: 1) a detailed study of the minimum energy configurations with explicit expressions for their energy and writhe and plots of the extension versus Link for these configurations. 2) a study of fluctuations around the local minima of energy and approximate analytical formulae for the free energy of stretched twisted polymers derived by the Gelfand Yaglom method. We use insights derived from our mechanical approach to suggest calculational schemes that lead to an improved treatment of thermal fluctuations. From the derived formulae, predictions of the WLC model for molecular elasticity can be worked out for comparison against numerical simulations and experiments.

  19. Force-induced rupture of a DNA duplex

    E-Print Network [OSTI]

    Mosayebi, Majid; Doye, Jonathan P K; Ouldridge, Thomas E

    2015-01-01T23:59:59.000Z

    The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex within a given experiment depends strongly on the time scale of observation. We use simple models of DNA to demonstrate that this approach naturally captures the experimentally observed dependence of the critical force on duplex length for a given observation time. In particular, the critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence o...

  20. Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

    SciTech Connect (OSTI)

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O.; Kasahara, Hideko; Nam, Hyun-Joo (BU-M); (Florida); (Texas)

    2012-10-16T23:59:59.000Z

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 {angstrom} resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  1. Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

    We introduce an extended version of oxDNA, a coarse-grained model of 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+]=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...

  2. Free energy landscape and characteristic forces for the initiation of DNA unzipping

    E-Print Network [OSTI]

    Mentes, Ahmet; Brunk, Elizabeth; Wereszczynski, Jeff; Joyeux, Marc; Andricioaei, Ioan

    2015-01-01T23:59:59.000Z

    DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular dynamics (MD) simulations, coarse-grained simulations and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. The calculation of the potential of mean force profiles for the initial separation of the first few terminal base pairs in a DNA oligomer reveal that forces ranging between 130 and 230 pN are needed to disrupt the first base pair, values of an order of magnitude larger than those needed to disrupt base pairs in partially unzipped DNA. The force peak has an "echo," of approximately 50 pN, at the distance that unzips the second base pair. We show that the high peak needed to initiate unzipping derives...

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

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06T23:59:59.000Z

    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.

  4. Crystal structures of [lamda] exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity

    SciTech Connect (OSTI)

    Zhang, Jinjin; McCabe, Kimberly A.; Bell, Charles E. (OSU)

    2011-08-10T23:59:59.000Z

    The {lambda} exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3' overhang. The crystal structure of {lambda} exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of {lambda} exonuclease in complex with DNA at 1.88-{angstrom} resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg{sup 2+} ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5' phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of {lambda} exonuclease operates not only at the level of the trimer, but also at the level of the monomer.

  5. Breaking Earth Poems

    E-Print Network [OSTI]

    Hernandez, Scott Mcnaul

    2012-01-01T23:59:59.000Z

    CALIFORNIA RIVERSIDE Breaking Earth Poems A Thesis submittedFestival……………………………………………………………………..…..14 Earth Against Mylittle else in their hands. Earth Against My Back I lay in

  6. WINTER BREAK HOUSING APPLICATION

    E-Print Network [OSTI]

    Hartman, Chris

    WINTER BREAK HOUSING APPLICATION RESIDENCE HALLS WILL BE CLOSED FROM 12:00PM (NOON), DECEMBER 19-6860 WWW.UAF.EDU/RESLIFE · EMAIL UAF-HOUSING@ALASKA.EDU TEL (907) 474-7247 · FAX (907) 474-6423 WINTER halls open need to complete the winter break housing application. Students that apply for housing before

  7. Biochemical and Developmental Characterization of a SNF2-like ATPase Amplified in Liver Cancer 1 (ALC1)

    E-Print Network [OSTI]

    Gottschalk, Aaron James

    2010-06-07T23:59:59.000Z

    . Ino80 and Swr1 complexes regulate double-strand break repair. ...........................................26 Figure 8. SNF2 ATPases have specialized modes of chromatin remodeling. Nucleosome......................28 Figure 9. Model for translocation... that the Snf2-related chromatin remodeling complexes Ino80 and Swr1 have essential roles in DNA damage and recombination [60]. An interesting characteristic of Ino80 and Swr1 type remodeling complexes is that each includes Ruv-B like helicases as subunits...

  8. Nanotechnology with DNA DNA Nanodevices

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

    Nanotechnology with DNA DNA Nanodevices Friedrich C. Simmel* and Wendy U. Dittmer A DNA actuator. Introduction.............285 2. Overview: DNA Nanotechnology.......285 3. Prototypes of Nanomechanical DNA overview of DNA nanotechnology as a whole is given. The most important properties of DNA molecules

  9. Self-avoiding worm-like chain model for dsDNA loop formation

    E-Print Network [OSTI]

    Yaroslav Pollak; Sarah Goldberg; Roee Amit

    2014-11-06T23:59:59.000Z

    We compute for the first time the effects of excluded volume on the probability for double-stranded DNA to form a loop. We utilize a Monte-Carlo algorithm for generation of large ensembles of self- avoiding worm-like chains, which are used to compute the J-factor for varying lengthscales. In the entropic regime, we confirm the scaling-theory prediction of a power-law drop off of -1.92, which is significantly stronger than the -1.5 power-law predicted by the non-self-avoiding worm-like chain model. In the elastic regime, we find that the angle-independent end-to-end chain distribution is highly anisotropic. This anisotropy, combined with the excluded volume constraints, lead to an increase in the J-factor of the self-avoiding worm-like chain by about half an order of magnitude relative to its non-self-avoiding counterpart. This increase could partially explain the anomalous results of recent cyclization experiments, in which short dsDNA molecules were found to have an increased propensity to form a loop.

  10. DNA microarray (spot) .

    E-Print Network [OSTI]

    1. DNA microarray DNA (spot) . DNA probe , probe (hybridization) . DNA microarray cDNA oligonucleotide oligonucleotide cDNA probe . oligonucleotide microarray , DNA , probe . oligonucleotide microarray probe

  11. Finite group symmetry breaking

    E-Print Network [OSTI]

    G. Gaeta

    2005-10-02T23:59:59.000Z

    Finite group symmetry is commonplace in Physics, in particular through crystallographic groups occurring in condensed matter physics -- but also through the inversions (C,P,T and their combinations) occurring in high energy physics and field theory. The breaking of finite groups symmetry has thus been thoroughly studied, and general approaches exist to investigate it. In Landau theory, the state of a system is described by a finite dimensional variable (the {\\it order parameter}), and physical states correspond to minima of a potential, invariant under a group. In this article we describe the basics of symmetry breaking analysis for systems described by a symmetric polynomial; in particular we discuss generic symmetry breakings, i.e. those determined by the symmetry properties themselves and independent on the details of the polynomial describing a concrete system. We also discuss how the plethora of invariant polynomials can be to some extent reduced by means of changes of coordinates, i.e. how one can reduce to consider certain types of polynomials with no loss of generality. Finally, we will give some indications on extension of this theory, i.e. on how one deals with symmetry breakings for more general groups and/or more general physical systems.

  12. SuperBreak: Using Interactivity to Enhance Ergonomic Typing Breaks

    E-Print Network [OSTI]

    Rajamani, Sriram K.

    SuperBreak: Using Interactivity to Enhance Ergonomic Typing Breaks Dan Morris, A.J. Bernheim Brush Repetitive strain injuries and ergonomics concerns have become increasingly significant health issues software mechanisms exist for managing ergonomics; the most well-known are "break-reminder" packages

  13. DNA Computing Hamiltonian path

    E-Print Network [OSTI]

    Hagiya, Masami

    2014 DNA DNA #12;DNA Computing · Feynman · Adleman · DNASIMD · ... · · · · · DNADNA #12;DNA · DNA · · · · DNA · · #12;2000 2005 2010 1995 Hamiltonian path DNA tweezers DNA tile DNA origami DNA box Sierpinski DNA tile self assembly DNA logic gates Whiplash PCR DNA automaton DNA spider MAYA

  14. DNA-nuclear matrix interactions and ionizing radiation sensitivity

    SciTech Connect (OSTI)

    Schwartz, J.L. (Argonne National Lab., IL (United States) Chicago Univ., IL (United States). Dept. of Radiation and Cellular Oncology); Vaughan, A.T.M. (Loyola Univ., Hines, IL (United States). Dept. of Radiotherapy)

    1993-01-01T23:59:59.000Z

    The association between inherent ionizing radiation sensitivity and DNA supercoil unwinding in mammalian cells suggests that the DNA-nuclear matrix attachment region (MAR) plays an important role in radiation response. In radioresistant cells, the MAR structure may exist in a more stable, open configuration, limiting DNA unwinding following strand break induction and maintaining DNA ends in close proximity for more rapid and accurate rejoining. In addition, the open configuration at these matrix attachment sites may serve to facilitate rapid DNA processing of breaks by providing (1) sites for repair proteins to collect and (2) energy to drive enzymatic reactions.

  15. DNA-nuclear matrix interactions and ionizing radiation sensitivity

    SciTech Connect (OSTI)

    Schwartz, J.L. [Argonne National Lab., IL (United States)]|[Chicago Univ., IL (United States). Dept. of Radiation and Cellular Oncology; Vaughan, A.T.M. [Loyola Univ., Hines, IL (United States). Dept. of Radiotherapy

    1993-03-01T23:59:59.000Z

    The association between inherent ionizing radiation sensitivity and DNA supercoil unwinding in mammalian cells suggests that the DNA-nuclear matrix attachment region (MAR) plays an important role in radiation response. In radioresistant cells, the MAR structure may exist in a more stable, open configuration, limiting DNA unwinding following strand break induction and maintaining DNA ends in close proximity for more rapid and accurate rejoining. In addition, the open configuration at these matrix attachment sites may serve to facilitate rapid DNA processing of breaks by providing (1) sites for repair proteins to collect and (2) energy to drive enzymatic reactions.

  16. The structural basis for partitioning of the XRCC1/DNA ligase III-[alpha] BRCT-mediated dimer complexes

    SciTech Connect (OSTI)

    Cuneo, Matthew J.; Gabel, Scott A.; Krahn, Joseph M.; Ricker, Melissa A.; London, Robert E. (NIH)

    2011-11-17T23:59:59.000Z

    The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase III-{alpha}. For efficient ligation, ligase III-{alpha} is constitutively bound to the scaffolding protein XRCC1 through interactions between the C-terminal BRCT domains of each protein. Although structural data for the individual domains has been available, no structure of the complex has been determined and several alternative proposals for this interaction have been advanced. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation. We report here the structures of both homodimer complexes as well as the heterodimer complex. Structural characterization of the heterodimer formed from a longer XRCC1 BRCT domain construct, including residues comprising the interdomain linker region, revealed an expanded heterodimer interface with the ligase III-{alpha} BRCT domain. This enhanced linker-mediated binding interface plays a significant role in the determination of heterodimer/homodimer selectivity. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex.

  17. The Structural Basis for Partitioning of the XRCC1/DNA Ligase III-alpha BRCT-mediated Dimer Complexes

    SciTech Connect (OSTI)

    M Cuneo; S Gabel; J Krahn; M Ricker; R London

    2011-12-31T23:59:59.000Z

    The ultimate step common to almost all DNA repair pathways is the ligation of the nicked intermediate to form contiguous double-stranded DNA. In the mammalian nucleotide and base excision repair pathways, the ligation step is carried out by ligase III-{alpha}. For efficient ligation, ligase III-{alpha} is constitutively bound to the scaffolding protein XRCC1 through interactions between the C-terminal BRCT domains of each protein. Although structural data for the individual domains has been available, no structure of the complex has been determined and several alternative proposals for this interaction have been advanced. Interpretation of the models is complicated by the formation of homodimers that, depending on the model, may either contribute to, or compete with heterodimer formation. We report here the structures of both homodimer complexes as well as the heterodimer complex. Structural characterization of the heterodimer formed from a longer XRCC1 BRCT domain construct, including residues comprising the interdomain linker region, revealed an expanded heterodimer interface with the ligase III-{alpha} BRCT domain. This enhanced linker-mediated binding interface plays a significant role in the determination of heterodimer/homodimer selectivity. These data provide fundamental insights into the structural basis of BRCT-mediated dimerization, and resolve questions related to the organization of this important repair complex.

  18. 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 (Emory-MED); (NE Biolabs)

    2014-07-03T23:59:59.000Z

    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 Ĺ, 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.

  19. APPROVED Tie-Breaking Procedures

    E-Print Network [OSTI]

    Iglesia, Enrique

    a public school applicant attends a low API school (1-4), or if a private school to the rest of the tie-break pool. Spring Admission Applicants recommended, relative to the rest of the tie-break pool. #12;APPROVED Denied Admission

  20. Solvatochromism and time-resolved fluorescence of the antitumor agent mitoxantrone and its analogues in solution and in DNA

    SciTech Connect (OSTI)

    Su Lin; Struve, W.S. (Ames Lab., IA (United States))

    1991-03-21T23:59:59.000Z

    The electronic spectroscopy and fluorescence kinetics of 1,4-dihydroxy-5,8-(2-(2-((2-hydroxyethyl)amino)ethyl)amino)-9,10-anthracenedione (mitoxantrone) and three closely related analogues have been studied in several solvents. The small solvatochromic blue shifts of their visible charge-transfer absorption bands in protic solvents are dominated by interactions with a solvent H-bonding donor, rather than by dipole-dielectric solute-solvent electrostatics. These interactions are unrelated to the phenolic hydroxy groups or the distal N atoms on the side chains but must be localized to the carbonyl groups. The fluorescence decays of all four anthraquinones are controlled by subnanosecond nonradiative relaxation in all solvents studied. At least two decay mechanisms contribute to the observed fluorescence kinetics in solution: (a) subnanosecond internal conversion that is accelerated relative to that in 1,4-diaminoanthraquinone by the presence of the flexible 1,4-side chains in mitoxantrone and its analogues; (b) an additional decay mode that is accentuated in H-bonding solvents. A substantial normal isotope effect occurs in the fluorescence lifetimes of mitoxantrone in perdeuterated water and methanol but not in aprotic solvents. When bound to double-stranded calf thymus DNA, mitoxantrone displays a fluorescence lifetime similar to that in aprotic solvents, suggesting that H-bonding interactions with water are precluded by chromophore intercalation. DNA-bound ametantrone exhibits a lifetime longer than that in either H-bonding or aprotic solvents, indicating that immobilization of the side chains through binding of the distal N atoms to the DNA backbone may influence the decay kinetics. This technique therefore shows potential for elucidating the DNA binding modes for a large class of intercalative drugs.

  1. DNA Copyright

    E-Print Network [OSTI]

    Torrance, Andrew W.

    2011-01-01T23:59:59.000Z

    of architecture and computer software. Sequences of DNA should also be acknowledged as eligible for copyright protection. Unaltered genomic DNA sequences would seem poor candidates for copyright protection. The case is stronger for copyright protection...

  2. DNA demethylation by DNA repair

    E-Print Network [OSTI]

    Gehring, Mary

    Active DNA demethylation underlies key facets of reproduction in flowering plants and mammals and serves a general genome housekeeping function in plants. A family of 5-methylcytosine DNA glycosylases catalyzes plant ...

  3. DNA Pendant

    E-Print Network [OSTI]

    Hacker, Randi; Tsutsui, William

    2007-11-14T23:59:59.000Z

    Broadcast Transcript: It's a symbol of commitment. It's a memento mori. It's the DNA pendant offered by Japan's Eiwa Industry and it's two, two, two things in one. Using genetic extraction, Eiwa removes the DNA from, say, a strand of hair or a...

  4. Chiral Symmetry Breaking in Graphene

    E-Print Network [OSTI]

    Gordon W. Semenoff

    2011-08-19T23:59:59.000Z

    The question of whether the Coulomb interaction is strong enough to break the sublattice symmetry of un-doped graphene is discussed. We formulate a strong coupling expansion where the ground state of the Coulomb Hamiltonian is found exactly and the kinetic hopping Hamiltonian is treated as a perturbation. We argue that many of the properties of the resulting system would be shared by graphene with a Hubbard model interaction. In particular, the best candidate sublattice symmetry breaking ground state is an antiferromagnetic Mott insulator. We discuss the results of some numerical simulations which indicate that the Coulomb interaction is indeed subcritical. We also point out the curious fact that, if the electron did not have spin degeneracy, the tendency to break chiral symmetry would be much greater and even relatively weak Coulomb interactions would likely gap the spectrum.

  5. Dependence of DNA persistence length on ionic strength of solutions with monovalent and divalent salts: a joint theory-experiment study

    E-Print Network [OSTI]

    Brunet, Annaël; Salomé, Laurence; Rousseau, Philippe; Destainville, Nicolas; Manghi, Manoel

    2015-01-01T23:59:59.000Z

    Using high-throughput Tethered Particle Motion single molecule experiments, the double-stranded DNA persistence length, $L_p$, is measured in solutions with Na$^+$ and Mg$^{2+}$ ions of various ionic strengths, $I$. Several theoretical equations for $L_p(I)$ are fitted to the experimental data, but no decisive theory is found which fits all the $L_p$ values for the two ion valencies. Properly extracted from the particle trajectory using simulations, $L_p$ varies from 30~nm to 55~nm, and is compared to previous experimental results. For the Na$^+$ only case, $L_p$ is an increasing concave function of $I^{-1}$, well fitted by Manning's electrostatic stretching approach, but not by classical Odjik-Skolnick-Fixman theories with or without counter-ion condensation. With added Mg$^{2+}$ ions, $L_p$ shows a marked decrease at low $I$, interpreted as an ion-ion correlation effect, with an almost linear law in $I^{-1}$, fitted by a proposed variational approach.

  6. Journal of the Mechanics and Physics of Solids 51 (2003) 18151847

    E-Print Network [OSTI]

    Ortiz, Michael

    2003-01-01T23:59:59.000Z

    of the DNA is de˙ned as a functional of the director ˙eld which accounts for bending, torsion years, the structure of the portal motor which translocates double-stranded DNA into the capsid

  7. Elucidation of the Mechanisms of Nucleosome Binding and Repositioning by a Chromatin Remodeler: Monomeric ISWI Remodels Nucleosomes Through a Random Walk

    E-Print Network [OSTI]

    Al-Ani, Gada K.

    2014-05-31T23:59:59.000Z

    remodeler ISWI with fluorophore-labeled nucleosomes and DNA through associated changes in fluorescence anisotropy of the fluorophore upon ISWI binding to these substrates. We determined that one ISWI molecule binds to a 20 bp double stranded DNA substrate...

  8. Baryon and chiral symmetry breaking

    SciTech Connect (OSTI)

    Gorsky, A. [Institute for Theoretical and Experimental Physics (ITEP), Moscow, Russia and Moscow Institute of Physics and Technology (MIPT), Dolgoprudny (Russian Federation); Krikun, A. [NORDITA, KTH Royal Institute of Technology and Stockholm University Stockholm, Sweden and Institute for Theoretical and Experimental Physics (ITEP), Moscow (Russian Federation)

    2014-07-23T23:59:59.000Z

    We briefly review the generalized Skyrmion model for the baryon recently suggested by us. It takes into account the tower of vector and axial mesons as well as the chiral symmetry breaking. The generalized Skyrmion model provides the qualitative explanation of the Ioffe’s formula for the baryon mass.

  9. Symmetry breaking in laser cavities

    E-Print Network [OSTI]

    Malomed, Boris A

    2015-01-01T23:59:59.000Z

    A brief introduction to the topic of spontaneous symmetry breaking (SSB) in conservative and dissipative nonlinear systems with an underlying double-well-potential structure is given. The reason is a discussion of a recent observation of the SSB a dual-core nanolaser cavity [5]. The effect is illustrated by means of a simple semi-analytically-tractable model (Fig. 1).

  10. Function of the ATR N-terminal domain revealed by an ATM/ATR chimera

    SciTech Connect (OSTI)

    Chen Xinping [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States); Zhao Runxiang [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States); Glick, Gloria G. [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States); Cortez, David [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States)]. E-mail: david.cortez@vanderbilt.edu

    2007-05-01T23:59:59.000Z

    The ATM and ATR kinases function at the apex of checkpoint signaling pathways. These kinases share significant sequence similarity, phosphorylate many of the same substrates, and have overlapping roles in initiating cell cycle checkpoints. However, they sense DNA damage through distinct mechanisms. ATR primarily senses single stranded DNA (ssDNA) through its interaction with ATRIP, and ATM senses double strand breaks through its interaction with Nbs1. We determined that the N-terminus of ATR contains a domain that binds ATRIP. Attaching this domain to ATM allowed the fusion protein (ATM*) to bind ATRIP and associate with RPA-coated ssDNA. ATM* also gained the ability to localize efficiently to stalled replication forks as well as double strand breaks. Despite having normal kinase activity when tested in vitro and being phosphorylated on S1981 in vivo, ATM* is defective in checkpoint signaling and does not complement cellular deficiencies in either ATM or ATR. These data indicate that the N-terminus of ATR is sufficient to bind ATRIP and to promote localization to sites of replication stress.

  11. DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics

    E-Print Network [OSTI]

    DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo­Yong Shin 1 , Eun Jeong the complexity of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

  12. DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics

    E-Print Network [OSTI]

    DNA Computing Complexity Analysis Using DNA/DNA Hybridization Kinetics Soo-Yong Shin1 , Eun Jeong of DNA computing. The complexity of any computational algorithm is typically measured in terms of time and space. In DNA computing, the time complexity can be measured by the total reaction time

  13. CTRLWORK AND MACBREAKZ ERGONOMIC BREAK REMINDER SOFTWARE

    E-Print Network [OSTI]

    California at Santa Barbara, University of

    CTRLWORK AND MACBREAKZ ERGONOMIC BREAK REMINDER SOFTWARE SOFTWARE FEATURES: Analyzes your for installation assistance. 1. Please uninstall the former ergonomic break software, RSIGuard, if currently instructions on the screen. For more information, contact the UCSB Ergonomics Program at Ergonomics

  14. (gene expression) DNA (DNA microarrays).

    E-Print Network [OSTI]

    Athens, University of

    Lymphoblastic Leukemia - ALL, 25 Acute Myeloid Leukemia - AML) µ 7129 [10]. µ µ µ µ µ µ µ µ DNA. 62 µ, 22 40 , µ 2000 [6]. µ 72 µ µ (47 Acute

  15. Chaotic inflation and supersymmetry breaking

    SciTech Connect (OSTI)

    Kallosh, Renata; Linde, Andrei; Rube, Tomas [Stanford Institute of Theoretical Physics and Department of Physics, Stanford University, Stanford, California 94305 (United States); Olive, Keith A. [William I. Fine Theoretical Physics Institute, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    2011-10-15T23:59:59.000Z

    We investigate the recently proposed class of chaotic inflation models in supergravity with an arbitrary inflaton potential V({phi}). These models are extended to include matter fields in the visible sector and we employ a mechanism of supersymmetry breaking based on a particular phenomenological version of the KKLT mechanism (the KL model). We describe specific features of reheating in this class of models and show how one can solve the cosmological moduli and gravitino problems in this context.

  16. ##### SAT Engine ####### _ ############ DNA ###### _

    E-Print Network [OSTI]

    Hagiya, Masami

    ##### SAT Engine ####### _ ############ DNA ###### _ # # # #y # # #yy # # # #yy ###### DNA #################################### ############### ##################### 6 ## 10 ##### ### DNA ############### (Sakamoto et al., Science, Vol.288, pp.1223-122* *6

  17. Unparticles and electroweak symmetry breaking

    SciTech Connect (OSTI)

    Lee, Jong-Phil [Korea Institute for Advanced Study, Seoul 130-722 (Korea, Republic of)

    2008-11-23T23:59:59.000Z

    We investigate a scalar potential inspired by the unparticle sector for the electroweak symmetry breaking. The scalar potential contains the interaction between the standard model fields and unparticle sector. It is described by the non-integral power of fields that originates from the nontrivial scaling dimension of the unparticle operator. It is found that the electroweak symmetry is broken at tree level when the interaction is turned on. The scale invariance of unparticle sector is also broken simultaneously, resulting in a physical Higgs and a new lighter scalar particle.

  18. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA

    E-Print Network [OSTI]

    1. Adleman[1] 1994 DNA Hamiltonian Path Problem , DNA DNA [2]. DNA DNA , . , , 2 , DNA 4 . DNA 4 A(Adenine), C(Cytosine), G(Guanine), T(Thymine) 2 4 . , . 1 mole 6x10 23 DNA DNA . , . DNA NP-complete [1, 2], [2

  19. DNA Topology: Fundamentals

    E-Print Network [OSTI]

    Mirkin, Sergei

    DNA Topology: Fundamentals Sergei M Mirkin, University of Illinois at Chicago, Illinois, USA Topological characteristics of DNA and specifically DNA supercoiling influence all major DNA transactions in living cells. DNA supercoiling induces the formation of unusual secondary structure by specific DNA

  20. Degeneracy Breaking of Hydrogen Atom

    E-Print Network [OSTI]

    Agung Trisetyarso; Pantur Silaban

    2014-11-21T23:59:59.000Z

    The three dimensional rotation group, SO(3), is a symmetry group of the normal hydrogen atom. Each reducible representation of this group can be associated with a degenerate energy level. If this atom is placed in an external magnetic field, the interaction between the orbital magnetic moment with this field will lead to a symmetry breaking where the symmetry group of the atom is a new group distinct from the SO(3) group. This phenomenon describes the normal Zeeman effect, where a degenerate energy level splits into several new energy levels. It is explicitly shown that each of the new energy levels can be associated with an irreducible representation of the new symmetry group.

  1. Alan Turing as a Statistician: Breaking the Code by Breaking the Bayesian Egg

    E-Print Network [OSTI]

    Wolfe, Patrick J.

    Alan Turing as a Statistician: Breaking the Code by Breaking the Bayesian Egg Joseph K. Blitzstein, Harvard University Alan Turing is widely considered the father of computer science. Yet even

  2. Amino Triazole : A New Abscission Chemical and Growth Inhibitor. 

    E-Print Network [OSTI]

    Leinweber, C. L. (Charles Lee); Johnson, S. P. (Samuel Park); Hall, Wayne C. (Wayne Clark)

    1954-01-01T23:59:59.000Z

    Most bacteriophages release progeny virions at the end of the infection cycle by lysis of the host. Large phages with double-stranded DNA genomes use a multigene strategy based on holins, small membrane proteins, and ...

  3. Genes and structural proteins of the phage SYN5 of the marine cyanobacteria, Synechococcus

    E-Print Network [OSTI]

    Pope, Welkin Hazel

    2005-01-01T23:59:59.000Z

    Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10łą particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed ...

  4. DNA polymerase with modified processivity

    DOE Patents [OSTI]

    Bedford, Ella (Brookline, MA); Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

    1999-01-01T23:59:59.000Z

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

  5. Vanadium catalysts break down biomass for fuels

    E-Print Network [OSTI]

    - 1 - Vanadium catalysts break down biomass for fuels March 26, 2012 Vanadium catalysts break down biomass into useful components Due to diminishing petroleum reserves, non-food biomass (lignocellulose) is an attractive alternative as a feedstock for the production of renewable chemicals and fuels. The Department

  6. Gauge symmetry breaking in orbifold model building

    E-Print Network [OSTI]

    Michele Trapletti

    2006-11-02T23:59:59.000Z

    We review the gauge symmetry breaking mechanism due to orbifold projections in orbifold model building. We explicitly show the existence of a scale of breaking if such a symmetry breaking is due to freely-acting orbifold operators only, i.e. in case the breaking is realized non-locally in the internal space. We show that such a scale is related to the compactification moduli only, and that there are no extra continuous parameters, at least in semirealistic models with N=1 SUSY in four dimensions. In this sense, the mechanism is peculiarly different from the standard Higgs (or Hosotani) symmetry breaking mechanism. We show that the mechanism also differs from that present in standard orbifold models where, even in presence of discrete Wilson lines, a scale of breaking is generically missing, since the breaking is localized in specific points in the internal space. We review a set of background geometries where the described non-local breaking is realized, both in the case of two and six extra dimensions. In the latter case, relevant in string model building, we consider both heterotic and open string compactifications.

  7. Laboratory Directed Research and Development Program. Annual report

    SciTech Connect (OSTI)

    Ogeka, G.J.; Romano, A.J.

    1992-12-01T23:59:59.000Z

    This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium.

  8. Laboratory Directed Research and Development Program

    SciTech Connect (OSTI)

    Ogeka, G.J.; Romano, A.J.

    1992-12-01T23:59:59.000Z

    This report briefly discusses the following research: Advances in Geoexploration; Transvenous Coronary Angiography with Synchrotron X-Rays; Borehole Measurements of Global Warming; Molecular Ecology: Development of Field Methods for Microbial Growth Rate and Activity Measurements; A New Malaria Enzyme - A Potential Source for a New Diagnostic Test for Malaria and a Target for a New Antimalarial Drug; Basic Studies on Thoron and Thoron Precursors; Cloning of the cDNA for a Human Serine/Threonine Protein Kinase that is Activated Specifically by Double-Stranded DNA; Development of an Ultra-Fast Laser System for Accelerator Applications; Cluster Impact Fusion; Effect of a Bacterial Spore Protein on Mutagenesis; Structure and Function of Adenovirus Penton Base Protein; High Resolution Fast X-Ray Detector; Coherent Synchrotron Radiation Longitudinal Bunch Shape Monitor; High Grain Harmonic Generation Experiment; BNL Maglev Studies; Structural Investigations of Pt-Based Catalysts; Studies on the Cellular Toxicity of Cocaine and Cocaethylene; Human Melanocyte Transformation; Exploratory Applications of X-Ray Microscopy; Determination of the Higher Ordered Structure of Eukaryotic Chromosomes; Uranium Neutron Capture Therapy; Tunneling Microscopy Studies of Nanoscale Structures; Nuclear Techiques for Study of Biological Channels; RF Sources for Accelerator Physics; Induction and Repair of Double-Strand Breaks in the DNA of Human Lymphocytes; and An EBIS Source of High Charge State Ions up to Uranium.

  9. Advance the DNA computing 

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30T23:59:59.000Z

    DNA computer. The existing models from which a few DNA computing algorithms have been developed are not sufficiently powerful and robust, however, to attract potential users. This thesis has described research performed to build a new DNA computing...

  10. Explicit versus Spontaneous Diffeomorphism Breaking in Gravity

    E-Print Network [OSTI]

    Robert Bluhm

    2015-04-02T23:59:59.000Z

    Gravitational theories with fixed background fields break local Lorentz and diffeomorphism invariance either explicitly or spontaneously. In the case of explicit breaking it is known that conflicts can arise between the dynamics and geometrical constraints, while spontaneous breaking evades this problem. It is for this reason that in the gravity sector of the Standard-Model Extension (SME) it is assumed that the background fields (SME coefficients) originate from spontaneous symmetry breaking. However, in other examples, such as Chern-Simons gravity and massive gravity, diffeomorphism invariance is explicitly broken by the background fields, and the potential conflicts between the dynamics and geometry can be avoided in most cases. An analysis of how this occurs is given, and the conditions that are placed on the metric tensor and gravitational structure as a result of the presence of an explicit-breaking background are described. The gravity sector of the SME is then considered for the case of explicit breaking. However, it is found that a useful post-Newtonian limit is only obtained when the symmetry breaking is spontaneous.

  11. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

    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.

  12. Symmetry Breaking Revisited Jean-Francois Puget

    E-Print Network [OSTI]

    Flener, Pierre

    Symmetry Breaking Revisited Jean-Fran¸cois Puget ILOG, 9 avenue de Verdun, 94253 Gentilly, France, puget@ilog.fr Abstract. Symmetries in constraint satisfaction problems (CSPs) are one

  13. Holographic realization of gauge mediated supersymmetry breaking

    E-Print Network [OSTI]

    Kostas Skenderis; Marika Taylor

    2012-09-10T23:59:59.000Z

    The general gauge mediation scenario provides a framework in which properties of a visible sector with soft supersymmetry breaking are computed from current correlation functions in the supersymmetry breaking hidden sector. In this paper we will use holography to model strongly coupled hidden sectors by weakly curved geometries and describe how the current correlators relevant for general gauge mediation are computed by holographic methods. We illustrate the general setup by a toy example which captures most of the relevant features.

  14. Breaking Parity Symmetry Using Extra Dimensions

    E-Print Network [OSTI]

    R. N. Mohapatra; A. Pérez-Lorenzana

    1999-11-17T23:59:59.000Z

    We present a new way to break parity symmetry in left-right symmetric models using boundary conditions on the fields residing in the fifth dimension. We also discuss the connection between the limits on the size of extra dimensions and the scale of right handed symmetry breaking obtained from the analysis of neutrinoless double beta decay in the case where the righthanded gauge symmetry is in the bulk.

  15. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

    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.

  16. Natural DNA sequencing by synthesis

    E-Print Network [OSTI]

    Roller, Eric E.

    2011-01-01T23:59:59.000Z

    labeled nucleotides by DNA polymerases. Biotechniques, 2005.S.A. , et al. , Multiplexed DNA sequencing-by-synthesis.Assembly of High-Density DNA Arrays for Genomic Analyses.

  17. DNA conjugation andDNA conjugation and reversibility onreversibility on

    E-Print Network [OSTI]

    Rubloff, Gary W.

    DNA conjugation andDNA conjugation and reversibility onreversibility on chitosan surfaceschitosan surfaceschitosan surfaceschitosan surfaces Rubloff Research Group Accomplishments #12;DNA conjugation and reversibility onDNA conjugation and reversibility on chitosan surfaceschitosan surfaces Accomplishment Single

  18. Chimera Death: Symmetry Breaking in Dynamical Networks

    E-Print Network [OSTI]

    Anna Zakharova; Marie Kapeller; Eckehard Schöll

    2014-02-03T23:59:59.000Z

    For a network of generic oscillators with nonlocal topology and symmetry-breaking coupling we establish novel partially coherent inhomogeneous spatial patterns, which combine the features of chimera states (coexisting incongruous coherent and incoherent domains) and oscillation death (oscillation suppression), which we call chimera death. We show that due to the interplay of nonlocality and breaking of rotational symmetry by the coupling two distinct scenarios from oscillatory behavior to a stationary state regime are possible: a transition from an amplitude chimera to chimera death via in-phase synchronized oscillations, and a direct abrupt transition for larger coupling strength.

  19. Gauge mediated supersymmetry breaking and moduli stabilization

    SciTech Connect (OSTI)

    Alwis, S. P. de [Physics Department, University of Colorado, Boulder, Colorado 80309 (United States)

    2007-10-15T23:59:59.000Z

    A generic lesson of string theory is that the coupling constants of an effective low energy theory are determined by the vacuum values of a set of fields - the so-called moduli - some of which are stabilized at relatively low masses by nonperturbative effects. We argue that the physics of these moduli cannot be separated from the issues of dynamical and gauge mediated supersymmetry breaking. To illustrate this point we present a modified version of the type IIB Kachru-Kallosh-Linde-Trivedi model where the criteria for gauge mediated supersymmetry breaking may be realized.

  20. Meta-DNA: synthetic biology via DNA nanostructures and

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: synthetic biology via DNA nanostructures and hybridization reactions Harish Chandran1 of DNA manipulations achieved by protein enzymes be simulated via simple DNA hybridization chemistry? In this work, we develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based on strands

  1. Quantitive DNA Fiber Mapping

    E-Print Network [OSTI]

    Lu, Chun-Mei

    2009-01-01T23:59:59.000Z

    of California. Lu et al. : DNA Fiber Mapping page - 35 Lu etal. : DNA Fiber Mapping page - 36 a b c d e f g OV P1 cloneSp6 end T7 end Lu et al. : DNA Fiber Mapping page - 37 a b c

  2. Symmetry-Breaking Constraints for Matrix Models

    E-Print Network [OSTI]

    Flener, Pierre

    -breaking constraints. Experimental re- sults confirm their value. 1 Introduction Symmetry in a CSP model is an important issue as the exploration of symmet- ric but essentially equivalent branches in a search tree may techniques have been developed to address the issue of eliminating symmetry in CSP models. An important class

  3. Viscoplastic dam breaks and the Bostwick consistometer

    E-Print Network [OSTI]

    Balmforth, Neil

    Viscoplastic dam breaks and the Bostwick consistometer N. J. Balmforth, a R. V. Craster, b P'Informazione, Universit`a di Milano, Crema, Italy Abstract We present a theoretical and experimental analysis of the dam the broken dam) that may assist an experimentalist to unravel those dependences. Experiments are conducted

  4. Long Wave Breaking Effects on Fringing Reefs

    E-Print Network [OSTI]

    Goertz, John 1985-

    2012-12-12T23:59:59.000Z

    Calculated HRMS .................................................... 20? Figure 7: HRMS of JB07 vs. Directly Calculated HRMS ..................................................... 21? Figure 8: Dissipation Zones for Combined Probabilistic Model.... To find a better estimation of the constraints in this steep slope area, Janssen and Battjes (2007; hereafter JB07) can be used to estimate bulk dissipation. However, it is possible to investigate the breaking process at levels deeper than bulk...

  5. Radiation physics, biophysics, and radiation biology. Progress report, December 1, 1992--November 30, 1993

    SciTech Connect (OSTI)

    Hall, E.J.; Zaider, M.

    1993-05-01T23:59:59.000Z

    Research at the Center for Radiological Research is a multidisciplenary blend of physics, chemistry and biology aimed at understanding the mechanisms involved in the health problems resulting from human exposure to ionizing radiations. The focus is increased on biochemistry and the application of the techniques of molecular biology to the problems of radiation biology. Research highlights of the program from the past year are described. A mathematical model describing the production of single-strand and double-strand breaks in DNA as a function radiation quality has been completed. For the first time Monte Carlo techniques have been used to obtain directly the spatial distribution of DNA moieties altered by radiation. This information was obtained by including the transport codes a realistic description of the electronic structure of DNA. We have investigated structure activity relationships for the potential oncogenicity of a new generation of bioreductive drugs that function as hypoxic cytotoxins. Experimental and theoretical investigation of the inverse dose rate effect, whereby medium LET radiations actually produce an c effect when the dose is protracted, is now at a point where the basic mechanisms are reasonably understood and the complex interplay between dose, dose rate and radiation quality which is necessary for the effect to be present can now be predicted at least in vitro. In terms of early radiobiological damage, a quantitative link has been established between basic energy deposition and locally multiply damaged sites, the radiochemical precursor of DNA double strand breaks; specifically, the spatial and energy deposition requirements necessary to form LMDs have been evaluated. For the first time, a mechanically understood ``biological fingerprint`` of high-LET radiation has been established. Specifically measurement of the ratio of inter-to intra-chromosomal aberrations produces a unique signature from alpha-particles or neutrons.

  6. Radiation physics, biophysics, and radiation biology

    SciTech Connect (OSTI)

    Hall, E.J.; Zaider, M.

    1993-05-01T23:59:59.000Z

    Research at the Center for Radiological Research is a multidisciplenary blend of physics, chemistry and biology aimed at understanding the mechanisms involved in the health problems resulting from human exposure to ionizing radiations. The focus is increased on biochemistry and the application of the techniques of molecular biology to the problems of radiation biology. Research highlights of the program from the past year are described. A mathematical model describing the production of single-strand and double-strand breaks in DNA as a function radiation quality has been completed. For the first time Monte Carlo techniques have been used to obtain directly the spatial distribution of DNA moieties altered by radiation. This information was obtained by including the transport codes a realistic description of the electronic structure of DNA. We have investigated structure activity relationships for the potential oncogenicity of a new generation of bioreductive drugs that function as hypoxic cytotoxins. Experimental and theoretical investigation of the inverse dose rate effect, whereby medium LET radiations actually produce an c effect when the dose is protracted, is now at a point where the basic mechanisms are reasonably understood and the complex interplay between dose, dose rate and radiation quality which is necessary for the effect to be present can now be predicted at least in vitro. In terms of early radiobiological damage, a quantitative link has been established between basic energy deposition and locally multiply damaged sites, the radiochemical precursor of DNA double strand breaks; specifically, the spatial and energy deposition requirements necessary to form LMDs have been evaluated. For the first time, a mechanically understood biological fingerprint'' of high-LET radiation has been established. Specifically measurement of the ratio of inter-to intra-chromosomal aberrations produces a unique signature from alpha-particles or neutrons.

  7. DNA Sequencing apparatus

    DOE Patents [OSTI]

    Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

    1992-01-01T23:59:59.000Z

    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.

  8. DNA: structure, dense phases, charges, interactions

    E-Print Network [OSTI]

    Potsdam, Universität

    DNA: structure, dense phases, charges, interactions #12;Outline 1. DNA: structure, charges, dense phases 2. Counterion and DNA condensation 3. ES DNA-DNA interactions 4. DNA toroidal structures 5. Interactions of real DNA helices 6. DNA-DNA ES recognition 7. DNA melting in aggregates 8. Azimuthal

  9. Assigning phrase breaks from part-of-speech sequences. 

    E-Print Network [OSTI]

    Black, Alan W; Taylor, Paul A

    1997-01-01T23:59:59.000Z

    One of the important stages in the process of turning unmarked text into speech is the assignment of appropriate phrase break boundaries. Phrase break boundaries are important to later modules including accent ...

  10. Winter Break 2011 (January) Knowledge is Power Program

    E-Print Network [OSTI]

    , TX) · Kentucky Equine Humane Center (Nicholsville, Kentucky) · Grand Canyon: Kane Ranch (Marble participants) · Community Collaborations, Flood Relief (Atlanta, GA) (10 participants) Weekend Breaks Fall 2009, San Juan, TX (10 participants) Weekend Break Fall 2008 (October)-12 participants · Cedar Rapids

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

    SciTech Connect (OSTI)

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

    2002-01-01T23:59:59.000Z

    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.

  12. Collective neutrino oscillations and spontaneous symmetry breaking

    E-Print Network [OSTI]

    Duan, Huaiyu

    2015-01-01T23:59:59.000Z

    Neutrino oscillations in a hot and dense astrophysical environment such as a core-collapse supernova pose a challenging, seven-dimensional flavor transport problem. To make the problem even more difficult (and interesting), neutrinos can experience collective oscillations through nonlinear refraction in the dense neutrino medium in this environment. Significant progress has been made in the last decade towards the understanding of collective neutrino oscillations in various simplified neutrino gas models with imposed symmetries and reduced dimensions. However, a series of recent studies seem to have "reset" this progress by showing that these models may not be compatible with collective neutrino oscillations because the latter can break the symmetries spontaneously if they are not imposed. We review some of the key concepts of collective neutrino oscillations by using a few simple toy models. We also elucidate the breaking of spatial and directional symmetries in these models because of collective oscillation...

  13. Gravity dual of metastable dynamical supersymmetry breaking

    SciTech Connect (OSTI)

    DeWolfe, Oliver [Department of Physics, 390 UCB, University of Colorado, Boulder, Colorado 80309 (United States); Kachru, Shamit; Mulligan, Michael [Department of Physics and SLAC, Stanford University, Stanford, California 94305/94309 (United States)

    2008-03-15T23:59:59.000Z

    Metastable, supersymmetry-breaking configurations can be created in flux geometries by placing antibranes in warped throats. Via gauge/gravity duality, such configurations should have an interpretation as supersymmetry-breaking states in the dual field theory. In this paper, we perturbatively determine the asymptotic supergravity solutions corresponding to D3-brane probes placed at the tip of the cascading warped deformed conifold geometry, which is dual to an SU(N+M)xSU(N) gauge theory. The backreaction of the antibranes has the effect of introducing imaginary anti-self-dual flux, squashing the compact part of the space and forcing the dilaton to run. Using the generalization of holographic renormalization to cascading geometries, we determine the expectation values of operators in the dual field theory in terms of the asymptotic values of the supergravity fields.

  14. (2) DNA O(n^5) Quorum-Sensing Lux

    E-Print Network [OSTI]

    Hagiya, Masami

    - 1 - ( ) ( ) DNA RNA DNA RNA DNA DNA 2 DNA #12;- 2 - 17 6 (1) (2) DNA O(n^5) (3) Quorum-Sensing Lux (4) (5) LMNtal ambient LMNtal (1) (2) DNA (3) DNA (4) DNA (5) DNA (1) DNA ANP-96 (Precision System Science ) (2) RTRACS DNA RTRACS (3) in vivo in vivo (4) DNA trans cis 1/10 (5) DNA-PNA DNA DNA DNA DNA DNA

  15. Navy Breaks World Record With Futuristic Free-Electron Laser...

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

    foxnews.comscitech20110218navy-breaks-world-record-futuristic-laser-getting-real Submitted: Sunday, February 20, 2011...

  16. Textural break foundation wall construction modules

    DOE Patents [OSTI]

    Phillips, Steven J. (Kennewick, WA)

    1990-01-01T23:59:59.000Z

    Below-grade, textural-break foundation wall structures are provided for inhibiting diffusion and advection of liquids and gases into and out from a surrounding hydrogeologic environment. The foundation wall structure includes a foundation wall having an interior and exterior surface and a porous medium disposed around a portion of the exterior surface. The structure further includes a modular barrier disposed around a portion of the porous medium. The modular barrier is substantially removable from the hydrogeologic environment.

  17. BREAK HOUSING HALLS NOTICE FOR SPRING SEMESTER HOUSING

    E-Print Network [OSTI]

    Massachusetts at Amherst, University of

    BREAK HOUSING HALLS NOTICE FOR SPRING SEMESTER HOUSING BRETT | LEWIS | PRINCE | CASHIN NORTH AREA APARTMENTS #12;If you are cancelling your Break Housing assignment for the spring semester, you have two will receive a $100 refund of the Break Housing fee to your fall Bursar account. 2. If you remain beyond 6:00pm

  18. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01T23:59:59.000Z

    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.

  19. Multiprotein DNA looping

    E-Print Network [OSTI]

    Jose M. G. Vilar; Leonor Saiz

    2006-06-19T23:59:59.000Z

    DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.

  20. Visualizing DNA What is it?

    E-Print Network [OSTI]

    Rose, Michael R.

    Visualizing DNA #12;What is it? Gel electrophoresis is one of the techniques scientists use to look at the DNA they have. This technique separates DNA by size. #12;How does it work? First a gel is prepared. Gels

  1. Breaking Barriers in Polymer Additive Manufacturing

    SciTech Connect (OSTI)

    Love, Lonnie J [ORNL; Duty, Chad E [ORNL; Post, Brian K [ORNL; Lind, Randall F [ORNL; Lloyd, Peter D [ORNL; Kunc, Vlastimil [ORNL; Peter, William H [ORNL; Blue, Craig A [ORNL

    2015-01-01T23:59:59.000Z

    Additive Manufacturing (AM) enables the creation of complex structures directly from a computer-aided design (CAD). There are limitations that prevent the technology from realizing its full potential. AM has been criticized for being slow and expensive with limited build size. Oak Ridge National Laboratory (ORNL) has developed a large scale AM system that improves upon each of these areas by more than an order of magnitude. The Big Area Additive Manufacturing (BAAM) system directly converts low cost pellets into a large, three-dimensional part at a rate exceeding 25 kg/h. By breaking these traditional barriers, it is possible for polymer AM to penetrate new manufacturing markets.

  2. Lattice String Breaking and Heavy Meson Decays

    E-Print Network [OSTI]

    I T Drummond; R R Horgan

    1998-11-11T23:59:59.000Z

    We show how string breaking on the lattice, treated as a mixing effect, can be related to decay rates for heavy quark systems. We use this to make a preliminary calculation of the energy split at maximum mixing for static quarks in QCD from the decay rate for $\\Upsilon(4S)\\to B{\\bar B}$. We extend the calculation to achieve rough estimates for the contributions of channels involving $B, B^*, B_s and B_s^*$ mesons to the width of the $\\Upsilon(5S)$.

  3. Dynamics of Symmetry Breaking and Tachyonic Preheating

    SciTech Connect (OSTI)

    Felder, Gary; Garcia-Bellido, Juan; Greene, Patrick B.; Kofman, Lev; Linde, Andrei; Tkachev, Igor

    2001-07-02T23:59:59.000Z

    We reconsider the old problem of the dynamics of spontaneous symmetry breaking (SSB) using 3D lattice simulations. We develop a theory of tachyonic preheating, which occurs due to the spinodal instability of the scalar field. Tachyonic preheating is so efficient that SSB typically completes within a single oscillation as the field rolls towards the minimum of its effective potential. We show that, contrary to previous expectations, preheating in hybrid inflation is typically tachyonic. Our results may also be relevant for the theory of the formation of topological defects and of disoriented chiral condensates in heavy ion collisions.

  4. Spontaneous Supersymmetry Breaking Induced by Vacuum Condensates

    E-Print Network [OSTI]

    Antonio Capolupo; Marco Di Mauro

    2012-08-29T23:59:59.000Z

    We propose a novel mechanism of spontaneous supersymmetry breaking which relies upon an ubiquitous feature of Quantum Field Theory, vacuum condensates. Such condensates play a crucial r\\^{o}le in many phenomena. Examples include Unruh effect, superconductors, particle mixing, and quantum dissipative systems. We argue that in all these phenomena supersymmetry, when present, is spontaneously broken. Evidence for our conjecture is given for the Wess--Zumino model, that can be considered an approximation to the supersymmetric extensions of the above mentioned systems. The magnitude of the effect is estimated for a recently proposed experimental setup based on an optical lattice.

  5. Site directed recombination

    DOE Patents [OSTI]

    Jurka, Jerzy W. (Los Altos, CA)

    1997-01-01T23:59:59.000Z

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  6. 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)

    2002-01-01T23:59:59.000Z

    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.

  7. Chip breaking system for automated machine tool

    DOE Patents [OSTI]

    Arehart, Theodore A. (Clinton, TN); Carey, Donald O. (Oak Ridge, TN)

    1987-01-01T23:59:59.000Z

    The invention is a rotary selectively directional valve assembly for use in an automated turret lathe for directing a stream of high pressure liquid machining coolant to the interface of a machine tool and workpiece for breaking up ribbon-shaped chips during the formation thereof so as to inhibit scratching or other marring of the machined surfaces by these ribbon-shaped chips. The valve assembly is provided by a manifold arrangement having a plurality of circumferentially spaced apart ports each coupled to a machine tool. The manifold is rotatable with the turret when the turret is positioned for alignment of a machine tool in a machining relationship with the workpiece. The manifold is connected to a non-rotational header having a single passageway therethrough which conveys the high pressure coolant to only the port in the manifold which is in registry with the tool disposed in a working relationship with the workpiece. To position the machine tools the turret is rotated and one of the tools is placed in a material-removing relationship of the workpiece. The passageway in the header and one of the ports in the manifold arrangement are then automatically aligned to supply the machining coolant to the machine tool workpiece interface for breaking up of the chips as well as cooling the tool and workpiece during the machining operation.

  8. Large-Field Inflation and Supersymmetry Breaking

    E-Print Network [OSTI]

    Wilfried Buchmuller; Emilian Dudas; Lucien Heurtier; Clemens Wieck

    2014-07-14T23:59:59.000Z

    Large-field inflation is an interesting and predictive scenario. Its non-trivial embedding in supergravity was intensively studied in the recent literature, whereas its interplay with supersymmetry breaking has been less thoroughly investigated. We consider the minimal viable model of chaotic inflation in supergravity containing a stabilizer field, and add a Polonyi field. Furthermore, we study two possible extensions of the minimal setup. We show that there are various constraints: first of all, it is very hard to couple an O'Raifeartaigh sector with the inflaton sector, the simplest viable option being to couple them only through gravity. Second, even in the simplest model the gravitino mass is bounded from above parametrically by the inflaton mass. Therefore, high-scale supersymmetry breaking is hard to implement in a chaotic inflation setup. As a separate comment we analyze the simplest chaotic inflation construction without a stabilizer field, together with a supersymmetrically stabilized Kahler modulus. Without a modulus, the potential of such a model is unbounded from below. We show that a heavy modulus cannot solve this problem.

  9. 1Ottawa 7/05 Structural Break DetectionStructural Break Detection

    E-Print Network [OSTI]

    ://www.stat.colostate.edu/~rdavis/lectures) This research supported in part by an IBM faculty award. #12;2Ottawa 7/05 Introduction Setup Examples AR GARCH for structural break estimation Simulation results Applications Simulation results for GARCH and SSM #12;3Ottawa/05 Examples (cont) 2. Segmented GARCH model: where 0 = 1

  10. 'Jet breaks' and 'missing breaks' in the X-Ray afterglow of Gamma Ray Bursts

    E-Print Network [OSTI]

    Dado, Shlomo; De Rújula, Alvaro

    2008-01-01T23:59:59.000Z

    The X-ray afterglows (AGs) of Gamma-Ray Bursts (GRBs) and X-Ray Flashes (XRFs) have, after the fast decline phase of their prompt emission, a temporal behaviour varying between two extremes. A large fraction of these AGs has a 'canonical' light curve which, after an initial shallow-decay 'plateau' phase, 'breaks smoothly' into a fast power-law decline. Very energetic GRBs, contrariwise, appear not to have a 'break', their AG declines like a power-law from the start of the observations. Breaks and 'missing breaks' are intimately related to the geometry and deceleration of the jets responsible for GRBs. In the frame of the 'cannonball' (CB) model of GRBs and XRFs, we analyze the cited extreme behaviours (canonical and pure power-law) and intermediate cases spanning the observed range of X-ray AG shapes. We show that the entire panoply of X-ray light-curve shapes --measured with Swift and other satellites-- are as anticipated, on very limpid grounds, by the CB model. We test the expected correlations between the...

  11. FIRST ATTEMPTS AT PREDICTION OF DNA STRAND-BREAK YIELDS USING NANODOSIMETRIC DATA

    E-Print Network [OSTI]

    an ion-cluster size distribution. This approach is the only one possible in case of unknown radiation data consist of ion-cluster size distributions [f(nion)], providing the absolute freq- uency of ion projectile particle. The SV can be approximated by a cylinder of 1.6 mm diam. (in 120 Pa propane gas) whose

  12. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12T23:59:59.000Z

    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.

  13. DNA chips --Integrated Chemical Circuits for DNADiagnosis and DNA computers

    E-Print Network [OSTI]

    Hagiya, Masami

    DNA chips -- Integrated Chemical Circuits for DNADiagnosis and DNA computers Akira Suyama, Associate Professor Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo DNA chips are si l i con­ or glass­based smal l surfaces on which many DNA ol i gonuc l eotides are i

  14. Focus: DNA probes

    SciTech Connect (OSTI)

    Not Available

    1986-11-01T23:59:59.000Z

    Progress in the development of DNA probes for the identification and quantitation of specific genetic sequences in biological samples is reviewed. Current research efforts in the development of DNA probes for the diagnosis of a wide variety of bacterial, viral, and other infectious diseases, such as herpes simplex and cytomegalovirus, and inherited genetic diseases such as cystic fibrosis and sickle cell anemia are discussed. Progress in development of DNA probe assays for cancer diagnosis, detection of Salmonella food poisoning, tissue typing (detection of histocompatibility antigens), mutagen screening, and animal diseases, among other applications is included.

  15. Dynamical electroweak symmetry breaking and the top quark

    SciTech Connect (OSTI)

    Chivukula, R.S. [Boston Univ., MA (United States)

    1997-01-01T23:59:59.000Z

    In this talk, I discuss theories of dynamical electroweak symmetry breaking, with emphasis on the implications of a heavy top quark on the weak interaction {rho} parameter.

  16. Understanding the Electroweak Symmetry Breaking: The Higgs Boson...

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

    Understanding the Electroweak Symmetry Breaking: The Higgs Boson and Beyond (Monday, March 2) DATE: Monday, March 2, 4:10 pm LOCATION: Physics 0003 Understanding the Electroweak...

  17. R-symmetry and Supersymmetry Breaking at Finite Temperature

    E-Print Network [OSTI]

    E. F. Moreno; F. A. Schaposnik

    2009-09-16T23:59:59.000Z

    We analyze the spontaneous $U(1)_R$ symmetry breaking at finite temperature for the simple O'Raifeartaigh-type model introduced in [1] in connection with spontaneous supersymmetry breaking. We calculate the finite temperature effective potential (free energy) to one loop order and study the thermal evolution of the model. We find that the R-symmetry breaking occurs through a second order phase transition. Its associated meta-stable supersymmetry breaking vacuum is thermodynamically favored at high temperatures and the model remains trapped in this state by a potential barrier, as the temperature lowers all the way until T=0.

  18. Isospin-Breaking quark condensates in Chiral Perturbation Theory

    E-Print Network [OSTI]

    A. Gomez Nicola; R. Torres Andres

    2011-11-14T23:59:59.000Z

    We analyze the isospin-breaking corrections to quark condensates within one-loop SU(2) and SU(3) Chiral Perturbation Theory including $m_u\

  19. Low energy dynamical supersymmetry breaking simplified

    SciTech Connect (OSTI)

    Dine, M. (Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, California 95064 (United States)); Nelson, A.E. (Department of Physics, FM-15, University of Washington, Seattle,Washington 98195 (United States)); Shirman, Y. (Santa Cruz Institute for Particle Physics, University of California, Santa Cruz, California 95064 (United States))

    1995-02-01T23:59:59.000Z

    We present a model in which supersymmetry is dynamically broken at comparatively low energies. Previous efforts to construct simple models of this sort have been hampered by the presence of axions. The present model, which exploits an observation of Bagger, Poppitz, and Randall to avoid this problem, is far simpler than previous constructions. Models of this kind do not suffer from the naturalness difficulties of conventional supergravity models, and make quite definite predictions for physics over a range of scales from 100's of GeV to 1000's of TeV. Thus renormalizable visible sector models'' are a viable alternative to more conventional approaches. Our approach also yields a viable example of hidden sector dynamical supersymmetry breaking.

  20. -DNA 1217 BK21-IT,

    E-Print Network [OSTI]

    - DNA 1217 BK21-IT, (MEC) (NRL) . . : : : : syshin@bi.snu.ac.kr ihlee@bi.snu.ac.kr btzhang@bi.snu.ac.kr 2004 9 16 2005 10 14 - DNA (DNA Sequence Design using -Multiobjective Evolutionary Algorithm) (Soo-Yong Shin) (In-Hee Lee) (Byoung-Tak Zhang) DNA

  1. Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

    E-Print Network [OSTI]

    Christian Matek; Thomas E. Ouldridge; Jonathan P. K. Doye; Ard A. Louis

    2014-04-10T23:59:59.000Z

    Biological information is not only stored in the digital chemical sequence of double helical DNA, but is also encoded in the mechanical properties of the DNA strands, which can influence biochemical processes involving its readout. For example, loop formation in the Lac operon can regulate the expression of key genes, and DNA supercoiling is closely correlated to rhythmic circardian gene expression in cyanobacteria. Supercoiling is also important for large scale organisation of the genome in both eukaryotic and prokaryotic cells. DNA can respond to torsional stress by writhing to form looped structures called plectonemes, thus transferring energy stored as twist into energy stored in bending. Denaturation bubbles can also relax torsional stress, with the enthalpic cost of breaking bonds being compensated by their ability to absorb undertwist. Here we predict a novel regime where bubbles form at the tips of plectonemes, and study its properties using coarse-grained simulations. These tip bubbles can occur for both positive and negative supercoiling and greatly reduce plectoneme diffusion by a pinning mechanism. They can cause plectonemes to preferentially localise to AT rich regions, because bubbles more easily form there. The tip-bubble regime occurs for supercoiling densities and forces that are typically encountered for DNA in vivo, and may be exploited for biological control of genomic processes.

  2. Intermediate DNA at low added salt: DNA bubbles slow the diffusion of short DNA fragments

    E-Print Network [OSTI]

    Tomislav Vuletic; Sanja Dolanski Babic; Ticijana Ban; Joachim Raedler; Francoise Livolant; Silvia Tomic

    2011-01-05T23:59:59.000Z

    We report a study of DNA (150 bp fragments) conformations in very low added salt $DNA concentration range $0.0015\\leq c \\leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 DNA has the diffusion coefficient, $D_p$ reduced below the values for both ssDNA coils and native dsDNA helices of similar polymerization degree $N$. Thus, this DNA population can not be a simple mix of dsDNA and of ssDNA which results from DNA melting. Here, melting occurs due to a reduction in screening concomitant with DNA concentration being reduced, in already very low salt conditions. The intermediate DNA is rationalized through the well known concept of fluctuational openings (DNA bubbles) which we postulate to form in AT-rich portions of the sequence, without the strands coming apart. Within the bubbles, DNA is locally stretched, while the whole molecule remains rod-like due to very low salt environment. Therefore, such intermediate DNA is elongated, in comparison to dsDNA, which accounts for its reduced $D_p$.

  3. Strandwise translocation of a DNA glycosylase on undamaged DNA

    SciTech Connect (OSTI)

    Qi, Yan; Nam, Kwangho; Spong, Marie C.; Banerjee, Anirban; Sung, Rou-Jia; Zhang, Michael; Karplus, Martin; Verdine, Gregory L. (Harvard)

    2012-05-14T23:59:59.000Z

    Base excision repair of genotoxic nucleobase lesions in the genome is critically dependent upon the ability of DNA glycosylases to locate rare sites of damage embedded in a vast excess of undamaged DNA, using only thermal energy to fuel the search process. Considerable interest surrounds the question of how DNA glycosylases translocate efficiently along DNA while maintaining their vigilance for target damaged sites. Here, we report the observation of strandwise translocation of 8-oxoguanine DNA glycosylase, MutM, along undamaged DNA. In these complexes, the protein is observed to translocate by one nucleotide on one strand while remaining untranslocated on the complementary strand. We further report that alterations of single base-pairs or a single amino acid substitution (R112A) can induce strandwise translocation. Molecular dynamics simulations confirm that MutM can translocate along DNA in a strandwise fashion. These observations reveal a previously unobserved mode of movement for a DNA-binding protein along the surface of DNA.

  4. Symmetry breaking and low energy conformational fluctuations in

    E-Print Network [OSTI]

    Drabold, David

    Symmetry breaking and low energy conformational fluctuations in amorphous graphene Y. Li and D. A. Drabold* Department of Physics and Astronomy, Condensed Matter Surface Science Program, Ohio University Published online 21 December 2012 Keywords amorphous graphene, low-energy excitation, symmetry breaking

  5. Nonequilibrium symmetry breaking and pattern formation in magnetic films

    E-Print Network [OSTI]

    Deutsch, Josh

    films. ­ p. 7/6 #12;Applications of Ferromagnetism Doodle Pads Refrigerator Magnets NonequilibriumNonequilibrium symmetry breaking and pattern formation in magnetic films Josh Deutsch University of California Santa Cruz Nonequilibrium symmetry breaking and pattern formation in magnetic films. ­ p. 1/6 #12

  6. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

    Doye, Jonathan P K; Louis, Ard A; Romano, Flavio; Sulc, Petr; Matek, Christian; Snodin, Benedict E K; Rovigatti, Lorenzo; Schreck, John S; Harrison, Ryan M; Smith, William P J

    2013-01-01T23:59:59.000Z

    To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

  7. Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection...

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

    Hairpin DNA Switch for Ultrasensitive Spectrophotometric Detection of DNA Hybridization Based on Gold Nanoparticles and Enzyme Hairpin DNA Switch for Ultrasensitive...

  8. Creaming and breaking of liquid emulsions: a free boundary problem 1 / 48 Creaming and breaking of liquid

    E-Print Network [OSTI]

    Rosso, Fabio

    , as opposite to the other case called instead a water-in-oil emulsion. #12;Creaming and breaking of liquid emulsions: a free boundary problem 4 / 48 What is an emulsion? Everyday life examples (a) water-in-oil of the model 5 A priori estimates 6 Existence and uniqueness #12;Creaming and breaking of liquid emulsions

  9. 1SCRA 2006 FIM XIII-PORTUGAL Structural Break Detection for a ClassStructural Break Detection for a Class

    E-Print Network [OSTI]

    1000 -4-202 Any breaks in this series? #12;5SCRA 2006 FIM XIII-PORTUGAL Introduction Examples AR GARCH for structural break estimation Simulation results Applications Simulation results for GARCH and SV models #12 (cont) 2. Segmented GARCH model: where 0 = 1

  10. 1NCAR-IMAGe 2006 Structural Break Detection in Time Series ModelsStructural Break Detection in Time Series Models

    E-Print Network [OSTI]

    -202 Any breaks in this series? #12;5NCAR-IMAGe 2006 Introduction Examples AR GARCH Stochastic volatility break estimation Simulation results Applications Simulation results for GARCH and SV models #12;6NCAR-tjptjptjjt tYYY jj GARCH model

  11. Charge symmetry breaking in $\\Lambda$ hypernuclei revisited

    E-Print Network [OSTI]

    Gal, Avraham

    2015-01-01T23:59:59.000Z

    The large charge symmetry breaking (CSB) implied by the $\\Lambda$ binding energy difference $\\Delta B^{4}_{\\Lambda}(0^+_{\\rm g.s.})\\equiv B_{\\Lambda}(_{\\Lambda}^4$He)$-$$B_{\\Lambda}(_{\\Lambda}^4$H) = 0.35$\\pm$0.06 MeV of the $A=4$ mirror hypernuclei ground states, determined from emulsion studies, has defied theoretical attempts to reproduce it in terms of CSB in hyperon masses and in hyperon-nucleon interactions, including one pion exchange arising from $\\Lambda-\\Sigma^0$ mixing. Using a schematic strong-interaction $\\Lambda N\\leftrightarrow\\Sigma N$ coupling model developed by Akaishi and collaborators for $s$-shell $\\Lambda$ hypernuclei, we revisit the evaluation of CSB in the $A=4$ $\\Lambda$ hypernuclei and extend it to $p$-shell mirror $\\Lambda$ hypernuclei. The model yields values of $\\Delta B^{4}_{\\Lambda} (0^+_{\\rm g.s.})\\sim 0.25$ MeV. Smaller size and mostly negative $p$-shell binding energy differences are calculated for the $A=7-10$ mirror hypernuclei, in rough agreement with the few available dat...

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

    DOE Patents [OSTI]

    Tabor, Stanley (Cambridge, MA); Richardson, Charles (Chestnut Hill, MA)

    1997-01-01T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25T23:59:59.000Z

    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.

  14. Developing Single-Molecule TPM Experiments for Direct Observation of Successful RecA-Mediated Strand

    E-Print Network [OSTI]

    Cox, Michael M.

    : This project is supported by National Science Council of Taiwan to HWL and the United States National information is crucial for cell survival. RecA-mediated homologous recombination repairs double-stranded (ds ssDNA and the dsDNA, with the ejection of the displaced strand, and (v) depolymerization of RecA from

  15. Searching for DNA Lesions: Structural Evidence for Lower- and Higher-Affinity DNA Binding Conformations of Human Alkyladenine DNA Glycosylase

    E-Print Network [OSTI]

    Drennan, Catherine L.

    To efficiently repair DNA, human alkyladenine DNA glycosylase (AAG) must search the million-fold excess of unmodified DNA bases to find a handful of DNA lesions. Such a search can be facilitated by the ability of glycosylases, ...

  16. Dynamical chiral symmetry breaking in strangelets at finite temperature

    E-Print Network [OSTI]

    Chang-Qun Ma; Chun-Yuan Gao

    2009-12-08T23:59:59.000Z

    A model for strangelets at finite temperature is built, in which the quark masses are dynamically generated. The dynamical chiral symmetry breaking inside strangelets at finite temperature is investigated. It is found that the chiral symmetry is going to break spontaneously inside the strangelets at some finite temperature, and then the masses of strange quarks inside the strangelets increase as the temperature rises. The phenomenon that strange quark mass increases with temperature after the chiral symmetry breaks spontaneously is illustrated by some typical numerical examples.

  17. DNA Damage Induced by Low-Energy Electrons: Electron Transfer and Diffraction

    SciTech Connect (OSTI)

    Zheng Yi; Wagner, J. Richard; Sanche, Leon [Groupe de Recherche en Sciences des Radiations, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, QC J1H 5N4 (Canada)

    2006-05-26T23:59:59.000Z

    Thin films of the short single strand of DNA, GCAT, in which guanine (G) or adenine (A) have been removed, were bombarded under vacuum by 4 to 15 eV electrons. The fragments corresponding to base release and strand breaks (SB) were analyzed by high performance liquid chromatography and their yields compared with those obtained from unmodified GCAT. From such a comparison, it is shown that, using GCAT as a model system (1) most SB result from electron capture by DNA bases followed by electron transfer to the phosphate group and (2) the initial capture probability depends on the coherence of the electron wave within the tetramer.

  18. DNA Structural Nanotechnology Duke University

    E-Print Network [OSTI]

    Reif, John H.

    DNA Structural Nanotechnology John Reif Duke University Graduate Students: Harish Chandran&Caltech Tube Lattices #12;Ned Seeman New York University, USA Ned Seeman: Father of DNA Nanotechnology His Initial Ideas & Motivation for DNA Nanotechnology #12;Cube Chen & Seeman, Nature350:631 (1991) Truncated

  19. Sensing DNA - DNA as nanosensor: a perspective towards nanobiotechnology

    E-Print Network [OSTI]

    Ralf Metzler; Tobias Ambjoernsson

    2005-08-20T23:59:59.000Z

    Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA may be used as a local sensor. Employing single molecule fluorescence methods, we propose to make use of the physics of DNA denaturation nanoregions to find out about the solvent conditions such as ionic strength, presence of binding proteins, etc. By measuring dynamical quantities in particular, rather sensitive nanoprobes may be constructed with contemporary instruments.

  20. Adenoviral E4orf3 and E4orf6 Proteins, But Not E1B55K, Increase Killing of Cancer Cells by Radiotherapy in vivo

    SciTech Connect (OSTI)

    Liikanen, Ilkka; Dias, Joao D.; Nokisalmi, Petri; Sloniecka, Marta; Kangasniemi, Lotta; Rajecki, Mari [Cancer Gene Therapy Group, Molecular Cancer Biology Program and Transplantation Laboratory and Haartman Institute and Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki (Finland); HUSLAB, Helsinki University Central Hospital, Helsinki (Finland); Dobner, Thomas [Heinrich Pette Institute for Experimental Virology and Immunology, Hamburg (Germany); Tenhunen, Mikko [Department of Oncology, Helsinki University Central Hospital, Helsinki (Finland); Kanerva, Anna [Cancer Gene Therapy Group, Molecular Cancer Biology Program and Transplantation Laboratory and Haartman Institute and Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki (Finland); Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki (Finland); Pesonen, Sari [Cancer Gene Therapy Group, Molecular Cancer Biology Program and Transplantation Laboratory and Haartman Institute and Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki (Finland); HUSLAB, Helsinki University Central Hospital, Helsinki (Finland); Ahtiainen, Laura Ph.D., E-mail: laura.ahtiainen@helsinki.f [Cancer Gene Therapy Group, Molecular Cancer Biology Program and Transplantation Laboratory and Haartman Institute and Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki (Finland); HUSLAB, Helsinki University Central Hospital, Helsinki (Finland); Hemminki, Akseli, E-mail: akseli.hemminki@helsinki.f [Cancer Gene Therapy Group, Molecular Cancer Biology Program and Transplantation Laboratory and Haartman Institute and Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki (Finland); HUSLAB, Helsinki University Central Hospital, Helsinki (Finland)

    2010-11-15T23:59:59.000Z

    Purpose: Radiotherapy is widely used for treatment of many tumor types, but it can damage normal tissues. It has been proposed that cancer cells can be selectively sensitized to radiation by adenovirus replication or by using radiosensitizing transgenes. Adenoviral proteins E1B55K, E4orf3, and E4orf6 play a role in radiosensitization, by targeting the Mre11, Rad50, and NBS1 complex (MRN) and inhibiting DNA double-strand break (DSB) repair. We hypothesize that combined with irradiation, these adenoviral proteins increase cell killing through the impairment of DSB repair. Methods and Materials: We assessed the radiosensitizing/additive potential of replication-deficient adenoviruses expressing E1B55K, E4orf3, and E4orf6 proteins. Combination treatments with low-dose external photon beam radiotherapy were studied in prostate cancer (PC-3MM2 and DU-145), breast cancer (M4A4-LM3), and head and neck cancer (UT-SCC8) cell lines. We further demonstrated radiosensitizing or additive effects in mice with PC-3MM2 tumors. Results: We show enhanced cell killing with adenovirus and radiation combination treatment. Co-infection with several of the viruses did not further increase cell killing, suggesting that both E4orf6 and E4orf3 are potent in MRN inhibition. Our results show that adenoviral proteins E4orf3 and E4orf6, but not E1B55K, are effective also in vivo. Enhanced cell killing was due to inhibition of DSB repair resulting in persistent double-strand DNA damage, indicated by elevated phospho-H2AX levels at 24 h after irradiation. Conclusions: This knowledge can be applied for improving the treatment of malignant tumors, such as prostate cancer, for development of more effective combination therapies and minimizing radiation doses and reducing side effects.

  1. Petra Nova Project Breaks Ground on World's Largest Post-Combustion...

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

    Petra Nova Project Breaks Ground on World's Largest Post-Combustion Carbon Capture Project Petra Nova Project Breaks Ground on World's Largest Post-Combustion Carbon Capture...

  2. SciTech Connect: Sphericity and symmetry breaking in the formation...

    Office of Scientific and Technical Information (OSTI)

    and symmetry breaking in the formation of FrankKasper phases from one component materials Citation Details In-Document Search Title: Sphericity and symmetry breaking in the...

  3. Wave breaking along the stratospheric polar vortex as seen in ERA-40 data

    E-Print Network [OSTI]

    Abatzoglou, John T; Magnusdottir, Gudrun

    2007-01-01T23:59:59.000Z

    1983), Breaking planetary waves in the stratosphere, Nature,structure of breaking Rossby waves in the polar wintertimecontrol of upward wave flux near the tropopause, Geophys.

  4. The Role of Pendant Amines in the Breaking and Forming of Molecular...

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

    Pendant Amines in the Breaking and Forming of Molecular Hydrogen Catalyzed by Nickel Complexes. The Role of Pendant Amines in the Breaking and Forming of Molecular Hydrogen...

  5. Dynamical R-parity Breaking at the LHC

    E-Print Network [OSTI]

    Chen, Shao-Long; Mohapatra, Rabindra N; Zhang, Yue

    2010-01-01T23:59:59.000Z

    In a class of extensions of the minimal supersymmetric standard model with (B-L)/left-right symmetry that explains the neutrino masses, breaking R-parity symmetry is an essential and dynamical requirement for successful gauge symmetry breaking. Two consequences of these models are: (i) a new kind of R-parity breaking interaction that protects proton stability but adds new contributions to neutrinoless double beta decay and (ii) an upper bound on the extra gauge and parity symmetry breaking scale which is within the large hadron collider (LHC) energy range. We point out that an important prediction of such theories is a potentially large mixing between the right-handed charged lepton ($e^c$) and the superpartner of the right-handed gauge boson ($\\widetilde W_R^+$), which leads to a brand new class of R-parity violating interactions of type $\\widetilde{\\mu^c}^\\dagger\

  6. Tackling Epistemological Problems (TEP) A didactical engineering to break through

    E-Print Network [OSTI]

    Spagnolo, Filippo

    Tackling Epistemological Problems (TEP) A didactical engineering to break through the amazing world, becomes a didactical obstacle for the learning of this geometry. We need to use 3D models and also dynamic

  7. Assigning phrase breaks from part-of-speech sequences 

    E-Print Network [OSTI]

    Taylor, Paul; Black, Alan W

    This paper presents an algorithm for automatically assigning phrase breaks to unrestricted text for use in a text-to-speech synthesizer. Text is first converted into a sequence of part-of-speech tags. Next a Markov model ...

  8. Sets of Symmetry Breaking Constraints Barbara M. Smith

    E-Print Network [OSTI]

    Smith, Barbara M.

    Sets of Symmetry Breaking Constraints Barbara M. Smith Cork Constraint Computation Centre, University College Cork, Ireland b.m.smith@4c.ucc.ie Abstract [Puget, 2004] has shown that if the symmetry

  9. Holographic theories of electroweak symmetry breaking without a Higgs Boson

    E-Print Network [OSTI]

    Burdman, Gustavo; Nomura, Yasunori

    2003-01-01T23:59:59.000Z

    Breaking without a Higgs Boson Gustavo Burdman a and1] or theories where the Higgs boson arises as a compositeto build models of a composite Higgs boson [4] and dynamical

  10. The Independent Caucus: Breaking the Rubber Stamp Mold

    E-Print Network [OSTI]

    Illinois at Chicago, University of

    The Independent Caucus: Breaking the Rubber Stamp Mold Chicago City Council Report May 21, 2007 in its voting patterns. It remains to be seen if this new oppositional bloc will undermine the rubber

  11. Novel Thermal Break with Simplified Manufacturing for R7 Commercial...

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

    (R5 OptiQ-Ultra Thermal Windows). Windows incorporating the foam-based sandwich-type thermal-break would achieve U-Factor of 0.14 Btuhr-ft2-F (R7 or better) with...

  12. Dynamics of Wave Breaking at a Coastal Sea Wall

    E-Print Network [OSTI]

    Antoine, Arthur L.

    2010-07-14T23:59:59.000Z

    etc). Even the "Factor of Safety" which is regularly used in designs to account for unknown and/or unforeseen situations which might occur implies a degree of uncertainty about the dynamic scenario of breaking waves in the coastal environment...

  13. Synchronous Symmetry Breaking in Neurons with Different Neurite Counts

    E-Print Network [OSTI]

    Wissner-Gross, Zachary D.

    As neurons develop, several immature processes (i.e., neurites) grow out of the cell body. Over time, each neuron breaks symmetry when only one of its neurites grows much longer than the rest, becoming an axon. This symmetry ...

  14. 1Kaiserslautern 9/05 Structural Break Detection in Time Series ModelsStructural Break Detection in Time Series Models

    E-Print Network [OSTI]

    Regressive Modeling 4 pieces, 2.58 seconds. #12;4Kaiserslautern 9/05 Introduction Examples AR GARCH Stochastic for structural break estimation Simulation results Applications Simulation results for GARCH and SSM #12. Segmented GARCH model: where 0 = 1

  15. DNA decontamination: DNA-ExitusPlus in comparison with conventional reagents

    E-Print Network [OSTI]

    Cai, Long

    DNA decontamination: DNA-ExitusPlus in comparison with conventional reagents Here we present a completely new DNA decontamination reagent DNA-ExitusPlus. In comparison with conventional products, DNA solutions for effective DNA decontamination. DNA decontamination reagents use three different molecular prin

  16. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01T23:59:59.000Z

    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.

  17. Tops and Writhing DNA

    E-Print Network [OSTI]

    Joseph Samuel; Supurna Sinha

    2010-11-30T23:59:59.000Z

    The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.

  18. DNA waves and water

    E-Print Network [OSTI]

    L. Montagnier; J. Aissa; E. Del Giudice; C. Lavallee; A. Tedeschi; G. Vitiello

    2010-12-23T23:59:59.000Z

    Some bacterial and viral DNA sequences have been found to induce low frequency electromagnetic waves in high aqueous dilutions. This phenomenon appears to be triggered by the ambient electromagnetic background of very low frequency. We discuss this phenomenon in the framework of quantum field theory. A scheme able to account for the observations is proposed. The reported phenomenon could allow to develop highly sensitive detection systems for chronic bacterial and viral infections.

  19. Monosporascus root rot/vine decline: a study of double-stranded (DS) RNA and its role in the pathogenesis of Monosporascus cannonballus on muskmelon

    E-Print Network [OSTI]

    Batten, Jeffrey Samuel

    1997-01-01T23:59:59.000Z

    dodecyl sulfate (SDS), and 10 mg of carborundum (Sigma Chemical Co. , St. Louis, MO) for 1 min and incubated for 30 min at 37'C to allow for degradation of host RNAs. Nucleic acids were extracted with an equal volume of TE saturated phenol...

  20. Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families

    SciTech Connect (OSTI)

    Carbonell, Alberto; Martinez de Alba, Angel-Emilio [Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politecnica, Avenida de los Naranjos, s/n, 46022 Valencia (Spain); Flores, Ricardo [Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politecnica, Avenida de los Naranjos, s/n, 46022 Valencia (Spain)], E-mail: rflores@ibmcp.upv.es; Gago, Selma [Instituto de Biologia Molecular y Celular de Plantas (UPV-CSIC), Campus Universidad Politecnica, Avenida de los Naranjos, s/n, 46022 Valencia (Spain)

    2008-02-05T23:59:59.000Z

    Infection by viroids, non-protein-coding circular RNAs, occurs with the accumulation of 21-24 nt viroid-derived small RNAs (vd-sRNAs) with characteristic properties of small interfering RNAs (siRNAs) associated to RNA silencing. The vd-sRNAs most likely derive from dicer-like (DCL) enzymes acting on viroid-specific dsRNA, the key elicitor of RNA silencing, or on the highly structured genomic RNA. Previously, viral dsRNAs delivered mechanically or agroinoculated have been shown to interfere with virus infection in a sequence-specific manner. Here, we report similar results with members of the two families of nuclear- and chloroplast-replicating viroids. Moreover, homologous vd-sRNAs co-delivered mechanically also interfered with one of the viroids examined. The interference was sequence-specific, temperature-dependent and, in some cases, also dependent on the dose of the co-inoculated dsRNA or vd-sRNAs. The sequence-specific nature of these effects suggests the involvement of the RNA induced silencing complex (RISC), which provides sequence specificity to RNA silencing machinery. Therefore, viroid titer in natural infections might be regulated by the concerted action of DCL and RISC. Viroids could have evolved their secondary structure as a compromise between resistance to DCL and RISC, which act preferentially against RNAs with compact and relaxed secondary structures, respectively. In addition, compartmentation, association with proteins or active replication might also help viroids to elude their host RNA silencing machinery.

  1. The horizontal dam break problem for slow non-Newtonian power-law fluids

    E-Print Network [OSTI]

    The horizontal dam break problem for slow non-Newtonian power-law fluids P. Saramito a C. Smutek bLaboratoire g´eosciences ­ IPGP et universit´e de La R´eunion, France Abstract ­ The dam break problem shallow for the horizontal dam break problem. Keywords ­ viscoplastic fluid; dam break problem; shallow flows. 1

  2. Explicit Supersymmetry Breaking on Boundaries of Warped Extra Dimensions

    SciTech Connect (OSTI)

    Hall, Lawrence J.; Nomura, Yasunori; Okui, Takemichi; Oliver, Steven J.

    2003-02-25T23:59:59.000Z

    Explicit supersymmetry breaking is studied in higher dimensional theories by having boundaries respect only a subgroup of the bulk symmetry. If the boundary symmetry is the maximal subgroup allowed by the boundary conditions imposed on the fields, then the symmetry can be consistently gauged; otherwise gauging leads to an inconsistent theory. In a warped fifth dimension, an explicit breaking of all bulk supersymmetries by the boundaries is found to be inconsistent with gauging; unlike the case of flat 5D, complete supersymmetry breaking by boundary conditions is not consistent with supergravity. Despite this result, the low energy effective theory resulting from boundary supersymmetry breaking becomes consistent in the limit where gravity decouples, and such models are explored in the hope that some way of successfully incorporating gravity can be found. A warped constrained standard model leads to a theory with one Higgs boson with mass expected close to the experimental limit. A unified theory in a warped fifth dimension is studied with boundary breaking of both SU(5) gauge symmetry and supersymmetry. The usual supersymmetric predictionfor gauge coupling unification holds even though the TeV spectrum is quite unlike the MSSM. Such a theory may unify matter and Higgs in the same SU(5) hypermultiplet.

  3. Gel and process for preventing carbon dioxide break through

    SciTech Connect (OSTI)

    Sandiford, B.B.; Zillmer, R.C.

    1987-06-16T23:59:59.000Z

    A process is described for retarding the flow of carbon dioxide in carbon dioxide break-through fingers in a subterranean formation, the process comprising: (a) introducing a gas selected from the group consisting of carbon dioxide and gases containing carbon dioxide into a subterranean deposit containing carbon dioxide break-through fingers; (b) after the carbon dioxide break-through fingers have sorbed a predetermined amount of the gas, stopping the flow of the gas into the subterranean formation, (c) after stopping the flow of the gas into the subterranean formation, introducing an effective amount of a gel-forming composition into the subterranean formation and into the carbon dioxide break-through fingers, the gel-forming composition being operable, when contacting carbon dioxide break-through fingers containing the brine which has absorbed substantial amounts of carbon dioxide to form a gel in the fingers which is operable for retarding the flow of the gas in the finger. The gel-forming composition comprises: i. an aqueous solution comprising a first substance selected from the group consisting of polyvinyl alcohols, polyvinyl alcohol copolymers, and mixtures thereof, and ii. an amount of a second substance selected from the group consisting of aldehydes, aldehyde generating substances, acetals, acetal generating substances, and mixtures thereof.

  4. Interstrand DNA-DNA Cross-Link Formation Between Adenine Residues and Abasic Sites in Duplex DNA

    E-Print Network [OSTI]

    Gates, Kent. S.

    Interstrand DNA-DNA Cross-Link Formation Between Adenine Residues and Abasic Sites in Duplex DNA of DNA is a common event that generates an abasic (Ap) site (1). Ap sites exist as an equilibrating that can form covalent adducts with nucleophilic sites in DNA. Thus, Ap sites present a potentially

  5. DNA attachment to support structures

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

    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).

  6. A Model for Structure and Thermodynamics of ssDNA and dsDNA Near...

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

    Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse Grained Approach. A Model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface:A Coarse...

  7. B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynami...

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

    B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations. B-DNA Under Stress: Over- and Untwisting of DNA during MolecularDynamics Simulations....

  8. Controlling DNA Methylation

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration would likeConstitution And BylawsMetal-Organic FrameworksControlling DNA

  9. Application of break preclusion concept in German nuclear power plants

    SciTech Connect (OSTI)

    Roos, E. [Energie-Versorgung Schwaben AG, Stuttgart (Germany); Maier, V. [Bayernwerk AG, Muenchen (Germany); Nagel, G. [PraussenElektra AG, Hannover (Germany)] [and others

    1997-04-01T23:59:59.000Z

    The break preclusion concept is based on {open_quotes}KTA rules{close_quotes}, {open_quotes}RSK guidelines{close_quotes} and {open_quotes}Rahmenspeziflkation Basissicherheit{close_quotes}. These fundamental rules containing for example requirements on material, design, calculation, manufacturing and testing procedures are explained and the technical realisation is shown by means of examples. The proof of the quality of these piping systems can be executed by means of fracture mechanics calculations by showing that in every case the leakage monitoring system already detect cracks which are clearly smaller than the critical crack. Thus the leak before break behavior and the break preclusion concept is implicitly affirmed. In order to further diminish conservativities in the fracture mechanics procedures, specific research projects are executed which are explained in this contribution.

  10. Lorentz symmetry breaking as a quantum field theory regulator

    SciTech Connect (OSTI)

    Visser, Matt [School of Mathematics, Statistics, and Operations Research, Victoria University of Wellington, Wellington 6140 (New Zealand)

    2009-07-15T23:59:59.000Z

    Perturbative expansions of quantum field theories typically lead to ultraviolet (short-distance) divergences requiring regularization and renormalization. Many different regularization techniques have been developed over the years, but most regularizations require severe mutilation of the logical foundations of the theory. In contrast, breaking Lorentz invariance, while it is certainly a radical step, at least does not damage the logical foundations of the theory. I shall explore the features of a Lorentz symmetry breaking regulator in a simple polynomial scalar field theory and discuss its implications. In particular, I shall quantify just 'how much' Lorentz symmetry breaking is required to fully regulate the quantum theory and render it finite. This scalar field theory provides a simple way of understanding many of the key features of Horava's recent article [Phys. Rev. D 79, 084008 (2009)] on 3+1 dimensional quantum gravity.

  11. Break modeling for RELAP5 analyses of ISP-27 Bethsy

    SciTech Connect (OSTI)

    Petelin, S.; Gortnar, O.; Mavko, B.; Parzer, I.

    1992-01-01T23:59:59.000Z

    This paper presents pre- and posttest analyses of International Standard Problem (ISP) 27 on the Bethsy facility and separate RELAP5 break model tests considering the measured boundary condition at break inlet. This contribution also demonstrates modifications which have assured the significant improvement of model response in posttest simulations. Calculations were performed using the RELAP5/MOD2/36.05 and RELAP5/MOD3.5M5 codes on the MicroVAX, SUN, and CONVEX computers. Bethsy is an integral test facility that simulates a typical 900-MW (electric) Framatome pressurized water reactor. The ISP-27 scenario involves a 2-in. cold-leg break without HPSI and with delayed operator procedures for secondary system depressurization.

  12. Comparing Measured Fluorocarbon Leader Breaking Strength with Manufacturer Claims

    E-Print Network [OSTI]

    Haight, Christine; McQueeney, Kathleen; Courtney, Ya'el

    2012-01-01T23:59:59.000Z

    The experiment reported in this article addresses manufacturer claims of fluorocarbon leader material strength versus experimental tests of leaders strength. Breaking strength of fishing line is the most common specification when marketing fishing line. In this study, eight leaders rated near 15 pounds by their manufacturers were tested. Each leader was tested with a knot in the line and without a knot in the line. The strongest leader tested without a knot was Cabela's Seaguar fluorocarbon and the weakest leader tested without a knot was Cabela's Premier leader. The highest strength of leaders with a knot was the Ande Monofilament Fluorocarbon and the lowest breaking strength of leaders with a knot was the Seaguar Grand Max Fluorocarbon. Few published studies actually test the breaking strength of a leader to determine the accuracy of manufacturers' claims. Tensile strengths are also reported.

  13. Break-up stage restoration in multifragmentation reactions

    E-Print Network [OSTI]

    Ad. R. Raduta; E. Bonnet; B. Borderie; N. Le Neindre; S. Piantelli; M. F. Rivet

    2007-02-05T23:59:59.000Z

    In the case of Xe+Sn at 32 MeV/nucleon multifragmentation reaction break-up fragments are built-up from the experimentally detected ones using evaluations of light particle evaporation multiplicities which thus settle fragment internal excitation. Freeze-out characteristics are extracted from experimental kinetic energy spectra under the assumption of full decoupling between fragment formation and energy dissipated in different degrees of freedom. Thermal kinetic energy is determined uniquely while for freeze-out volume - collective energy a multiple solution is obtained. Coherence between the solutions of the break-up restoration algorithm and the predictions of a multifragmentation model with identical definition of primary fragments is regarded as a way to select the true value. The broad kinetic energy spectrum of $^3$He is consistent with break-up genesis of this isotope.

  14. Breaking anchored droplets in a microfluidic Hele-Shaw cell

    E-Print Network [OSTI]

    Amselem, Gabriel; Gallaire, François; Baroud, Charles N

    2015-01-01T23:59:59.000Z

    We study microfluidic self digitization in Hele-Shaw cells using pancake droplets anchored to surface tension traps. We show that above a critical flow rate, large anchored droplets break up to form two daughter droplets, one of which remains in the anchor. Below the critical flow velocity for breakup the shape of the anchored drop is given by an elastica equation that depends on the capillary number of the outer fluid. As the velocity crosses the critical value, the equation stops admitting a solution that satisfies the boundary conditions; the drop breaks up in spite of the neck still having finite width. A similar breaking event also takes place between the holes of an array of anchors, which we use to produce a 2D array of stationary drops in situ.

  15. Symmetry Breaking and False Vacuum Decay after Hybrid Inflation

    E-Print Network [OSTI]

    Juan Garcia-Bellido; Margarita Garcia Perez; Antonio Gonzalez-Arroyo

    2003-03-25T23:59:59.000Z

    We discuss the onset of symmetry breaking from the false vacuum in generic scenarios in which the mass squared of the symmetry breaking (Higgs) field depends linearly with time, as it occurs, via the evolution of the inflaton, in models of hybrid inflation. We show that the Higgs fluctuations evolve from quantum to classical during the initial stages. This justifies the subsequent use of real-time lattice simulations to describe the fully non-perturbative and non-linear process of symmetry breaking. The early distribution of the Higgs field is that of a smooth classical gaussian random field, and consists of lumps whose shape and distribution is well understood analytically. The lumps grow with time and develop into ``bubbles'' which eventually collide among themselves, thus populating the high momentum modes, in their way towards thermalization at the true vacuum. With the help of some approximations we are able to provide a quasi-analytic understanding of this process.

  16. Charge Symmetry Breaking and Parity Violating Electron-Proton Scattering

    E-Print Network [OSTI]

    Michael Wagman; Gerald A. Miller

    2014-12-16T23:59:59.000Z

    Charge symmetry breaking contributions to the proton's neutral weak form factors must be understood in order for future measurements of parity violating electron-proton scattering to be definitively interpreted as evidence of proton strangeness. We calculate these charge symmetry breaking form factor contributions using chiral perturbation theory with resonance saturation estimates for unknown low-energy constants. The uncertainty of the leading-order resonance saturation estimates is reduced by incorporating nuclear physics constraints. Higher-order contributions are investigated through phenomenological vertex form factors. We predict that charge symmetry breaking form factor contributions are an order of magnitude larger than expected from naive dimensional analysis but are still an order of magnitude smaller than current experimental bounds on proton strangeness. This is consistent with previous calculations using chiral perturbation theory with resonance saturation.

  17. Color breaking in the quantum leaped stop decay

    E-Print Network [OSTI]

    Imre Czovek

    2015-04-12T23:59:59.000Z

    The superfield propagator contains a measurable quantum leap, which comes from the definition of SUSY. In the sfermion -> Goldstino + fermion vertex change: 1. the spin of sparticle with discrete 1/2, 2. the Grassman superspace with the Goldstino shift operator. 3. the spacetime as the result of extra dimensional leap. The leap nature of SUSY transformations appears in the squark decay, it is the analog definition of SUSY. The quantum leaped outgoing propagators are determined and break locally the energy and the charge. Like to the teleportation the entangled pairs are here the b quark and the Goldstino. The dominant stop production is from gluons. The stop-antistop pair decay to quantum leaped b (c or t) quark, and the decay break the color. I get for the (color breaking) quantum leap: 10^-18 m !!! And 10^-11 m color breaking would be needed for a color breaking chain reaction. The open question is: Are the colliders going to produce supersymmetry charge? Because some charges in QGP can make long color breaking and a chain reaction. A long color broken QGP state in the re-Big Bang theory could explain the near infinite energy and the near infinite mass of the universe: - at first was random color QGP in the flat space-time, - at twice the color restoration in the curved space-time, which eats the Goldstinos, - and finally the baryon genesis. The re Big Bang make a supernova like collapse and a flat explosion of Universe. This explanation of SUSY hides the Goldstone fermion in the extra dimensions, the Goldstino propagate only in superspace and it is a not observable dark matter. PACS: 12.60.Jv

  18. Margins in high temperature leak-before-break assessments

    SciTech Connect (OSTI)

    Budden, P.J.; Hooton, D.G.

    1997-04-01T23:59:59.000Z

    Developments in the defect assessment procedure R6 to include high-temperature mechanisms in Leak-before-Break arguments are described. In particular, the effect of creep on the time available to detect a leak and on the crack opening area, and hence leak rate, is discussed. The competing influence of these two effects is emphasized by an example. The application to Leak-before-Break of the time-dependent failure assessment diagram approach for high temperature defect assessment is then outlined. The approach is shown to be of use in assessing the erosion of margins by creep.

  19. DNA-DNA interactions Helmut H Strey*t, Rudi Podgornik* ,

    E-Print Network [OSTI]

    Podgornik, Rudolf

    309 DNA-DNA interactions Helmut H Strey*t, Rudi Podgornik* , Parsegian The forces that govern DNA interactions - such as electrostatic interactions, hydration, and fluctuation forces - that treat DNA about the physical forces and energies that involve DNA molecules is to ask whether there is more to DNA

  20. Nuclear apoJ: A low dose radiation inducible regulator of cell death. Final report for period September 15, 1998 - September 14, 2001

    SciTech Connect (OSTI)

    Aronow, Bruce J.

    2002-04-19T23:59:59.000Z

    This project was based on preliminary data that was published by Dr. Boothman (Yang et al. 2000) which indicated a strong induction of apoJ gene expression, increased secretion of the protein, and accumulation of an apparently somewhat different form of the apoJ protein in the nucleus of MCF-7 breast carcinoma cells undergoing response to DNA damage. A clone expressing apoJ protein was isolated that was capable of interacting with Ku80, a component of the double strand break repair complex that is essential for the successful repair of rearranging immunoglobulin and T-cell receptor genes as evidenced by failure to produce mature B and T cells in the absence of Ku70. ApoJ clones isolated and characterized by Dr. Boothman bound strongly to a Ku-70 ''bait'' protein. Over-expression of these same clones in a cell line was capable of killing the cell. ApoJ is very strongly induced in many instances of programmed cell death and has been proposed repeatedly to play some sort of effector role in the process. Our principle hypothesis for this study was that the strong induction of the apoJ gene and the particular expression of a nuclear form of the protein was potentially a causal factor in the decision point made by the cell as it attempts to repair double-strand breakage based DNA damage. The hypothesis was that if sufficiently high damage occurred, it would be deleterious to maintain the cell's viability through continued DNA repair. One method to inhibit DNA repair might be by inhibiting proteins such as Ku-70 that are necessary for double-strand break repair. If apoJ does play a critical role in tipping the decision balance over to cell death, we reasoned that deficiency of apoJ would cause increased accumulation of cells with DNA damage and that this might decrease cell death in response to DNA damage and increase tumor occurrence rates. To test this hypothesis and its potential implications, we exposed wildtype and apoJ deficient animals that we constructed through gene targeting to increasing levels of ionizing radiation from a Cesium source. Data gathered under the support of this grant application initially indicated that apoJ deficient animals were more resistant to radiation, but as we accumulated more and more data points and covered a tighter exposure range, the genotype-based differences became insignificant. However, the possibility existed that because mortality based radiation-resistance could be attributable to mechanism for which nuclear apoJ was not rate determining, we maintained a very large of colony of apoJ knockout and wildtype animals in both the C57/B16 and Cv129 strain backgrounds that were exposed to sub-lethal levels of ionizing radiation to monitor for the occurrence of tumors. These animals were allowed to fully recover and age normally in either germ free or normal animal housing. Our results demonstrated no significant differences between wildtype and apoJ knockout animals over a period that extended up to 30 months for individual animals. We recorded similar weight gain, a relatively low mortality rate, and a similar mixture and rate of sarcoma and adenocarcinomas after surviving the initial ionizing radiation exposures. Thus we conclude that apoJ gene function, which was totally eliminated by our gene targeting, did not influence radiation sensitivity or serve as a tumor suppressor in response to DNA damage.

  1. ADVERTISMENT Home > News > Breaking news 20 May 2009

    E-Print Network [OSTI]

    Espinosa, Horacio D.

    ADVERTISMENT Home > News > Breaking news 20 May 2009 New tool for next-generation cancer treatments 2 of 2 Prostate Cancer Options Most advanced prostate cancer treatments in Chicago's NW suburbs www.nch.org/northwestcommunityhosp New Cancer Treatments Discover The 12 Most Effective Cancer Treatments In Existence! Ultimate-Cancer

  2. Structural Testing at the Micro and Nano Scales: Breaking

    E-Print Network [OSTI]

    Ballarini, Roberto

    Structural Testing at the Micro and Nano Scales: Breaking Invisible Specimens With Zero Force). "Nano measurements with micro devices: mechanical properties of hydrated collagen fibrils," J. of the R tangential slots · Fuel swirls in the spin chamber and exits through the orifice in a hollow conical spray

  3. EasyVoice: Breaking barriers for people with voice disabilities

    E-Print Network [OSTI]

    Condado, Paulo

    disabilities. With the advances in computing power, new applications have been developed for helping peopleEasyVoice: Breaking barriers for people with voice disabilities Paulo A. Condado and Fernando G,flobo}@ualg.pt Abstract. Text-to-speech technology has been broadly used to help people with voice disabilities

  4. Building Cathedrals and Breaking down Reinforced Concrete Walls

    E-Print Network [OSTI]

    Broué, Michel - Institut de Mathématiques de Jussieu, Université Paris 7

    Building Cathedrals and Breaking down Reinforced Concrete Walls Michel Brou´e Institut Henri distinction between great mathematicians Concrete walls breakers Michel Brou´e (Institut Henri Poincar´e) John Concrete walls breakers Cathedrals builders Michel Brou´e (Institut Henri Poincar´e) John Thompson

  5. Bootstrap Dynamical Symmetry Breaking with New Heavy Chiral Quarks

    E-Print Network [OSTI]

    Yukihiro Mimura; Wei-Shu Hou; Hiroaki Kohyama

    2013-01-31T23:59:59.000Z

    A Higgs-like new boson with mass around 126 GeV is now established, but its true nature probably cannot be settled with 2011--2012 LHC data. We assume it is a dilaton with couplings weaker than the Higgs boson (except to $\\gamma\\gamma$ and $gg$), and explore dynamical symmetry breaking (DSB) by strong Yukawa coupling of a yet unseen heavy chiral quark doublet $Q$. Assuming the actual Higgs boson to be heavy, the Goldstone boson $G$ of electroweak symmetry breaking still couples to $Q$ with Yukawa coupling $\\lambda_Q$. A ``bootstrap" gap equation without a Higgs particle is constructed. Electroweak symmetry breaking via strong $\\lambda_Q$ generates both heavy mass for $Q$, while self-consistently justifying $G$ as a massless Goldstone particle in the loop. The spontaneous breaking of scale invariance in principle \\emph{allows} for a dilaton. We numerically solve such a gap equation and find the mass of the heavy quark to be a couple of TeV. We offer a short critique on the results of the scale-invariant model of Hung and Xiong, where a similar gap equation is built with a massless scalar doublet. Through this we show that a light SM Higgs at 126 GeV cannot be viable within our approach to DSB, while a dilaton with weaker couplings is consistent with our main result.

  6. BREAKING WITH OR BUILDING ON THE PAST? REFORMING IRISH PUBLIC

    E-Print Network [OSTI]

    of the application of new public management styles to Ireland. Particular attention is paid to the public serviceBREAKING WITH OR BUILDING ON THE PAST? REFORMING IRISH PUBLIC ADMINISTRATION: 1958-2008 Niamh? REFORMING IRISH PUBLIC ADMINISTRATION: 1958-2008 Niamh Hardiman and Muiris MacCarthaigh Working Papers

  7. Mechanisms of cellular symmetry breaking in S. cerevisiae

    E-Print Network [OSTI]

    Smith, Sarah Ellen

    2013-12-31T23:59:59.000Z

    ………………… … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … …..1 Chapter 2: Non ?uniform membrane diffusion enables steady?state cell polarization via vesicular trafficking………………………… … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … …..34 Chapter 3: Independence of symmetry breaking on... Bem1?mediated autocatalytic activation of Cdc42……………………… … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … … ….88 Chapter 4: Preliminary data on Cdc42 microdomains in the presence of Rdi1 feedback………..135 Chapter 5...

  8. Vacuum condensates, flavor mixing and spontaneous supersymmetry breaking

    E-Print Network [OSTI]

    Antonio Capolupo; Marco Di Mauro

    2013-01-05T23:59:59.000Z

    Spontaneous supersymmetry (SUSY) breaking is revealed in all phenomena in which vacuum condensates are physically relevant. The dynamical breakdown of SUSY is generated by the condensates themselves, which lift the zero point energy. Evidence is presented in the case of the Wess-Zuimino model, and the flavor mixing case is treated in detail.

  9. Timber + TouchPads: How Education Will Make or Break

    E-Print Network [OSTI]

    Pulfrey, David L.

    Timber + TouchPads: How Education Will Make or Break BC's Emerging Smart Economy Vancouver Board the health of the soil and human health and survival. Right here at home, Business in Vancouver founder Peter-wide collective of farmers' markets. The BC government just announced $2 million dollars in funding for local food

  10. Researcher breaks new ground in understanding chemical reaction process

    E-Print Network [OSTI]

    Glaser, Rainer

    Researcher breaks new ground in understanding chemical reaction process Study of diazonium rewrites about a common, basic chemical process using diazonium ions as the example. These ions are used in nature. Now, a professor of chemistry has found that this chemical process has been incorrectly described

  11. Towards Automatic Detecting of Overlapping Genes -Clustered BLAST Analysis of Viral

    E-Print Network [OSTI]

    Reiterer, Harald

    overlaps. In case of short, trivial overlaps, the #12;2 Neuhaus et al. Fig. 1. A double strand of DNA overlapping genes has been modeled by mutational events, which displace the start or stop codons [3­9]. The focus of this project, however, is on embedded genes which encode two completely different functional

  12. The Polymerase Chain Reaction and Branching Processes Fengzhu Sun

    E-Print Network [OSTI]

    Sun, Fengzhu - Sun, Fengzhu

    The Polymerase Chain Reaction and Branching Processes Fengzhu Sun Department of Mathematics, DRB is studied. We also study the distribution of the Hamming distance between two randomly chosen sequences long. The double-stranded DNA molecules are heated to near boiling temperature so that the double

  13. Gene Assembly from Chip-Synthesized Oligonucleotides

    E-Print Network [OSTI]

    Church, George M.

    molecular biology laboratory. The major stages of our synthesis pipeline are computational design, chip of the constructs. The key principle is that well-designed primers can amplify a desired subset of oligonucleotides synthesis of long double-stranded DNA constructs has a myriad of applications in biology and biological

  14. Condensation of circular DNA

    E-Print Network [OSTI]

    E. L. Starostin

    2013-04-05T23:59:59.000Z

    A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and torsional elastic components and the effective self-attraction energy. The model includes a relative orientation or sequence dependence of the effective attraction forces between different pieces of the polymer chain. Two series of conformations are analysed: a multicovered circle (a toroid) and a multifold two-headed racquet. The results are presented as a diagram of state. It is suggested that the stability of particular conformations may be controlled by proper adjustment of the primary structure. Application of the model to other semi-flexible polymers is considered.

  15. FastFEM: Breaking Wave Impact on Ships Wave breaking and wave impact on maritime structures are difficult to model

    E-Print Network [OSTI]

    Wirosoetisno, Djoko

    are difficult to model mathematically and numerically. The challenge is that nonlinear and breaking waves with fine-scale dynamic air-water interfaces need to be modelled efficiently, including their interactions measurements in wave basins. These potential flow models will be developed further at the University of Twente

  16. 1Banff 6/06 Structural Break Detection in Time Series ModelsStructural Break Detection in Time Series Models

    E-Print Network [OSTI]

    breaks in this series? #12;5Banff 6/06 Introduction Examples AR GARCH Stochastic volatility State space Simulation results Applications Simulation results for GARCH and SV models #12;6Banff 6/06 Examples 1 ),,( 1 jjpj K #12;7Banff 6/06 Examples (cont) 2. Segmented GARCH model: where 0 = 1

  17. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K. (Chicago, IL)

    1998-01-01T23:59:59.000Z

    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. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10T23:59:59.000Z

    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.

  19. Normalized cDNA libraries

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

    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.

  20. DNA UPTAKE BY TRANSFORMABLE BACTERIA

    SciTech Connect (OSTI)

    LACKS,S.A.

    1999-09-07T23:59:59.000Z

    The various processes of DNA uptake by cells can be categorized as: viral DNA entry, conjugation, or transformation. Within each category, a variety of mechanisms have been found. However, considerable similarities occur among the different mechanisms of conjugation and, especially, transformation. All of these natural mechanisms of DNA transfer are quite elaborate and involve multiple protein components, as the case may be, of the virus, the donor cell, and the recipient cell. The mechanisms of viral infection and conjugation will be discussed mainly with respect to their relevance to transformation.

  1. Navier-Stokes simulations of steep breaking water waves with a coupled air-water interface

    E-Print Network [OSTI]

    Hendrickson, Kelli L

    2005-01-01T23:59:59.000Z

    Wave breaking on the ocean surface significantly facilitates the transfer of mass, momentum, heat and energy across the air-sea interface. In the context of the near field flow about a surface ship, the breaking bow wave ...

  2. Coastal Wave Generation and Wave Breaking over Terrain: Two Problems in Mesoscale Wave Dynamics 

    E-Print Network [OSTI]

    Qian, Tingting

    2010-07-14T23:59:59.000Z

    Two problems in mesoscale wave dynamics are addressed: (i) wave-turbulence interaction in a breaking mountain wave and (ii) gravity wave generation associated with coastal heating gradients. The mean and turbulent structures in a breaking mountain...

  3. Quantitative imaging of the air-water flow fields formed by unsteady breaking waves

    E-Print Network [OSTI]

    Belden, Jesse (Jesse Levi)

    2009-01-01T23:59:59.000Z

    An experimental method for simultaneously measuring the velocity fields on the air and water side of unsteady breaking waves is presented. The method is applied to breaking waves to investigate the physics of the air and ...

  4. Experimental investigation of small-scale breaking waves : flow visualization across the air-water interface

    E-Print Network [OSTI]

    McDonald, Angus Kai

    2005-01-01T23:59:59.000Z

    The dynamics of breaking waves significantly affect air-sea fluxes of heat, momentum, mass and energy across the ocean interface. Breaking waves also contribute considerable loading to offshore and coastal structures, and ...

  5. Three dimensional effects in analysis of PWR steam line break accident

    E-Print Network [OSTI]

    Tsai, Chon-Kwo

    A steam line break accident is one of the possible severe abnormal transients in a pressurized water reactor. It is required to present an analysis of a steam line break accident in the Final Safety Analysis Report (FSAR) ...

  6. U.S. Department of Energy Breaks Ground on State-of-the-Art Wind...

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

    U.S. Department of Energy Breaks Ground on State-of-the-Art Wind Turbine Test Facility U.S. Department of Energy Breaks Ground on State-of-the-Art Wind Turbine Test Facility...

  7. Coastal Wave Generation and Wave Breaking over Terrain: Two Problems in Mesoscale Wave Dynamics

    E-Print Network [OSTI]

    Qian, Tingting

    2010-07-14T23:59:59.000Z

    Two problems in mesoscale wave dynamics are addressed: (i) wave-turbulence interaction in a breaking mountain wave and (ii) gravity wave generation associated with coastal heating gradients. The mean and turbulent structures in a breaking mountain...

  8. Transcriptional Control of DNA-Based Nanomachines

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

    on responses to stimuli or the cell's environ- ment. So far, nanomachines have been controlled with DNA rather be performed by these devices in well-defined steps. Recently, a DNA machine that binds, carries, and releases the manual addition of a "fuel" strand, consisting of single stranded DNA (ssDNA) that affects

  9. Unnatural nucleotides for DNA sequencing

    E-Print Network [OSTI]

    Jacutin, Swanee E

    1997-01-01T23:59:59.000Z

    Fluorescent nucleotide analogs were prepared and tested to find surrogate structures that are: (i) incorporated by DNA polymerases; (ii) spectroscopically distinct for each fluorescent tag; and (iii) easily deprotected at the 3'-position under mild...

  10. Mammalian DNA Repair. Final Report

    SciTech Connect (OSTI)

    None

    2003-01-24T23:59:59.000Z

    The Gordon Research Conference (GRC) on Mammalian DNA Repair was held at Harbortown Resort, Ventura Beach, CA. Emphasis was placed on current unpublished research and discussion of the future target areas in this field.

  11. The Environmental Impact of Lyman-break Galaxies

    E-Print Network [OSTI]

    Elizabeth J. Tasker; Greg L. Bryan

    2006-04-11T23:59:59.000Z

    We perform cosmological simulations of galaxies forming at z=3 using the hydrodynamics grid code, Enzo. By selecting the largest galaxies in the volume to correspond to Lyman-break galaxies, we construct observational spectra of the HI flux distribution around these objects, as well as column densities of CIV and OVI throughout a refined region. We successfully reproduce the most recent observations of the mean HI flux in the close vicinity of Lyman-break galaxies but see no evidence for the proximity effect in earlier observations. While our galaxies do return metals to the IGM, their quantity and volume appears to be somewhat less than observed. We conclude that either we do not adequately resolve galactic winds, or that at least some of the intergalactic metal enrichment is by early epoch objects whose mass is smaller than our minimum resolved halo mass.

  12. Breaking discrete symmetries in the effective field theory of inflation

    E-Print Network [OSTI]

    Dario Cannone; Jinn-Ouk Gong; Gianmassimo Tasinato

    2015-05-29T23:59:59.000Z

    We study the phenomenon of discrete symmetry breaking during the inflationary epoch, using a model-independent approach based on the effective field theory of inflation. We work in a context where both time reparameterization symmetry and spatial diffeomorphism invariance can be broken during inflation. We determine the leading derivative operators in the quadratic action for fluctuations that break parity and time-reversal. Within suitable approximations, we study their consequences for the dynamics of linearized fluctuations. Both in the scalar and tensor sectors, we show that such operators can lead to new direction-dependent phases for the modes involved. They do not affect the power spectra, but can have consequences for higher correlation functions. Moreover, a small quadrupole contribution to the sound speed can be generated.

  13. Pipe break frequency estimation for Nuclear Power Plants

    SciTech Connect (OSTI)

    Wright, R.E.; Steverson, J.A.; Zuroff, W.F.

    1987-05-01T23:59:59.000Z

    This study empirically develops frequencies of safety-significant pipe failures in commercial nuclear power plants (NPPs). Its primary purpose is to update the pipe break frequencies reported in the Reactor Safety Study, WASH-1400, which are used in many risk analyses. The study involved reviewing various data sources for actual piping failure events of significant magnitude. When extant in the documentation reviewed, information was extracted concerning conditional factors such as the system in which the failure occurred, operational mode of the plant, and size of the pipe involved to estimate conditional pipe break frequencies useful to risk analysts. Because of the high quality piping used in NPPs, there have been few significant pipe failures. An attempt was made to augment the analysis with synthetic data from a Delphi approach, but the wide uncertainty bounds on the resulting estimates rendered the results unsuitable for combining data.

  14. Density driven symmetry breaking and Butterfly effect in holographic superconductors

    E-Print Network [OSTI]

    Youngman Kim; Yumi Ko; Sang-Jin Sin

    2009-12-01T23:59:59.000Z

    We study the density driven symmetry breaking in holographic superconductors by considering the positive mass squared case. We show that even for the positive $m^2$, a scalar condensation still forms, provided the chemical potential is high enough. As $m^2$ increases, the phase space folds due to the non-linearity of the equations of motion, and two nearby points in the phase space can represent symmetry breaking and preserving configurations respectively. The phase space defined by the set of initial conditions of field variables at the horizon undergoes a non-linear radial evolution to result in the phase space folding, a characteristic phenomenon in a non-linear system. We then calculate the specific heat, which characterizes superconductors and has been measured in experiments.We observe a discontinuity in the specific heat at the transition point and compare our results with experimentally observed numbers. The electrical conductivity for various $m^2$ is also calculated.

  15. A Gravity Dual of Metastable Dynamical Supersymmetry Breaking

    SciTech Connect (OSTI)

    DeWolfe, Oliver; /Colorado U.; Kachru, Shamit; Mulligan, Michael; /Stanford U., Phys. Dept. /SLAC

    2008-02-04T23:59:59.000Z

    Metastable, supersymmetry-breaking configurations can be created in flux geometries by placing antibranes in warped throats. Via gauge/gravity duality, such configurations should have an interpretation as supersymmetry-breaking states in the dual field theory. In this paper, we perturbatively determine the asymptotic supergravity solutions corresponding to D3-brane probes placed at the tip of the cascading warped deformed conifold geometry, which is dual to an SU(N+M) x SU(N) gauge theory. The backreaction of the antibranes has the effect of introducing imaginary anti-self-dual flux, squashing the compact part of the space and forcing the dilaton to run. Using the generalization of holographic renormalization to cascading geometries, we determine the expectation values of operators in the dual field theory in terms of the asymptotic values of the supergravity fields.

  16. Electroweak Symmetry Breaking without the $\\mu^2$ Term

    E-Print Network [OSTI]

    Goertz, Florian

    2015-01-01T23:59:59.000Z

    We demonstrate that from a low energy perspective a viable electroweak symmetry breaking can be achieved without the (negative sign) $\\mu^2$ mass term in the Higgs potential, thereby avoiding completely the appearance of relevant operators. We show that such a setup is self consistent and not ruled out by Higgs physics. In particular, we point out that it is the lightness of the Higgs boson that allows for the electroweak symmetry to be broken dynamically via operators of $D\\geq 4$, consistent with the power expansion. Beyond that, we entertain how this scenario might even be preferred phenomenologically compared to the ordinary mechanism of electroweak symmetry breaking, as realized in the Standard Model, and argue that it can be fully tested at the LHC. In an appendix, we classify UV completions that could lead to such a setup, considering also the option of generating all scales dynamically.

  17. RR Flux on Calabi-Yau and Partial Supersymmetry Breaking

    E-Print Network [OSTI]

    T. R. Taylor; C. Vafa

    2000-01-26T23:59:59.000Z

    We show how turning on Flux for RR (and NS-NS) field strengths on non-compact Calabi-Yau 3-folds can serve as a way to partially break supersymmetry from N=2 to N=1 by mass deformation. The freezing of the moduli of Calabi-Yau in the presence of the flux is the familiar phenomenon of freezing of fields in supersymmetric theories upon mass deformations.

  18. Gauge/gravity Duality and MetastableDynamical Supersymmetry Breaking

    SciTech Connect (OSTI)

    Argurio, Riccardo; Bertolini, Matteo; Franco, Sebastian; Kachru, Shamit

    2006-10-24T23:59:59.000Z

    We engineer a class of quiver gauge theories with several interesting features by studying D-branes at a simple Calabi-Yau singularity. At weak 't Hooft coupling we argue using field theory techniques that these theories admit both supersymmetric vacua and meta-stable non-supersymmetric vacua, though the arguments indicating the existence of the supersymmetry breaking states are not decisive. At strong 't Hooft coupling we find simple candidate gravity dual descriptions for both sets of vacua.

  19. S-Dual Gaugino Condensation and Supersymmetry Breaking

    E-Print Network [OSTI]

    Z. Lalak; A. Niemeyer; H. P. Nilles

    1994-10-27T23:59:59.000Z

    The principle of S-duality is used to incorporate gaugino condensates into effective supergravity (superstring) Lagrangians. We discuss two implementations of S-duality which differ in the way the coupling constant is transformed. Both solve the problem of the runaway dilaton and lead to satisfactory supersymmetry breaking in models with a {\\em single} gaugino condensate. The breakdown of supersymmetry is intimately related to a nontrivial transformation of the condensate under T-duality.

  20. Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and Is DNA Leaching a Factor?

    E-Print Network [OSTI]

    Shapiro, Beth

    reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even for vertical migration of aDNA across strata. To assess the extent of this problem, we extracted aDNA from (Lydolph et al. 2005). Also uncertain is whether the DNA is extracellular and bound to clay minerals

  1. Meta-DNA: A DNA-Based Approach to Synthetic Harish Chandran1

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: A DNA-Based Approach to Synthetic Biology Harish Chandran1 harish@cs.duke.edu Nikhil taken here is to develop a biochemical system which we call meta-DNA (abbre- viated as mDNA), based entirely on strands of DNA as the only component molecules. Our work leverages prior work

  2. Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions

    E-Print Network [OSTI]

    Reif, John H.

    Meta-DNA: Synthetic Biology via DNA Nanostructures and Hybridization Reactions Harish Chandran for desired functionality. The approach of this paper is to develop a biochemical system which we call meta-DNA (abbreviated as mDNA), based entirely on strands of DNA as the only component molecule. Our work leverages

  3. Impact of DNA Twist Accumulation on Progressive Helical Wrapping of Torsionally Constrained DNA

    E-Print Network [OSTI]

    Wang, Wei Hua

    Impact of DNA Twist Accumulation on Progressive Helical Wrapping of Torsionally Constrained DNA Wei (Received 17 July 2012; published 20 November 2012) DNA wrapping is an important mechanism for chromosomal DNA packaging in cells and viruses. Previous studies of DNA wrapping have been performed mostly

  4. DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays

    E-Print Network [OSTI]

    DNA Word Design Strategy for Creating Sets of Non-interacting Oligonucleotides for DNA Microarrays-interacting DNA oligonucleotides for applications in DNA arrays and biosensors is demonstrated. This strategy mismatches with the complements of all the other members in the set. These "DNA word" sets are denoted as nbm

  5. FLASH predictions of the MB-2 steam line break tests

    SciTech Connect (OSTI)

    Lincoln, F.W.; Coffield, R.D.; Johnson, E.G.

    1992-12-31T23:59:59.000Z

    If a main steam line from a pressurized water reactor (PWR) steam generator were to rupture, the effect would be a depressurization of the secondary side and a consequential overcooling transient on the primary side. Analyses must accurately predict the effects of the rapid cooldown of the reactor vessel coolant on positive nuclear-kinetic reactivity feedback to the core plus thermal shock to the reactor vessel and other primary system components. Many early studies of the steam line break (SLB) transient made extremely conservative assumptions to maximize the primary to secondary heat transfer which in turn maximized the reactor vessel cooldown rate. Among the more significant of these assumptions was that flow from the break was pure steam and that the tube bundle remained covered until the secondary mass inventory was significantly reduced. The Model F commercial PWR steam generator testing performed in the Model Boiler No. 2 (MB-2) facility located at the Westinghouse Engineering Test Facility in Tampa, Florida provided data to better qualify the actual variation in these key parameters. A conclusion of this analysis is that the MB-2 steam line break data base is accurate and of sufficient detail to provide a valuable basis for making comparisons relative to code predictions. Results obtained using the FLASH transient safety analysis code were found to be in excellent agreement with the data.

  6. Peccei-Quinn Symmetry from Dynamical Supersymmetry Breaking

    E-Print Network [OSTI]

    Harigaya, Keisuke; Schmitz, Kai; Yanagida, Tsutomu T

    2015-01-01T23:59:59.000Z

    The proximity of the Peccei-Quinn scale to the scale of supersymmetry breaking in models of pure gravity mediation hints at a common dynamical origin of these two scales. To demonstrate how to make such a connection manifest, we embed the Peccei-Quinn mechanism into the vector-like model of dynamical supersymmetry breaking a la IYIT. Here, we rely on the anomaly-free discrete Z4R symmetry required in models of pure gravity mediation to solve the mu problem to protect the Peccei-Quinn symmetry from the dangerous effect of higher-dimensional operators. This results in a rich phenomenology featuring a QCD axion with a decay constant of O(10^10) GeV and mixed WIMP/axion dark matter. In addition, exactly five pairs of extra 5 and 5* matter multiplets, directly coupled to the supersymmetry breaking sector and with masses close to the gravitino mass, m3/2 ~ 100 TeV, are needed to cancel the Z4R anomalies.

  7. Peccei-Quinn Symmetry from Dynamical Supersymmetry Breaking

    E-Print Network [OSTI]

    Keisuke Harigaya; Masahiro Ibe; Kai Schmitz; Tsutomu T. Yanagida

    2015-05-27T23:59:59.000Z

    The proximity of the Peccei-Quinn scale to the scale of supersymmetry breaking in models of pure gravity mediation hints at a common dynamical origin of these two scales. To demonstrate how to make such a connection manifest, we embed the Peccei-Quinn mechanism into the vector-like model of dynamical supersymmetry breaking a la IYIT. Here, we rely on the anomaly-free discrete Z4R symmetry required in models of pure gravity mediation to solve the mu problem to protect the Peccei-Quinn symmetry from the dangerous effect of higher-dimensional operators. This results in a rich phenomenology featuring a QCD axion with a decay constant of O(10^10) GeV and mixed WIMP/axion dark matter. In addition, exactly five pairs of extra 5 and 5* matter multiplets, directly coupled to the supersymmetry breaking sector and with masses close to the gravitino mass, m3/2 ~ 100 TeV, are needed to cancel the Z4R anomalies.

  8. Dynamical evolution of supernova remnants breaking through molecular clouds

    E-Print Network [OSTI]

    Cho, Wankee; Koo, Bon-Chul

    2015-01-01T23:59:59.000Z

    We carry out three-dimensional hydrodynamic simulations of the supernova remnants (SNRs) produced inside molecular clouds (MCs) near their surface using the HLL code (Harten et al. 1983). We explore the dynamical evolution and the X-ray morphology of SNRs after breaking through the MC surface for ranges of the explosion depths below the surface and the density ratios of the clouds to the intercloud media (ICM). We find that if an SNR breaks out through an MC surface in its Sedov stage, the outermost dense shell of the remnant is divided into several layers. The divided layers are subject to the Rayleigh-Taylor instability and fragmented. On the other hand, if an SNR breaks through an MC after the remnant enters the snowplow phase, the radiative shell is not divided to layers. We also compare the predictions of previous analytic solutions for the expansion of SNRs in stratified media with our onedimensional simulations. Moreover, we produce synthetic X-ray surface brightness in order to research the center-bri...

  9. Modeling suggests that oblique extension facilitates rifting and continental break-up

    E-Print Network [OSTI]

    Kaus, Boris

    Modeling suggests that oblique extension facilitates rifting and continental break-up Sascha Brune; accepted 5 June 2012; published 2 August 2012. [1] In many cases the initial stage of continental break-up was and is associated with oblique rifting. That includes break-up in the Southern and Equatorial Atlantic, separation

  10. GENTLE IONISATION AND VIOLENT BREAK-UP OF MOLECULES USING SOFT X-RAYS

    E-Print Network [OSTI]

    Bapat, Bhas

    GENTLE IONISATION AND VIOLENT BREAK-UP OF MOLECULES USING SOFT X-RAYS Bhas Bapat PRL, Ahmedabad RRCAT Indore, June 2012 BHAS BAPAT (PRL, AHMEDABAD) BREAK-UP OF MOLECULES USING SOFT X-RAYS RRCAT INDORE INVESTIGATED RECENT RESULTS BHAS BAPAT (PRL, AHMEDABAD) BREAK-UP OF MOLECULES USING SOFT X-RAYS RRCAT INDORE

  11. Lack of Bystander Effects From High LET Radiation For Early Cytogenetic Endpoints.

    SciTech Connect (OSTI)

    Groesser, Torsten; Cooper, Brian; Rydberg, Bjorn

    2008-05-07T23:59:59.000Z

    The aim of this work was to study radiation-induced bystander effects for early cytogenetic end points in various cell lines using the medium transfer technique after exposure to high- and low-LET radiation. Cells were exposed to 20 MeV/ nucleon nitrogen ions, 968 MeV/nucleon iron ions, or 575 MeV/nucleon iron ions followed by transfer of the conditioned medium from the irradiated cells to unirradiated test cells. The effects studied included DNA double-strand break induction, {gamma}-H2AX focus formation, induction of chromatid breaks in prematurely condensed chromosomes, and micronucleus formation using DNA repair-proficient and -deficient hamster and human cell lines (xrs6, V79, SW48, MO59K and MO59J). Cell survival was also measured in SW48 bystander cells using X rays. Although it was occasionally possible to detect an increase in chromatid break levels using nitrogen ions and to see a higher number of {gamma}-H2AX foci using nitrogen and iron ions in xrs6 bystander cells in single experiments, the results were not reproducible. After we pooled all the data, we could not verify a significant bystander effect for any of these end points. Also, we did not detect a significant bystander effect for DSB induction or micronucleus formation in these cell lines or for clonogenic survival in SW48 cells. The data suggest that DNA damage and cytogenetic changes are not induced in bystander cells. In contrast, data in the literature show pronounced bystander effects in a variety of cell lines, including clonogenic survival in SW48 cells and induction of chromatid breaks and micronuclei in hamster cells. To reconcile these conflicting data, it is possible that the epigenetic status of the specific cell line or the precise culture conditions and medium supplements, such as serum, may be critical for inducing bystander effects.

  12. Enhancement of the RAD51 Recombinase Activity by the Tumor Suppressor PALB2

    SciTech Connect (OSTI)

    Dray, Eloise; Etchin, Julia; Wiese, Claudia; Saro, Dorina; Williams, Gareth J.; Hammel, Michal; Yu, Xiong; Galkin, Vitold E.; Liu, Dongqing; Tsai, Miaw-Sheue; Sy, Shirley M-H.; Egelman, Edward; Chen, Junjie; Sung, Patrick; Schild, D.

    2010-08-24T23:59:59.000Z

    Homologous recombination mediated by the RAD51 recombinase helps eliminate chromosomal lesions, such as DNA double-stranded breaks induced by radiation or arising from injured DNA replication forks. The tumor suppressors BRCA2 and PALB2 act together to deliver RAD51 to chromosomal lesions to initiate repair. Here we document a new function of PALB2 in the enhancement of RAD51's ability to form the D-loop. We show that PALB2 binds DNA and physically interacts with RAD51. Importantly, while PALB2 alone stimulates D-loop formation, a cooperative effect is seen with RAD51AP1, an enhancer of RAD51. This stimulation stems from PALB2's ability to function with RAD51 and RAD51AP1 to assemble the synaptic complex. Our results help unveil a multi-faceted role of PALB2 in chromosome damage repair. Since PALB2 mutations can cause breast and other tumors or lead to Fanconi anemia, our findings are important for understanding the mechanism of tumor suppression in humans.

  13. 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)

    2001-01-01T23:59:59.000Z

    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.

  14. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01T23:59:59.000Z

    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.

  15. Regulation of DNA damage tolerance : studies of the translesion synthesis DNA ploymerase eta in Saccharomyces cerevisiae

    E-Print Network [OSTI]

    Woodruff, Rachel Van Etten

    2008-01-01T23:59:59.000Z

    All organisms must control the effects of DNA damage to protect the integrity of their genomes. In addition to DNA repair, this requires DNA damage tolerance pathways, which allow the continuation of essential processes ...

  16. DNA Strands Attached Inside Single Conical Nanopores: Ionic Pore Characteristics and Insight into DNA Biophysics

    E-Print Network [OSTI]

    Nguyen, Gael; Howorka, Stefan; Siwy, Zuzanna S.

    2011-01-01T23:59:59.000Z

    Nonexponential kinetics of DNA escape from alpha-hemolysin2010), (iii) the speed of DNA transport (Meller et al. 2001;0AJ, UK G. Nguyen et al. : DNA Strands in Single Nanopores

  17. DNA binding specificity of the p73 DNA-binding domain

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

    interactions of p53 with DNA: when flexibility serves2006). Structural basis of DNA recognition by p53 tetramers.Z. (2010). Diversity in DNA recognition by p53 revealed by

  18. DNA repair is the target of novel antibiotics

    E-Print Network [OSTI]

    Gunderson, Carl Wayne

    2007-01-01T23:59:59.000Z

    W. & A. M. Segall, (2006) DNA repair, a novel antibacterialjunction-trapping peptides induce DNA damage and chromosomePeptide inhibitors of DNA cleavage by tyrosine recombinases

  19. DNA Guided Self-Assembly of Nanocrystals for Optoelectronic Devices /

    E-Print Network [OSTI]

    Noh, Hyunwoo

    2013-01-01T23:59:59.000Z

    Lithographically Confined DNA Origami. Nat. Nanotech. 2010,and Orientation of Individual DNA Shapes on LithographicallyB. ; Yan, H. ; Liu, Y. DNA-Origami-Directed Self- Assembly

  20. Leak before break application in French PWR plants under operation

    SciTech Connect (OSTI)

    Faidy, C. [EDF SEPTEN, Villeurbanne (France)

    1997-04-01T23:59:59.000Z

    Practical applications of the leak-before break concept are presently limited in French Pressurized Water Reactors (PWR) compared to Fast Breeder Reactors. Neithertheless, different fracture mechanic demonstrations have been done on different primary, auxiliary and secondary PWR piping systems based on similar requirements that the American NUREG 1061 specifications. The consequences of the success in different demonstrations are still in discussion to be included in the global safety assessment of the plants, such as the consequences on in-service inspections, leak detection systems, support optimization,.... A large research and development program, realized in different co-operative agreements, completes the general approach.

  1. Charge symmetry breaking in n p --> d pi^0

    E-Print Network [OSTI]

    A. K. Opper; E. Korkmaz; D. A. Hutcheon; R. Abegg; C. A. Davis; R. W. Finlay; P. W. Green; L. G. Greeniaus; D. V. Jordan; J. A. Niskanen; G. V. O'Rielly; T. A. Porcelli; S. D. Reitzner; P. L. Walden; S. Yen

    2003-06-19T23:59:59.000Z

    The forward--backward asymmetry in n p --> d pi^0, which must be zero in the center-of-mass system if charge symmetry is respected, has been measured to be [17.2 +/- 8 (stat) +/- 5.5 (sys)] * 10^{-4}, at an incident neutron energy of 279.5 MeV. This charge symmetry breaking observable was extracted by fitting the data with GEANT-based simulations and is compared to recent chiral effective field theory calculations, with implications regarding the value of the u d quark mass difference.

  2. Low-energy Supersymmetry Breaking Without the Gravitino Problem

    E-Print Network [OSTI]

    Hook, Anson

    2015-01-01T23:59:59.000Z

    In models of low-energy gauge mediation, the observed Higgs mass is in tension with the cosmological limit on the gravitino mass $m_{3/2} \\lesssim 16$ eV. We present an alternative mediation mechanism of supersymmetry breaking via a $U(1)$ $D$-term with an $E_6$-inspired particle content, which we call "vector mediation". The gravitino mass can be in the eV range. The sfermion masses are at the 10 TeV scale, while gauginos around a TeV. This mechanism also greatly ameliorates the $\\mu$-problem.

  3. A dynamical symmetry breaking model in Weyl space

    E-Print Network [OSTI]

    A. Feoli; W. R. Wood; G. Papini

    1998-05-11T23:59:59.000Z

    The dynamical process following the breaking of Weyl geometry to Riemannian geometry is considered by studying the motion of de Sitter bubbles in a Weyl vacuum. The bubbles are given in terms of an exact, spherically symmetric thin shell solution to the Einstein equations in a Weyl-Dirac theory with a time-dependent scalar field of the form beta = f(t)/r. The dynamical solutions obtained lead to a number of possible applications. An important feature of the thin shell model is the manner in which beta provides a connection between the interior and exterior geometries since information about the exterior geometry is contained in the boundary conditions for beta.

  4. Symmetry Breaking of H2 Dissociation by a Single Photon

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level:Energy: Grid Integration Redefining What'sis Taking Over Our InstagramStructureProposed Action Title:SustainableDepartmentSymmetry Breaking

  5. System Break-Out Session | Department of Energy

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn'tOriginEducationVideoStrategic SafetyGeothermal/Ground-Source HeatSweptCathodeSyntheticBreak-Out

  6. High-Fidelity DNA Hybridization Using Programmable Molecular DNA Devices

    E-Print Network [OSTI]

    Reif, John H.

    of complementary nucleic acid strands is the most basic of all reactions involving nucleic acids, but has a major specific high-fidelity DNA hybridization reactions for tar- get strands of arbitrary length. Our protocol acid strands is the most basic of all reactions involving nucleic acids and a major component of most

  7. Pulsar Emission above the Spectral Break - A Stacked Approach

    E-Print Network [OSTI]

    McCann, Andrew

    2015-01-01T23:59:59.000Z

    NASA's Fermi space telescope has provided us with a bountiful new population of gamma-ray sources following its discovery of 150 new gamma-ray pulsars. One common feature exhibited by all of these pulsars is the form of their spectral energy distribution, which can be described by a power law followed by a spectral break occurring between $\\sim$1 and $\\sim$8 GeV. The common wisdom is that the break is followed by an exponential cut-off driven by radiation/reaction-limited curvature emission. The discovery of pulsed gamma rays from the Crab pulsar, the only pulsar so far detected at very high energies (E$>$100GeV), contradicts this "cutoff" picture. Here we present a new stacked analysis with an average of 4.2 years of data on 115 pulsars published in the 2nd LAT catalog of pulsars. This analysis is sensitive to low-level $\\sim$100 GeV emission which cannot be resolved in individual pulsars but can be detected from an ensemble.

  8. The gravitational wave spectrum from cosmological B-L breaking

    SciTech Connect (OSTI)

    Buchmüller, W.; Domcke, V.; Kamada, K. [Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg (Germany); Schmitz, K., E-mail: buchmuwi@mail.desy.de, E-mail: valerie.domcke@desy.de, E-mail: kohei.kamada@desy.de, E-mail: kai.schmitz@ipmu.jp [Kavli IPMU (WPI), University of Tokyo, Kashiwa 277-8583 (Japan)

    2013-10-01T23:59:59.000Z

    Cosmological B-L breaking is a natural and testable mechanism to generate the initial conditions of the hot early universe. If B-L is broken at the grand unification scale, the false vacuum phase drives hybrid inflation, ending in tachyonic preheating. The decays of heavy B-L Higgs bosons and heavy neutrinos generate entropy, baryon asymmetry and dark matter and also control the reheating temperature. The different phases in the transition from inflation to the radiation dominated phase produce a characteristic spectrum of gravitational waves. We calculate the complete gravitational wave spectrum due to inflation, preheating and cosmic strings, which turns out to have several features. The production of gravitational waves from cosmic strings has large uncertainties, with lower and upper bounds provided by Abelian Higgs strings and Nambu-Goto strings, implying ?{sub GW}h{sup 2} ? 10{sup ?13}–10{sup ?8}, much larger than the spectral amplitude predicted by inflation. Forthcoming gravitational wave detectors such as eLISA, advanced LIGO, ET, BBO and DECIGO will reach the sensitivity needed to test the predictions from cosmological B-L breaking.

  9. Bending-induced Symmetry Breaking of Lithiation in Germanium Nanowires

    SciTech Connect (OSTI)

    Gu, Meng; Yang, Hui; Perea, Daniel E.; Zhang, Jiguang; Zhang, Sulin; Wang, Chong M.

    2014-08-01T23:59:59.000Z

    From signal transduction of living cells to oxidation and corrosion of metals, mechanical stress intimately couples with chemical reactions, regulating these biological and physiochemical processes. The coupled effect is particularly evident in electrochemical lithiation/delithiation cycling of high-capacity electrodes, such as silicon (Si), where on one hand lithiation-generated stress mediates lithiation kinetics, and on the other electrochemical reaction rate regulates stress generation and mechanical failure of the electrodes. Here we report for the first time the evidence on the controlled lithiation in germanium nanowires (GeNWs) through external bending. Contrary to the symmetric core-shell lithiation in free-standing GeNWs, we show bending GeNWs breaks the lithiation symmetry, speeding up lithaition at the tensile side while slowing down at the compressive side of the GeNWs. The bending-induced symmetry breaking of lithiation in GeNWs is further corroborated by chemomechanical modeling. In the light of the coupled effect between lithiation kinetics and mechanical stress in the electrochemical cycling, our findings shed light on strain/stress engineering of durable high-rate electrodes and energy harvesting through mechanical motion.

  10. Aerosol cluster impact and break-up : model and implementation.

    SciTech Connect (OSTI)

    Lechman, Jeremy B.

    2010-10-01T23:59:59.000Z

    In this report a model for simulating aerosol cluster impact with rigid walls is presented. The model is based on JKR adhesion theory and is implemented as an enhancement to the granular (DEM) package within the LAMMPS code. The theory behind the model is outlined and preliminary results are shown. Modeling the interactions of small particles is relevant to a number of applications (e.g., soils, powders, colloidal suspensions, etc.). Modeling the behavior of aerosol particles during agglomeration and cluster dynamics upon impact with a wall is of particular interest. In this report we describe preliminary efforts to develop and implement physical models for aerosol particle interactions. Future work will consist of deploying these models to simulate aerosol cluster behavior upon impact with a rigid wall for the purpose of developing relationships for impact speed and probability of stick/bounce/break-up as well as to assess the distribution of cluster sizes if break-up occurs. These relationships will be developed consistent with the need for inputs into system-level codes. Section 2 gives background and details on the physical model as well as implementations issues. Section 3 presents some preliminary results which lead to discussion in Section 4 of future plans.

  11. Micropatterned cell arrays for detecting DNA damage

    E-Print Network [OSTI]

    Mittal, Sukant

    2008-01-01T23:59:59.000Z

    Numerous agents are capable of interacting with DNA and damaging it. Permanent changes in the DNA structure can be both mutagenic and cytotoxic; therefore, methods to measure the susceptibility of cells to mutations are ...

  12. Towards Privacy Preserving of Forensic DNA Databases

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14T23:59:59.000Z

    Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...

  13. Co-targeting Deoxyribonucleic Acid–Dependent Protein Kinase and Poly(Adenosine Diphosphate-Ribose) Polymerase-1 Promotes Accelerated Senescence of Irradiated Cancer Cells

    SciTech Connect (OSTI)

    Azad, Arun, E-mail: arun.azad@bccancer.bc.ca [Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria (Australia); Department of Pathology, St. Vincent's Hospital, University of Melbourne, Parkville, Victoria (Australia); Bukczynska, Patricia; Jackson, Susan [Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria (Australia); Haput, Ygal; Cullinane, Carleen [Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria (Australia); Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria (Australia); McArthur, Grant A.; Solomon, Benjamin [Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria (Australia); Division of Cancer Medicine, Peter MacCallum Cancer Centre, East Melbourne, Victoria (Australia); Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, Victoria (Australia); Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria (Australia)

    2014-02-01T23:59:59.000Z

    Purpose: To examine the effects of combined blockade of DNA-dependent protein kinase (DNA-PK) and poly(adenosine diphosphate-ribose) polymerase-1 (PARP-1) on accelerated senescence in irradiated H460 and A549 non-small cell lung cancer cells. Methods and Materials: The effects of KU5788 and AG014699 (inhibitors of DNA-PK and PARP-1, respectively) on clonogenic survival, DNA double-strand breaks (DSBs), apoptosis, mitotic catastrophe, and accelerated senescence in irradiated cells were examined in vitro. For in vivo experiments, H460 xenografts established in athymic nude mice were treated with BEZ235 (a DNA-PK, ATM, and phosphatidylinositol 3-kinase/mammalian target of rapamycin inhibitor) and AG014699 to determine effects on proliferation, DNA DSBs, and accelerated senescence after radiation. Results: Compared with either inhibitor alone, combination treatment with KU57788 and AG014699 reduced postradiation clonogenic survival and significantly increased persistence of Gamma-H2AX (?H2AX) foci in irradiated H460 and A549 cells. Notably, these effects coincided with the induction of accelerated senescence in irradiated cells as reflected by positive ?-galactosidase staining, G2-M cell-cycle arrest, enlarged and flattened cellular morphology, increased p21 expression, and senescence-associated cytokine secretion. In irradiated H460 xenografts, concurrent therapy with BEZ235 and AG014699 resulted in sustained Gamma-H2AX (?H2AX) staining and prominent ?-galactosidase activity. Conclusion: Combined DNA-PK and PARP-1 blockade increased tumor cell radiosensitivity and enhanced the prosenescent properties of ionizing radiation in vitro and in vivo. These data provide a rationale for further preclinical and clinical testing of this therapeutic combination.

  14. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

    Christian, Allen T. (Tracy, CA); Coleman, Matthew A. (Livermore, CA); Tucker, James D. (Livermore, CA)

    2002-01-01T23:59:59.000Z

    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.

  15. DNA Microarrays An R Tutorial

    E-Print Network [OSTI]

    Qiu, Weigang

    Analysis & R Tutorial #12;DNA Microarrays An R Tutorial R: Graphics and Statistics beyond Excel R: an Open Source statistical package (http://www.r-project.org) RStudio: a Graphic User Interface to R (http(stock) # median > range(stock) # mim and max > sum(stock) # sum > var(stock) # variance > sd(stock) # standard

  16. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

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

    1991-01-01T23:59:59.000Z

    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. Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids

    E-Print Network [OSTI]

    Podgornik, Rudolf

    Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids Ame, University of Ljubljana, Ljubljana, Slovenia ABSTRACT DNA toroids that form inside the bacteriophage capsid glycol to the bathing solution. Spermine-DNA toroids present a convex, faceted section with no or minor

  18. Probe and method for DNA detection

    SciTech Connect (OSTI)

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

    2013-07-02T23:59:59.000Z

    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.

  19. DNA Sequencing via Electron Tunneling Michael Zwolak

    E-Print Network [OSTI]

    Zwolak, Michael

    DNA Sequencing via Electron Tunneling Michael Zwolak Department of Physics Oregon State University-cost DNA sequencing methods would revolutionize medicine: a person could have his/her full genome sequenced of "personalized medicine" is hampered today by the high cost and slow speed of DNA sequencing methods. We

  20. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11T23:59:59.000Z

    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.

  1. Influence of steam generator plugging and break size on large-break loss-of-collant accidents

    SciTech Connect (OSTI)

    Stritar, A.; Mavko, B. [Jozef Stefan Institute, Ljubljana (El Salvador)

    1991-07-01T23:59:59.000Z

    The large-break loss-of-coolant accident (LBLOCA) is the design-basis accident in the Krsko pressurized-water reactor, the only power reactor in Slovenia. Because numbers of steam generator tubes are plugged as the steam generator ages, and this directly influences the primary system behavior during an LBLOCA, this accident was re-examined assuming various proportions of blocked tube from 0 to 22%. The size of the break was changes from 25 to 45% of the initial cold-leg cross section. The analysis was made with RELAP4/MOD6 as the main code in the conservative mode rather than as the best-estimate code. The methodology separately considers the blowdown phase, the refill phase, and the reflood phase. It was found that the peak clad temperature rises as plugging increases up to about 10% plugging and tends to be constant or even decrease as the plugging increases beyond this point. It was also found that results are strongly dependent on the methodology used. 17 refs., 9 figs., 3 tabs.

  2. Mobilization of Viable Tumor Cells Into the Circulation During Radiation Therapy

    SciTech Connect (OSTI)

    Martin, Olga A. [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC (Australia); Anderson, Robin L. [The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC (Australia); Metastasis Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Russell, Prudence A. [Department of Anatomical Pathology, St. Vincent Hospital, Fitzroy, VIC (Australia); Ashley Cox, R. [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Ivashkevich, Alesia [Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Laboratory of DNA Repair and Genomics, Centre for Innate Immunity and Infectious Disease, Monash Institute for Medical Research, Monash University, Clayton, VIC (Australia); Swierczak, Agnieszka; Doherty, Judy P. [Metastasis Research Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Jacobs, Daphne H.M. [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Smith, Jai [Molecular Radiation Biology Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Siva, Shankar; Daly, Patricia E. [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); Ball, David L. [Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, East Melbourne, VIC (Australia); The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC (Australia); and others

    2014-02-01T23:59:59.000Z

    Purpose: To determine whether radiation therapy (RT) could mobilize viable tumor cells into the circulation of non-small cell lung cancer (NSCLC) patients. Methods and Materials: We enumerated circulating tumor cells (CTCs) by fluorescence microscopy of blood samples immunostained with conventional CTC markers. We measured their DNA damage levels using ?-H2AX, a biomarker for radiation-induced DNA double-strand breaks, either by fluorescence-activated cell sorting or by immunofluorescence microscopy. Results: Twenty-seven RT-treated NSCLC patients had blood samples analyzed by 1 or more methods. We identified increased CTC numbers after commencement of RT in 7 of 9 patients treated with palliative RT, and in 4 of 8 patients treated with curative-intent RT. Circulating tumor cells were also identified, singly and in clumps in large numbers, during RT by cytopathologic examination (in all 5 cases studied). Elevated ?-H2AX signal in post-RT blood samples signified the presence of CTCs derived from irradiated tumors. Blood taken after the commencement of RT contained tumor cells that proliferated extensively in vitro (in all 6 cases studied). Circulating tumor cells formed ?-H2AX foci in response to ex vivo irradiation, providing further evidence of their viability. Conclusions: Our findings provide a rationale for the development of strategies to reduce the concentration of viable CTCs by modulating RT fractionation or by coadministering systemic therapies.

  3. Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis

    SciTech Connect (OSTI)

    Kramer, J.M. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)

    1991-01-01T23:59:59.000Z

    X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs.

  4. SU(3) and Isospin Breaking Effects on B to PPP Amplitudes

    E-Print Network [OSTI]

    He, Xiao-Gang; Xu, Dong

    2014-01-01T23:59:59.000Z

    Several modes of $B$ decays into three pesudoscalar octet mesons PPP have been measured. These decays have provided useful information for B decays in the standard model (SM). Some of powerful tools in analyzing B decays are flavor $SU(3)$ and isospin symmetries. Such analyses are usually hampered by $SU(3)$ breaking effects due to a relatively large strange quark mass which breaks SU(3) symmetry down to isospin symmetry. The isospin symmetry also breaks down when up and down quark mass difference is non-zero. It is therefore interesting to find relations which are not sensitive to $SU(3)$ and isospin breaking effects. We find that the relations among several fully-symmetric $B \\to PPP$ decay amplitudes are immuned from $SU(3)$ breaking effects due a non-zero strange quark mass, and also some of them are not affected by isospin breaking effects. Measurements for these relations can provide important information about B decays in the SM.

  5. Analytical Derivation of Three Dimensional Vorticity Function for wave breaking in Surf Zone

    E-Print Network [OSTI]

    Dutta, R

    2015-01-01T23:59:59.000Z

    In this report, Mathematical model for generalized nonlinear three dimensional wave breaking equations was de- veloped analytically using fully nonlinear extended Boussinesq equations to encompass rotational dynamics in wave breaking zone. The three dimensional equations for vorticity distributions are developed from Reynold based stress equations. Vorticity transport equations are also developed for wave breaking zone. This equations are basic model tools for numerical simulation of surf zone to explain wave breaking phenomena. The model reproduces most of the dynamics in the surf zone. Non linearity for wave height predictions is also shown close to the breaking both in shoaling as well as surf zone. Keyword Wave breaking, Boussinesq equation, shallow water, surf zone. PACS : 47.32-y

  6. DNA and the Genetic Code June 14, 2011

    E-Print Network [OSTI]

    Guevara-Vasquez, Fernando

    DNA and the Genetic Code June 14, 2011 DNA and the Genetic Code #12;Protein synthesis The genetic synthesis requires two steps: transcription and translation. DNA and the Genetic Code #12;DNA DNA development. DNA is comprised of 4 bases: guanine (G), adenine (A), cytosine (C), and thymine (T). The bases

  7. ON THE EVOLUTION OF THE SPECTRAL BREAK IN THE AFTERGLOW OF GAMMA-RAY BURSTS

    SciTech Connect (OSTI)

    Dado, Shlomo; Dar, Arnon [Physics Department, Technion, Haifa 32000 (Israel)

    2012-02-20T23:59:59.000Z

    The temporal evolution of the spectral break in the time-resolved spectral energy density of the broadband afterglow of gamma-ray bursts (GRBs) 091127 and 080319B was shown recently to be inconsistent with that expected for the cooling break in the standard fireball model of GRBs. Here we show that it is, however, in good agreement with the predicted temporal evolution of the smooth injection break/bend in the cannonball model of GRBs.

  8. Bubbles Help Break Energy Storage Record for Lithium Air-Batteries

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

    Bubbles Help Break Energy Storage Record for Lithium Air-Batteries Foam-base graphene keeps oxygen flowing in batteries that holds promise for electric vehicles January...

  9. 466, 347 (2010) Intra-unit-cell Electronic C4 Symmetry Breaking

    E-Print Network [OSTI]

    Davis, James C.

    2010-01-01T23:59:59.000Z

    )]( ~ )( ~ )( ~ )( ~ [ 2 1 ][ QQ QQ QQ OyOxCux MMMM +-=)( ~ Q ~M(Qy ) = MCu + MOx - MOy Detecting IUC C4 symmetry breaking

  10. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

    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.

  11. Spontaneous symmetry breaking in a generalized orbital compass model

    E-Print Network [OSTI]

    Lukasz Cincio; Jacek Dziarmaga; Andrzej M. Oles

    2010-09-10T23:59:59.000Z

    We introduce a generalized two-dimensional orbital compass model, which interpolates continuously from the classical Ising model to the orbital compass model with frustrated quantum interactions, and investigate it using the multiscale entanglement renormalization ansatz (MERA). The results demonstrate that increasing frustration of exchange interactions triggers a second order quantum phase transition to a degenerate symmetry broken state which minimizes one of the interactions in the orbital compass model. Using boson expansion within the spin-wave theory we unravel the physical mechanism of the symmetry breaking transition as promoted by weak quantum fluctuations and explain why this transition occurs only surprisingly close to the maximally frustrated interactions of the orbital compass model. The spin waves remain gapful at the critical point, and both the boson expansion and MERA do not find any algebraically decaying spin-spin correlations in the critical ground state.

  12. Spontaneous breaking of spatial symmetries in collective neutrino oscillations

    E-Print Network [OSTI]

    Huaiyu Duan; Shashank Shalgar

    2014-12-22T23:59:59.000Z

    A dense neutrino medium can experience collective oscillations or self-induced flavor transformation through nonlinear neutrino-neutrino refraction. To make the problem of collective neutrino oscillations more tractable, all previous studies on this subject have assumed some spatial symmetry or symmetries in the neutrino medium (e.g., translation symmetries in the early universe and spherical symmetry in core-collapse supernovae). We point out that the collective oscillation modes studied in such models are very special. Using a simple toy model we show that spatial symmetries can be broken spontaneously in collective neutrino oscillations. We also show that the spatial-symmetry-breaking (SSB) modes of neutrino oscillations can exist for both neutrino mass hierarchies and even in the regimes where collective neutrino oscillations were previously thought to be suppressed. This finding calls for study of collective neutrino oscillations in multi-dimensional models.

  13. Spontaneous breaking of spatial symmetries in collective neutrino oscillations

    E-Print Network [OSTI]

    Duan, Huaiyu

    2014-01-01T23:59:59.000Z

    A dense neutrino medium can experience collective oscillations or self-induced flavor transformation through nonlinear neutrino-neutrino refraction. To make the problem of collective neutrino oscillations more tractable, all previous studies on this subject have assumed some spatial symmetry or symmetries in the neutrino medium (e.g., translation symmetries in the early universe and spherical symmetry in core-collapse supernovae). We point out that the collective oscillation modes studied in such models are very special. Using a simple toy model we show that spatial symmetries can be broken spontaneously in collective neutrino oscillations. We also show that the spatial-symmetry-breaking (SSB) modes of neutrino oscillations can exist for both neutrino mass hierarchies and even in the regimes where collective neutrino oscillations were previously thought to be suppressed. This finding calls for study of collective neutrino oscillations in multi-dimensional models.

  14. Radiative PQ Breaking and the Higgs Boson Mass

    E-Print Network [OSTI]

    D'Eramo, Francesco; Pappadopulo, Duccio

    2015-01-01T23:59:59.000Z

    The small and negative value of the Standard Model Higgs quartic coupling at high scales can be understood in terms of anthropic selection on a landscape where large and negative values are favored: most universes have a very short-lived electroweak vacuum and typical observers are in universes close to the corresponding metastability boundary. We provide a simple example of such a landscape with a Peccei-Quinn symmetry breaking scale generated through dimensional transmutation and supersymmetry softly broken at an intermediate scale. Large and negative contributions to the Higgs quartic are typically generated on integrating out the saxion field. Cancellations among these contributions are forced by the anthropic requirement of a sufficiently long-lived electroweak vacuum, determining the multiverse distribution for the Higgs quartic in a similar way to that of the cosmological constant. This leads to a statistical prediction of the Higgs boson mass that, for a wide range of parameters, yields the observed v...

  15. Inertial blob-hole symmetry breaking in magnetised plasma filaments

    E-Print Network [OSTI]

    Kendl, Alexander

    2015-01-01T23:59:59.000Z

    Symmetry breaking between the propagation velocities of magnetised plasma filaments with large positive (blob) and negative (hole) amplitudes, as implied by a dimensional analysis scaling, is studied with global ("full-n") non-Boussinesq gyrofluid computations, which include finite inertia effects through nonlinear polarisation. Interchange blobs on a flat density background have higher inertia and propagate more slowly than holes. In the presence of a large enough density gradient, the effect is reversed: blobs accelerate down the gradient and holes are slowed in their propagation up the gradient. Drift wave blobs spread their initial vorticity rapidly into a fully developed turbulent state, whereas primary holes can remain coherent for many eddy turnover times. The results bear implications for plasma edge zonal flow evolution and tokamak scrape-off-layer transport.

  16. Crucial role of neutrinos in the electroweak symmetry breaking

    SciTech Connect (OSTI)

    Smetana, Adam [Institute of Experimental and Applied Physics, Czech Technical University in Prague, Horská 3a/22, 128 00 Prague 2 (Czech Republic)

    2013-12-30T23:59:59.000Z

    Not only the top-quark condensate appears to be the natural significant source of dynamical electroweak symmetry breaking. Provided the seesaw scenario, the neutrinos can have their Dirac masses large enough so that their condensates contribute significantly to the electroweak scale as well. We address the question of a phenomenological feasibility of the top-quark and neutrino condensation conspiracy against the electroweak symmetry within the simplifying two-composite-Higgs-doublet model. Mandatory is to reproduce the masses of electroweak gauge bosons, the top-quark mass and the recently observed scalar mass of 125 GeV, and to satisfy the upper limits on absolute value of active neutrino masses. To accomplish that, the number of right-handed neutrinos participating on the seesaw mechanism turns out to be rather large, O(100–1000)

  17. Control of coherent backscattering by breaking optical reciprocity

    E-Print Network [OSTI]

    Bromberg, Y; Popoff, S M; Cao, H

    2015-01-01T23:59:59.000Z

    Reciprocity is a universal principle that has a profound impact on many areas of physics. A fundamental phenomenon in condensed-matter physics, optical physics and acoustics, arising from reciprocity, is the constructive interference of quantum or classical waves which propagate along time-reversed paths in disordered media, leading to, for example, weak localization and metal-insulator transition. Previous studies have shown that such coherent effects are suppressed when reciprocity is broken. Here we show that by breaking reciprocity in a controlled manner, we can tune, rather than simply suppress, these phenomena. In particular, we manipulate coherent backscattering of light, also known as weak localization. By utilizing a non-reciprocal magneto-optical effect, we control the interference between time-reversed paths inside a multimode fiber with strong mode mixing, and realize a continuous transition from the well-known peak to a dip in the backscattered intensity. Our results may open new possibilities fo...

  18. Replicating the benefits of closed timelike curves without breaking causality

    E-Print Network [OSTI]

    Xiao Yuan; Syed M. Assad; Jayne Thompson; Jing Yan Haw; Vlatko Vedral; Timothy C. Ralph; Ping Koy Lam; Christian Weedbrook; Mile Gu

    2014-12-17T23:59:59.000Z

    In general relativity, closed timelike curves can break causality with remarkable and unsettling consequences. At the classical level, they induce causal paradoxes disturbing enough to motivate conjectures that explicitly prevent their existence. At the quantum level, resolving such paradoxes induce radical benefits - from cloning unknown quantum states to solving problems intractable to quantum computers. Instinctively, one expects these benefits to vanish if causality is respected. Here we show that in harnessing entanglement, we can efficiently solve NP-complete problems and clone arbitrary quantum states - even when all time-travelling systems are completely isolated from the past. Thus, the many defining benefits of closed timelike curves can still be harnessed, even when causality is preserved. Our results unveil the subtle interplay between entanglement and general relativity, and significantly improve the potential of probing the radical effects that may exist at the interface between relativity and quantum theory.

  19. Single particles accelerate final stages of capillary break up

    E-Print Network [OSTI]

    Lindner, Anke; Wagner, Christian

    2015-01-01T23:59:59.000Z

    Droplet formation of suspensions is present in many industrial and technological processes such as coating and food engineering. Whilst the finite time singularity of the minimum neck diameter in capillary break-up of simple liquids can be described by well known self-similarity solutions, the pinching of non-Brownian suspension depends in a complex way on the particle dynamics in the thinning thread. Here we focus on the very dilute regime where the filament contains only isolated beads to identify the physical mechanisms leading to the pronounced acceleration of the filament thinning observed. This accelerated regime is characterized by an asymmetric shape of the filament with an enhanced curvature that depends on the size and the spatial distribution of the particles within the capillary thread.

  20. Single particles accelerate final stages of capillary break up

    E-Print Network [OSTI]

    Anke Lindner; Jorge Eduardo Fiscina; Christian Wagner

    2015-06-12T23:59:59.000Z

    Droplet formation of suspensions is present in many industrial and technological processes such as coating and food engineering. Whilst the finite time singularity of the minimum neck diameter in capillary break-up of simple liquids can be described by well known self-similarity solutions, the pinching of non-Brownian suspension depends in a complex way on the particle dynamics in the thinning thread. Here we focus on the very dilute regime where the filament contains only isolated beads to identify the physical mechanisms leading to the pronounced acceleration of the filament thinning observed. This accelerated regime is characterized by an asymmetric shape of the filament with an enhanced curvature that depends on the size and the spatial distribution of the particles within the capillary thread.

  1. A Symmetry Breaking Model for X Chromosome Inactivation

    E-Print Network [OSTI]

    M. Nicodemi; A. Prisco

    2008-01-17T23:59:59.000Z

    In mammals, dosage compensation of X linked genes in female cells is achieved by inactivation of one of their two X chromosomes which is randomly chosen. The earliest steps in X-inactivation (XCI), namely the mechanism whereby cells count their X chromosomes and choose between two equivalent X, remain mysterious. Starting from the recent discovery of X chromosome colocalization at the onset of X-inactivation, we propose a Statistical Mechanics model of XCI, which is investigated by computer simulations and checked against experimental data. Our model describes how a `blocking factor' complex is self-assembled and why only one is formed out of many diffusible molecules, resulting in a spontaneous symmetry breaking (SB) in the binding to two identical chromosomes. These results are used to derive a scenario of biological implications describing all current experimental evidences, e.g., the importance of colocalization.

  2. Matter inflation with A{sub 4} flavour symmetry breaking

    SciTech Connect (OSTI)

    Antusch, Stefan [Department of Physics, University of Basel, Klingelbergstrasse 82, Basel, CH-4056 Switzerland (Switzerland); Nolde, David, E-mail: stefan.antusch@unibas.ch, E-mail: david.nolde@unibas.ch [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), Föhringer Ring 6, München, D-80805 Germany (Germany)

    2013-10-01T23:59:59.000Z

    We discuss model building in tribrid inflation, which is a framework for realising inflation in the matter sector of supersymmetric particle physics models. The inflaton is a D-flat combination of matter fields, and inflation ends by a phase transition in which some Higgs field obtains a vacuum expectation value. We first describe the general procedure for implementing tribrid inflation in realistic models of particle physics that can be applied to a wide variety of BSM particle physics models around the GUT scale. We then demonstrate how the procedure works for an explicit lepton flavour model based on an A{sub 4} family symmetry. The model is both predictive and phenomenologically viable, and illustrates how tribrid inflation connects cosmological and particle physics parameters. In particular, it predicts a relation between the neutrino Yukawa coupling and the running of the spectral index ?{sub s}. We also show how topological defects from the flavour symmetry breaking can be avoided automatically.

  3. Effects of Rotational Symmetry Breaking in Polymer-coated Nanopores

    E-Print Network [OSTI]

    Osmanovic, D; Eccleston, R C; Hoogenboom, B W; Ford, I J

    2015-01-01T23:59:59.000Z

    The statistical theory of polymers tethered around the inner surface of a cylindrical channel has traditionally employed the assumption that the equilibrium density of the polymers is independent of the azimuthal coordinate. However, simulations have shown that this rotational symmetry can be broken when there are attractive interactions between the polymers. We investigate the phases that emerge in these circumstances, and we quantify the effect of the symmetry assumption on the phase behavior of the system. In the absence of this assumption, one can observe large differences in the equilibrium densities between the rotationally symmetric case and the non-rotationally symmetric case. A simple analytical model is developed that illustrates the driving thermodynamic forces responsible for this symmetry breaking. Our results have implications for the current understanding of the polymer behavior in cylindrical nanopores.

  4. Cosmological moduli problem, supersymmetry breaking, and stability in postinflationary cosmology

    SciTech Connect (OSTI)

    Banks, T.; Berkooz, M. [Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08855-0849 (United States)] [Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08855-0849 (United States); Steinhardt, P.J. [Department of Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States)] [Department of Physics, University of Pennsylvania, Philadelphia, Pennsylvania 19104 (United States)

    1995-07-15T23:59:59.000Z

    We review scenarios that have been proposed to solve the cosmological problem caused by moduli in string theory, the postmodern Polonyi problem (PPP). In particular, we discuss the difficulties encountered by the apparently ``trivial`` solution of this problem, in which moduli masses are assumed to arise from nonperturbative, SUSY-preserving, dynamics at a scale higher than that of SUSY breaking. This suggests a powerful {ital cosmological} {ital vacuum} {ital selection} {ital principle} in superstring theory. However, we argue that if one eschews the possibility of cancellations between different exponentials of the inverse string coupling, the mechanism described above cannot stabilize the dilaton. Thus, even if supersymmetric dynamics gives mass to the other moduli in string theory, the dilaton mass must be generated by SUSY breaking, and dilaton domination of the energy density of the Universe cannot be avoided. We conclude that the only proposal for solving the PPP that works is the intermediate scale inflation scenario of Randall and Thomas. However, we point out that all extant models have ignored unavoidably large inhomogeneities in the cosmological moduli density at very early times, and speculate that the effects associated with nonlinear gravitational collapse of these inhomogeneities may serve as an efficient mechanism for converting moduli into ordinary matter. As an important by-product of this investigation we show that in a postinflationary universe minima of the effective potential with a negative cosmological constant are not stationary points of the classical equations of scalar field cosmology. Instead, such points lead to catastrophic gravitational collapse of that part of the Universe which is attracted to them. Thus postinflationary cosmology dynamically chooses non-negative values of the cosmological constant. This implies that supersymmetry {ital must} be broken in any sensible inflationary cosmology. (Abstract Truncated)

  5. 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)

    2002-01-01T23:59:59.000Z

    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.

  6. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01T23:59:59.000Z

    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.

  7. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13T23:59:59.000Z

    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.

  8. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-13T23:59:59.000Z

    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.

  9. Hydrogen bond breaking probed with multidimensional stimulated vibrational echo correlation spectroscopy

    E-Print Network [OSTI]

    Fayer, Michael D.

    Hydrogen bond breaking probed with multidimensional stimulated vibrational echo correlation September 2003 Hydrogen bond population dynamics are extricated with exceptional detail using ultrafast ( 50 of methanol­OD oligomers in CCl4 . Hydrogen bond breaking makes it possible to acquire data for times much

  10. Symmetry Breaking in Graphene Gregory S. Boebinger, National High Magnetic Field Laboratory

    E-Print Network [OSTI]

    Weston, Ken

    Symmetry Breaking in Graphene Gregory S. Boebinger, National High Magnetic Field Laboratory DMR. In this experiment, Landau levels in graphene were used to study the breaking of SU(4) symmetry--a higher dimensional states by their spin polarization. It was found that graphene turns into either a spin ferromagnet

  11. On the Modeling and Simulation of Non-Hydrostatic Dam Break Flows

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    by the failure of the dam structure. The determination of the potential consequences of a dam break requiresOn the Modeling and Simulation of Non-Hydrostatic Dam Break Flows Alexandre Caboussat S´ebastien Boyaval Alexandre Masserey January 1, 2013 Abstract The numerical simulation of three-dimensional dam

  12. Break-Even Cost for Residential Photovoltaics in the United States: Key Drivers and Sensitivities

    SciTech Connect (OSTI)

    Denholm, P.; Margolis, R. M.; Ong, S.; Roberts, B.

    2009-12-01T23:59:59.000Z

    Grid parity--or break-even cost--for photovoltaic (PV) technology is defined as the point where the cost of PV-generated electricity equals the cost of electricity purchased from the grid. Break-even cost is expressed in $/W of an installed system. Achieving break-even cost is a function of many variables. Consequently, break-even costs vary by location and time for a country, such as the United States, with a diverse set of resources, electricity prices, and other variables. In this report, we analyze PV break-even costs for U.S. residential customers. We evaluate some key drivers of grid parity both regionally and over time. We also examine the impact of moving from flat to time-of-use (TOU) rates, and we evaluate individual components of the break-even cost, including effect of rate structure and various incentives. Finally, we examine how PV markets might evolve on a regional basis considering the sensitivity of the break-even cost to four major drivers: technical performance, financing parameters, electricity prices and rates, and policies. We find that local incentives rather than ?technical? parameters are in general the key drivers of the break-even cost of PV. Additionally, this analysis provides insight about the potential viability of PV markets.

  13. A model for the ultrasonic detection of surface-breaking cracks by the Scanning

    E-Print Network [OSTI]

    Huerta, Antonio

    A model for the ultrasonic detection of surface-breaking cracks by the Scanning Laser Source, Northwestern University, Evanston, IL 60208, USA Abstract A model for the Scanning Laser Source (SLS) technique- breaking cracks. The generated ultrasonic signal is monitored as a line-focused laser is scanned over

  14. Dam breaking by wave-induced erosional incision N. J. Balmforth,1

    E-Print Network [OSTI]

    Balmforth, Neil

    Dam breaking by wave-induced erosional incision N. J. Balmforth,1 J. von Hardenberg,2 A. Provenzale displacement wave can lead to catastrophic erosional incision of a moraine damming a glacial lake that a single wave is generally unable to break the dam, but a sufficiently large disturbance in an almost

  15. The dynamic interplay between DNA damage and metabolism : the metabolic fate and transport of DNA lesions and novel DNA damage derived from intermediary metabolism

    E-Print Network [OSTI]

    Jumpathong, Watthanachai

    2014-01-01T23:59:59.000Z

    The work presented in this thesis explores two novel and complementary facets of endogenous DNA damage: the development of biomarkers of inflammation based on metabolites of DNA damage products and the formation of DNA ...

  16. Breaking FIR-Radio Correlation: The Case of Interacting Galaxies

    E-Print Network [OSTI]

    Donevski, Darko

    2015-01-01T23:59:59.000Z

    Far-infrared (FIR)--radio correlation is a well-established empirical connection between continuum radio and dust emission of star-forming galaxies, used as a tool in determining star-formation rates. Here we point out that in the case of interacting star-forming galaxies this tool might break. Galactic interactions and mergers have been known to give rise to tidal shocks and disrupt morphologies especially in the smaller of the interacting components. Moreover, these shocks can also heat the gas and dust and accelerate particles leading to tidal cosmic-ray population in addition to standard galactic cosmic rays. Both heating and additional non-thermal radiation will obviously affect the FIR-radio correlation of these systems. To test this hypothesis we have analyzed a sample of 43 infrared bright star-forming interacting galaxies at different merger stages. We have found that their FIR-radio correlation parameter and radio emission spectral index vary over different merger stages and behave as it would be ex...

  17. Break-even Costs for Cow/Calf Producers

    E-Print Network [OSTI]

    Sprott, L. R.

    1998-10-14T23:59:59.000Z

    $400 90/600 540 $0.19 $0.37 $0.56 $0.74 90/500 450 $0.22 $0.44 $0.66 $0.89 90/400 360 $0.28 $0.56 $0.83 $1.11 90/300 270 $0.37 $0.74 $1.11 $1.48 80/600 480 $0.21 $0.42 $0.63 $0.83 80/500 400 $0.25 $0.50 $0.75 $1.00 80/400 320 $0.31 $0.63 $0.94 $1.25 80.../300 240 $0.42 $0.83 $1.25 $1.67 70/600 420 $0.24 $0.48 $0.71 $0.95 70/500 350 $0.29 $0.57 $0.86 $1.14 70/400 280 $0.36 $0.71 $1.07 $1.43 70/300 210 $0.48 $0.95 $1.43 $1.90 Table 1 shows break-even costs for 12 production scenarios and four annual cash...

  18. Lyman-break galaxies are they young spheroids?

    E-Print Network [OSTI]

    Matteucci, F

    2002-01-01T23:59:59.000Z

    We have compared the results from a model for the chemical evolution of an elliptical galaxy with initial luminous mass of 2x10^10 M_sun and effective radius of 2 kpc with the recent abundance determinations for the Lyman-break galaxy MS 1512-cB58 at a redshift z=2.7276. After correcting the iron abundance determination for the presence of dust we concluded that the observed [Si/Fe], [Mg/Fe], [N/Fe] are consistent with our model when a galactic age between 20 and 35 Myr is assumed. Moreover, the [N/O] ratio also suggests the same age. This age is in very good agreement with other independent studies based on the analysis of the spectral energy distribution suggesting that this object is younger than 35 Myr. Therefore, we suggest that MS 1512-cB58 is a truly young normal elliptical galaxy experiencing its main episode of star formation and galactic wind.

  19. Breaking the Curse of Cardinality on Bitmap Indexes

    SciTech Connect (OSTI)

    Wu, Kesheng; Wu, Kesheng; Stockinger, Kurt; Shoshani, Arie

    2008-04-04T23:59:59.000Z

    Bitmap indexes are known to be efficient for ad-hoc range queries that are common in data warehousing and scientific applications. However, they suffer from the curse of cardinality, that is, their efficiency deteriorates as attribute cardinalities increase. A number of strategies have been proposed, but none of them addresses the problem adequately. In this paper, we propose a novel binned bitmap index that greatly reduces the cost to answer queries, and therefore breaks the curse of cardinality. The key idea is to augment the binned index with an Order-preserving Bin-based Clustering (OrBiC) structure. This data structure significantly reduces the I/O operations needed to resolve records that cannot be resolved with the bitmaps. To further improve the proposed index structure, we also present a strategy to create single-valued bins for frequent values. This strategy reduces index sizes and improves query processing speed. Overall, the binned indexes with OrBiC great improves the query processing speed, and are 3 - 25 times faster than the best available indexes for high-cardinality data.

  20. Physical Naturalness and Dynamical Breaking of Classical Scale Invariance

    E-Print Network [OSTI]

    Matti Heikinheimo; Antonio Racioppi; Martti Raidal; Christian Spethmann; Kimmo Tuominen

    2014-05-05T23:59:59.000Z

    We propose a model of a confining dark sector, dark technicolor, that communicates with the Standard Model through the Higgs portal. In this model electroweak symmetry breaking and dark matter share a common origin, and the electroweak scale is generated dynamically. Our motivation to suggest this model is the absense of evidence for new physics from recent LHC data. Although the conclusion is far from certain at this point, this lack of evidence may suggest that no mechanism exists at the electroweak scale to stabilise the Higgs mass against radiative corrections from UV physics. The usual reaction to this puzzling situation is to conclude that the stabilising new physics is either hidden from us by accident, or that it appears at energies that are currently inaccessible, such that nature is indeed fine-tuned. In order to re-examine the arguments that have lead to this dichotomy, we review the concept of naturalness in effective field theories, discussing in particular the role of quadratic divergences in relation to different energy scales. This leads us to suggest classical scale invariance as a guidline for model building, implying that explicit mass scales are absent in the underlying theory.

  1. Non-equilibrium evolution of a "Tsunami" Dynamical Symmetry Breaking

    E-Print Network [OSTI]

    Boyanovsky, D; Holman, R; Kumar, S P; Pisarski, R D; Boyanovsky, Daniel; Vega, Hector J. de; Holman, Richard; Pisarski, Robert D.

    1998-01-01T23:59:59.000Z

    We propose to study the non-equilibrium features of heavy-ion collisions by following the evolution of an initial state with a large number of quanta with a distribution around a momentum |\\vec k_0| corresponding to a thin spherical shell in momentum space, a `tsunami'. An O(N); ({\\vec \\Phi}^2)^2 model field theory in the large N limit is used as a framework to study the non-perturbative aspects of the non-equilibrium dynamics including a resummation of the effects of the medium (the initial particle distribution). In a theory where the symmetry is spontaneously broken in the absence of the medium, when the initial number of particles per correlation volume is chosen to be larger than a critical value the medium effects can restore the symmetry of the initial state. We show that if one begins with such a symmetry-restored, non-thermal, initial state, non-perturbative effects automatically induce spinodal instabilities leading to a dynamical breaking of the symmetry. As a result there is explosive particle pro...

  2. Non-equilibrium evolution of a `Tsunami': Dynamical Symmetry Breaking

    E-Print Network [OSTI]

    Daniel Boyanovsky; Hector J. de Vega; Richard Holman; S. Prem Kumar; Robert D. Pisarski

    1997-11-06T23:59:59.000Z

    We propose to study the non-equilibrium features of heavy-ion collisions by following the evolution of an initial state with a large number of quanta with a distribution around a momentum |\\vec k_0| corresponding to a thin spherical shell in momentum space, a `tsunami'. An O(N); ({\\vec \\Phi}^2)^2 model field theory in the large N limit is used as a framework to study the non-perturbative aspects of the non-equilibrium dynamics including a resummation of the effects of the medium (the initial particle distribution). In a theory where the symmetry is spontaneously broken in the absence of the medium, when the initial number of particles per correlation volume is chosen to be larger than a critical value the medium effects can restore the symmetry of the initial state. We show that if one begins with such a symmetry-restored, non-thermal, initial state, non-perturbative effects automatically induce spinodal instabilities leading to a dynamical breaking of the symmetry. As a result there is explosive particle production and a redistribution of the particles towards low momentum due to the nonlinearity of the dynamics. The asymptotic behavior displays the onset of Bose condensation of pions and the equation of state at long times is that of an ultrarelativistic gas although the momentum distribution is non-thermal.

  3. Scales of Fermion Mass Generation and Electroweak Symmetry Breaking

    E-Print Network [OSTI]

    Duane A. Dicus; Hong-Jian He

    2005-06-11T23:59:59.000Z

    The scale of mass generation for fermions (including neutrinos) and the scale for electroweak symmetry breaking (EWSB) can be bounded from above by the unitarity of scattering involving longitudinal weak gauge bosons or their corresponding would-be Goldstone bosons. Including the exact n-body phase space we analyze the 2 --> n ($n \\geq 2$) processes for the fermion-(anti)fermion scattering into multiple gauge boson final states. Contrary to naive energy power counting, we demonstrate that as $n$ becomes large, the competition between an increasing energy factor and a phase-space suppression leads to a {\\it strong new upper bound} on the scale of fermion mass generation at a finite value $n=n_s$, which is {\\it independent of the EWSB scale,} $v = (\\sqrt{2}G_F)^{-1/2}$. For quarks, leptons and Majorana neutrinos, the strongest 2 --> n limits range from about 3TeV to 130-170TeV (with $2\\lesssim n_s \\lesssim 24$), depending on the measured fermion masses. Strikingly, given the tiny neutrino masses as constrained by the neutrino oscillations, neutrinoless double-beta decays and astrophysical observations, the unitarity violation of $\

  4. Symmetry Breaking and Topological Defect Formation in Ion Coulomb Crystals

    E-Print Network [OSTI]

    Pyka, Karsten; Partner, Heather L; Nigmatullin, Ramil; Burgermeister, Tobias; Meier, David-M; Kuhlmann, Kristijan; Retzker, Alex; Plenio, Martin B; Zurek, Wojciech H; del Campo, Adolfo; Mehlstäubler, Tanja E

    2013-01-01T23:59:59.000Z

    Symmetry breaking phase transitions play an important role in nature. When a system traverses such a transition at a finite rate, its causally disconnected regions choose the new broken symmetry state independently. Where such local choices are incompatible, defects will form with densities predicted to follow a power law scaling in the rate of the transition. The importance of this Kibble-Zurek mechanism (KZM) ranges from cosmology to condensed matter [1-4]. In previous tests in homogeneous systems, defect formation was seen, but weak dependence on the transition rate and limited control of external parameters so far prevented tests of KZM scaling. As recently predicted [5-9], in inhomogeneous systems propagation of the critical front enhances the role of causality and steepens scaling of defect density with the transition rate. We use ion Coulomb crystals in a harmonic trap to demonstrate, for the first time, scaling of the number of topological defects with the transition rate - the central prediction of K...

  5. Symmetry Breaking, Unification, and Theories Beyond the Standard Model

    SciTech Connect (OSTI)

    Nomura, Yasunori

    2009-07-31T23:59:59.000Z

    A model was constructed in which the supersymmetric fine-tuning problem is solved without extending the Higgs sector at the weak scale. We have demonstrated that the model can avoid all the phenomenological constraints, while avoiding excessive fine-tuning. We have also studied implications of the model on dark matter physics and collider physics. I have proposed in an extremely simple construction for models of gauge mediation. We found that the {mu} problem can be simply and elegantly solved in a class of models where the Higgs fields couple directly to the supersymmetry breaking sector. We proposed a new way of addressing the flavor problem of supersymmetric theories. We have proposed a new framework of constructing theories of grand unification. We constructed a simple and elegant model of dark matter which explains excess flux of electrons/positrons. We constructed a model of dark energy in which evolving quintessence-type dark energy is naturally obtained. We studied if we can find evidence of the multiverse.

  6. Noncommutative gauge theory and symmetry breaking in matrix models

    SciTech Connect (OSTI)

    Grosse, Harald; Steinacker, Harold [Department of Physics, University of Vienna, Boltzmanngasse5, A-1090 Vienna (Austria); Lizzi, Fedele [Dipartimento di Scienze Fisiche, Universita di Napoli Federico II and INFN, Sezione di Napoli, Via Cintia, 80126 Napoli (Italy); High Energy Physics Group, Departament d'Estructura i Constituents de la Materia and Institut de Ciencies del Cosmos Universitat de Barcelona Barcelona, Catalonia (Spain)

    2010-04-15T23:59:59.000Z

    We show how the fields and particles of the standard model can be naturally realized in noncommutative gauge theory. Starting with a Yang-Mills matrix model in more than four dimensions, an SU(n) gauge theory on a Moyal-Weyl space arises with all matter and fields in the adjoint of the gauge group. We show how this gauge symmetry can be broken spontaneously down to SU(3){sub c}xSU(2){sub L}xU(1){sub Q}[resp. SU(3){sub c}xU(1){sub Q}], which couples appropriately to all fields in the standard model. An additional U(1){sub B} gauge group arises which is anomalous at low energies, while the trace-U(1) sector is understood in terms of emergent gravity. A number of additional fields arise, which we assume to be massive, in a pattern that is reminiscent of supersymmetry. The symmetry breaking might arise via spontaneously generated fuzzy spheres, in which case the mechanism is similar to brane constructions in string theory.

  7. Treatment methods for breaking certain oil and water emulsions

    DOE Patents [OSTI]

    Sealock, Jr., L. John (W. Richland, WA); Baker, Eddie G. (Richland, WA); Elliott, Douglas C. (Richland, WA)

    1992-01-01T23:59:59.000Z

    Disclosed are treatment methods for breaking emulsions of petroleum oil and salt water, fatty oil and water, and those resulting from liquefication of organic material. The emulsions are broken by heating to a predetermined temperature at or above about 200.degree. C. and pressurizing to a predetermined pressure above the vapor pressure of water at the predetermined temperature to produce a heated and pressurized fluid. The heated and pressurized fluid is contained in a single vessel at the predetermined temperature and pressure for a predetermined period of time to effectively separate the emulsion into substantially distinct first and second phases, the first phase comprising primarily the petroleum oil, the second phase comprising primarily the water. The first and second phases are separately withdrawn from the vessel at a withdraw temperature between about 200.degree. C. and 374.degree. C. and a withdraw pressure above the vapor pressure of water at the withdraw temperature. Where solids are present in the certain emulsions, the above described treatment may also effectively separate the certain emulsion into a substantially distinct third phase comprising primarily the solids.

  8. DNA Bubble Life Time in Denaturation

    E-Print Network [OSTI]

    Zh. S. Gevorkian; Chin-Kun Hu

    2010-10-11T23:59:59.000Z

    We have investigated the denaturation bubble life time for a homogeneous as well as for a heterogeneous DNA within a Poland-Scheraga model. It is shown that at criticality the bubble life time for a homogeneous DNA is finite provided that the loop entropic exponent c>2 and has a scaling dependence on DNA length for c<2. Heterogeneity in the thermodynamical limit makes the bubble life time infinite for any entropic exponent.

  9. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

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

    2005-11-01T23:59:59.000Z

    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.

  10. Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation

    E-Print Network [OSTI]

    Shrivastav, Nidhi

    The reaction of DNA-damaging agents with the genome results in a plethora of lesions, commonly referred to as adducts. Adducts may cause DNA to mutate, they may represent the chemical precursors of lethal events and they ...

  11. DNA Directed Assembly Probe for Detecting DNA-Protein Interaction in Microarray Format

    E-Print Network [OSTI]

    Ng, Jin Kiat

    Quantifying DNA-protein interaction using DNA microarrays are gaining increasing attention due to their ability to profile specificity of interactions in a high-throughput manner. This paper describes a new approach that ...

  12. Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA

    E-Print Network [OSTI]

    Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore among individual nucleotides (nt). The system must be capable of differentiating among the four bases

  13. DNA binding specificity of the p73 DNA-binding domain

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

    of DNA recognition by p53 tetramers. Mol Cell 22, 741-753.site as a self-assembled tetramer. Structure 18, 246- Chene,structure of a p53 core tetramer bound to DNA. Oncogene 28,

  14. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18T23:59:59.000Z

    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.

  15. DNA: The Strand that Connects Us All

    SciTech Connect (OSTI)

    Kaplan, Matt (University of Arizona Genetics Core) [University of Arizona Genetics Core

    2011-03-29T23:59:59.000Z

    Learn how the methods and discoveries of human population genetics are applied for personal genealogical reconstruction and anthropological testing. Dr. Kaplan starts with a short general review of human genetics and the biology behind this form of DNA testing. He looks at how DNA testing is performed and how samples are processed in the University of Arizona laboratory. He also examines examples of personal genealogical results from Family Tree DNA and personal anthropological results from the Genographic Project. Finally, he describes the newest project in the UA laboratory, the DNA Shoah Project.

  16. SnapShot: DNA Polymerases II Mammals

    E-Print Network [OSTI]

    Foti, James J.

    DNA polymerases ensure the faithful duplication of genetic information inside the nuclease and mitochondria of eukaryotic cells and the nucleoid of prokaryotic cells. These remarkable enzymes synthesize polynucleotide ...

  17. 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)

    1992-01-01T23:59:59.000Z

    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.

  18. Nucleotide capacitance calculation for DNA sequencing

    SciTech Connect (OSTI)

    Lu, Jun-Qiang [ORNL; Zhang, Xiaoguang [ORNL

    2008-01-01T23:59:59.000Z

    Using a first-principles linear response theory, the capacitance of the DNA nucleotides, adenine, cytosine, guanine and thymine, are calculated. The difference in the capacitance between the nucleotides is studied with respect to conformational distortion. The result suggests that although an alternate current capacitance measurement of a single-stranded DNA chain threaded through a nano-gap electrodes may not sufficient to be used as a stand alone method for rapid DNA sequencing, the capacitance of the nucleotides should be taken into consideration in any GHz-frequency electric measurements and may also serve as an additional criterion for identifying the DNA sequence.

  19. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

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

    2013-07-16T23:59:59.000Z

    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.

  20. DNA

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

    algorithms that we have developed to see the inner workings of molecular machines," said Thomas Terwilliger, a senior Los Alamos scientist and Laboratory Fellow. In this case,...

  1. DNA

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power Administration wouldDECOMPOSITION OF CALCIUM SULFATE: A REVIEWThis rcportJ it cdrives

  2. DNA nanotechnology DOI: 10.1002/smll.200500464

    E-Print Network [OSTI]

    Li, Jiali

    DNA nanotechnology DOI: 10.1002/smll.200500464 Towards Rapid DNA Sequencing: Detecting Single- Stranded DNA with a Solid-State Nanopore Hao Yan* and Bingqian Xu* Keywords: · DNA · sequencing · single for rapid detection of single DNA molecules and their sequences. Two types of nanopores have been used

  3. Sequence specific alkylation of DNA by hairpin pyrroleimidazole polyamide conjugates

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Sequence specific alkylation of DNA by hairpin pyrrole­imidazole polyamide conjugates Nicholas R predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA for covalent reaction at specific DNA sequences and thereby inhibit DNA­protein interactions. Site

  4. Sequence Recognition of DNA by Protein-Induced Conformational Transitions

    E-Print Network [OSTI]

    Williams, Loren

    Sequence Recognition of DNA by Protein-Induced Conformational Transitions Derrick Watkins1 The binding of proteins to specific sequences of DNA is an important feature of virtually all DNA transactions. Proteins recognize specific DNA sequences using both direct readout (sensing types and positions of DNA

  5. 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.

    2013-05-14T23:59:59.000Z

    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.

  6. DNA Profiling Using Solid-State Nanopores: Detection of DNA-Binding

    E-Print Network [OSTI]

    Meller, Amit

    a 3.5 nm pore results from threading of a dye-intercalated DNA molecule, as compared to the typical for drug development, necessitating new in vitro methods for rapid and low-cost assessment of the binding molecules, which give the DNA/intercalator complex a bulkier structure than that of native DNA. Furthermore

  7. A DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation

    E-Print Network [OSTI]

    Deaton, Russell J.

    lelism, capacity, and power. This potential, however, is limited by the constraints imposed by the DNA chemistry 1]. Adleman 2] introduced a way to solve combina- torial optimization problems with DNA- mental reaction in DNA based computation is hydro- gen bonding between Watson-Crick complement base pairs

  8. Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving Stefan Bretschneider, Christian Eggeling, and Stefan W. Hell*

    E-Print Network [OSTI]

    Weeks, Eric R.

    Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving Stefan the breaking of the diffraction resolution barrier in far-field fluorescence microscopy by transiently shelving barrier by shelving the fluorophore in a metastable dark state, thereby effectively depleting

  9. Spontaneous Symmetry Breaking as a Basis of Particle Mass

    SciTech Connect (OSTI)

    Quigg, Chris; /Fermilab /CERN

    2007-04-01T23:59:59.000Z

    Electroweak theory joins electromagnetism with the weak force in a single quantum field theory, ascribing the two fundamental interactions--so different in their manifestations--to a common symmetry principle. How the electroweak gauge symmetry is hidden is one of the most urgent and challenging questions facing particle physics. The provisional answer incorporated in the ''standard model'' of particle physics was formulated in the 1960s by Higgs, by Brout & Englert, and by Guralnik, Hagen, & Kibble: The agent of electroweak symmetry breaking is an elementary scalar field whose self-interactions select a vacuum state in which the full electroweak symmetry is hidden, leaving a residual phase symmetry of electromagnetism. By analogy with the Meissner effect of the superconducting phase transition, the Higgs mechanism, as it is commonly known, confers masses on the weak force carriers W{sup {+-}} and Z. It also opens the door to masses for the quarks and leptons, and shapes the world around us. It is a good story--though an incomplete story--and we do not know how much of the story is true. Experiments that explore the Fermi scale (the energy regime around 1 TeV) during the next decade will put the electroweak theory to decisive test, and may uncover new elements needed to construct a more satisfying completion of the electroweak theory. The aim of this article is to set the stage by reporting what we know and what we need to know, and to set some ''Big Questions'' that will guide our explorations.

  10. The effects of similarity breaking on the intracluster medium

    E-Print Network [OSTI]

    E. J. Lloyd-Davies; R. G. Bower; T. J. Ponman

    2002-03-28T23:59:59.000Z

    We construct a family of simple analytical models of galaxy clusters at the present epoch and compare its predictions with observational data. We explore two processes that break the self-similarity of galaxy clusters: systematic variation in the dark matter halo concentration and energy injection into the intracluster gas, through their effects on the observed cluster properties. Three observed relations between cluster properties and temperature are employed to constrain the model; mass, slope of gas density profile (beta) and luminosity. The slope of the mass-temperature relation is found to be reproduced by our model when the observed variation in concentration is included, raising the slope from the self-similar prediction of 1.5, to that of the observed relation, ~ 2. Heating of the gas is observed to have little effect on the mass-temperature relation. The mean trend in the beta-temperature relation is reproduced by energy injection of 0.5-0.75 keV per particle, while concentration variation has only a small effect. Excess energies calculated for individual systems from the beta-temperature relation suggest that the lowest mass systems may have excess energies that are biased to lower values by selection effects. The observed properties of the luminosity-temperature relation are reproduced by the combined effects of excess energy and a trend in the dark matter concentration. At high masses the observed variation in dark matter concentration results a slope of ~ 2.7 compared to recent observations in the range 2.6-2.9, whilst the observed steepening in galaxy groups is predicted when heating of 0.5-0.75 keV per particle is included. Hence a combination of energy injection and dark matter concentration variation appears able to account for the mean trends in the observed relations.

  11. ADVANCES IN ATMOSPHERIC SCIENCES, VOL. 26, NO. 4, 2009, 701706 Variability of Northeast China River Break-up Date

    E-Print Network [OSTI]

    River Break-up Date WANG Huijun1,2 ( ˇ) and SUN Jianqi1,2 (ę ) 1 Institute of Atmospheric Physics investigates the variability of the break-up dates of the rivers in Northeast China from their icebound states for the period of 1957­2005 and explores some potential explanatory mechanisms. Results show that the break-up

  12. An adaptive time-space dual algorithm for shallow non-Newtonian power-law fluids: the horizontal dam break

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    dam break problem revisited P. Saramito a C. Smutek b B. Cordonnier b aLJK ­ CNRS et Universit´es de´eunion, France Abstract ­ The dam break problem shallow approximation for laminar flows of viscoplastic non equations for non-Newtonian fluids subject to the horizontal dam break problem. Keywords ­ viscoplastic

  13. Small break critical discharge: The roles of vapor and liquid entrainment in a stratified two-phase region upstream of the break

    SciTech Connect (OSTI)

    Schrock, V E; Revankar, S T; Mannheimer, R; Wang, C H

    1986-12-01T23:59:59.000Z

    The main objective of this research program was to perform an experimental investigation on the phenomena of two-phase critical flow through small break from a horizontal pipe which contained a stratified two phase flow. Stagnation conditions investigated were saturated steam-water, and air-cold water at pressures ranging from 0.37 MPa to 1.07 MPa. The small breaks employed were cylindrical tubes of diameters 3.96 mm, 6.32 mm, and 10.1 mm with sharp-edged entrance. For breaks resulting from a small hole in a primary coolant pipe or in a small pipe, a sharp-edged orifice or a sharp-edged tube can be the approximation.

  14. alkyladenine dna glycosylase: Topics by E-print Network

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

    recognition and repair by 3-methyladenine DNA glycosylase I (TAG) Audrey H Metz1II), Helicobacter pylori 3mA DNA glycosylase (MagIII), yeast methyladenine DNA glycosylase...

  15. Single Stranded DNA Induced Assembly of Gold Nanoparticles

    E-Print Network [OSTI]

    Yang, Jun

    The binding affinity of single stranded DNA (ssDNA) for gold nanoparticle surface is studied in this work. The data indicate that the strength of interaction between ssDNA and Au particle surface is closely related to the ...

  16. Single molecule analysis of DNA electrophoresis in microdevices

    E-Print Network [OSTI]

    Randall, Greg C

    2006-01-01T23:59:59.000Z

    Given that current electrophoresis technology is inadequate for mapping large O[100 kilobasepair] DNA, several promising lab-on-chip designs for DNA mapping have been recently proposed that require either 1) a DNA molecule ...

  17. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

    DNA topology confers sequence specificity to nonspecific architectural proteins Juan Weia , Luke of DNA change the disorder found in chain molecules randomly decorated by nonspecific, architectural, counter to expectations, in greater quantities and at particular sites along simulated DNA minicircles

  18. DNA Damage, Repair & Replication Using E. Coli Model Systems

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

    431. Kunkel, T.A. (2004) DNA replication fidelity. J Biol1996) Generation of an endogenous DNA- methylating agent bypombe Mag1 alkylpurine DNA glycosylase. EMBO Rep, 12, 1286-

  19. Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

    E-Print Network [OSTI]

    Dekker, Cees

    Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels Derek Stein,, Zeno Deurvorst on this understanding by demonstrating how a nanofluidic device with integrated electrodes can preconcentrate DNA. KEYWORDS Nanofluidic, DNA, electrokinetic, concentration M iniature fluidic devices are having an important

  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 Ř.; Voulgarakis, Nikolaos K.

    2015-03-12T23:59:59.000Z

    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. 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)

    1994-01-01T23:59:59.000Z

    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.

  2. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-10-18T23:59:59.000Z

    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.

  3. Dynamics and control of DNA sequence amplification

    SciTech Connect (OSTI)

    Marimuthu, Karthikeyan [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Chakrabarti, Raj, E-mail: raj@pmc-group.com, E-mail: rajc@andrew.cmu.edu [Department of Chemical Engineering and Center for Advanced Process Decision-Making, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213 (United States); Division of Fundamental Research, PMC Advanced Technology, Mount Laurel, New Jersey 08054 (United States)

    2014-10-28T23:59:59.000Z

    DNA amplification is the process of replication of a specified DNA sequence in vitro through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.

  4. DNA Motif Representation with Nucleotide Dependency

    E-Print Network [OSTI]

    Chin, Francis Y.L.

    DNA Motif Representation with Nucleotide Dependency Francis Chin1 and Henry Leung1 1 Department, these representations cannot model biological binding sites well because they fail to capture nucleotide interdependence. It has been pointed out by many researchers that the nucleotides of the DNA binding site cannot

  5. Subcellular Spatial Correlation of Particle Traversal and Biological Response in Clinical Ion Beams

    SciTech Connect (OSTI)

    Niklas, Martin, E-mail: m.niklas@dkfz.de [Division of Medical Physics in Radiation Oncology, German Cancer Research Center, Heidelberg (Germany); German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Abdollahi, Amir [German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Molecular and Translational Radiation Oncology, Heidelberg Ion-Beam Therapy Center, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg (Germany); Department of Radiation Oncology and Radiation Therapy, University Hospital Heidelberg, Heidelberg (Germany); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); Akselrod, Mark S. [Stillwater Crystal Growth Division, Landauer Inc, Stillwater, Oklahoma (United States); Debus, Jürgen [German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Molecular and Translational Radiation Oncology, Heidelberg Ion-Beam Therapy Center, University of Heidelberg Medical School and National Center for Tumor Diseases, German Cancer Research Center, Heidelberg (Germany); Department of Radiation Oncology and Radiation Therapy, University Hospital Heidelberg, Heidelberg (Germany); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); Jäkel, Oliver [Division of Medical Physics in Radiation Oncology, German Cancer Research Center, Heidelberg (Germany); German Cancer Consortium, National Center for Radiation Research in Oncology, Heidelberg Institute of Radiation Oncology, Heidelberg (Germany); Department of Radiation Oncology and Radiation Therapy, University Hospital Heidelberg, Heidelberg (Germany); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); and others

    2013-12-01T23:59:59.000Z

    Purpose: To report on the spatial correlation of physical track information (fluorescent nuclear track detectors, FNTDs) and cellular DNA damage response by using a novel hybrid detector (Cell-Fit-HD). Methods and Materials: The FNTDs were coated with a monolayer of human non-small cell lung carcinoma (A549) cells and irradiated with carbon ions (270.55 MeV u{sup ?1}, rising flank of the Bragg peak). Phosphorylated histone variant H2AX accumulating at the irradiation-induced double-strand break site was labeled (RIF). The position and direction of ion tracks in the FNTD were registered with the location of the RIF sequence as an ion track surrogate in the cell layer. Results: All RIF sequences could be related to their corresponding ion tracks, with mean deviations of 1.09 ?m and ?1.72 ?m in position and of 2.38° in slope. The mean perpendicular between ion track and RIF sequence was 1.58 ?m. The mean spacing of neighboring RIFs exhibited a regular rather than random spacing. Conclusions: Cell-Fit-HD allows for unambiguous spatial correlation studies of cell damage with respect to the intracellular ion traversal under therapeutic beam conditions.

  6. the Adaptive Response, Genetic Haplo-Insufficiency and Genomic Instability

    SciTech Connect (OSTI)

    Geard, Charles R.

    2014-12-12T23:59:59.000Z

    The linear no-threshold (LNT) hypothesis is the driving force in the establishment of radiation protection standards. However, the scientific basis for linearity has been brought into question, particularly due to the concerns about induced radiation resistance as it pertains to oxidative stress. Specifically, we investigated the observation that tumor hypoxia is associated with malignant progression, increased metastases, chemo- and radioresistance and poor prognosis. Experiments were conducted with non-malignant 3T3/NIH cells and normal human lung fibroblasts (NHLF) that were subjected to ?-irradiation under the levels of oxygen resembling those in growing tumors, and related our data to the concentrations of dissolved oxygen (DO), which is a better indicator of the amounts of residual oxygen inside the cells cultured in the hypoxic or anoxic atmosphere. We found that at DO levels about 0.5 mg/L cells subjected to both short-term (17 hours) and prolonged (48-72 hours) hypoxia continued to proliferate, and that apoptotic events were decreased at the early hours of hypoxic treatment. We showed that the short-term hypoxia up-regulated p53-binding protein 1 (53BP1) and resulted in facilitated 53BP1 nuclear foci formation and disappearance, thus indicating the higher efficiency of DNA double strand breaks repair processes. The latter was confirmed by the lower micronuclei incidence in irradiated hypoxic cells.

  7. Atomic force microscopy of biochemically tagged DNA

    SciTech Connect (OSTI)

    Ogletree, D.F.; Kolbe, W.; Spengler, S.; Salmeron, M. (Lawrence Berkeley Laboratory, CA (United States)); Hansma, H.G.; Bezanilla, M. (Univ. of California, Santa Barbara (United States)); Sano, T.; Smith, C.S.; Cantor, C.R. (Boston Univ., MA (United States))

    1993-05-01T23:59:59.000Z

    Small fragments of DNA of known length were made with the polymerase chain reaction. These fragments had biotin molecules covalently attached at their ends. They were subsequently labeled with a chimeric protein fusion between streptavidin and two immunoglobulin G-binding domains of staphyloccocal protein A. This tetrameric species was expected to bind up to four DNA molecules via their attached biotin moieties. The DNA-protein complex was deposited on mica and imaged with an atomic force microscope. The images revealed the protein chimera at the expected location at the ends of the strands of DNA as well as the expected dimers, trimers, and tetramers of DNA bound to a single protein. 25 refs., 5 figs.

  8. 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)

    2006-06-06T23:59:59.000Z

    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.

  9. Elastic and Proton Dynamics of the DNA

    E-Print Network [OSTI]

    V. L. Golo

    2008-03-28T23:59:59.000Z

    The subject of this report is the dynamics of elastic system in conjunction with hydrogen bonds of the DNA. We draw attention to the draw-back of the familiar rod model of the DNA, and make a case of constructing models that could accommodate the intrinsic structure of the DNA. In this respect studying the interplay among the elastic system and the protons of the DNA, is of interest, for it could accommodate the inter-strand as well as the tunneling modes of protons. Following this direction, we come to the conclusion that the elastic-proton dynamics may have a bearing on biophysics of the DNA. The phenomenon of point mutations is discussed within this framework.

  10. 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)

    2011-07-05T23:59:59.000Z

    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.

  11. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2006-08-01T23:59:59.000Z

    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.

  12. DNA tethering characterization, enzyme-mediated DNA looping under tension, and nucleosome stability in the force measuring optical tweezers

    E-Print Network [OSTI]

    Gemmen, Gregory John

    2006-01-01T23:59:59.000Z

    M. & Schiessel, H. (2004). DNA spools under tension. Phys.accessibility of nucleosomal DNA. Nat. Struct. Mol. Biol.elasticity of lambda-phage DNA. Science . 265 : 1599–1600.

  13. DNA Damage, Repair & Replication Using E. Coli Model Systems

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

    from DNA containing dIMP residues by the Escherichia coli,from DNA containing dIMP residues by the Escherichia coli,

  14. Constraint of DNA on Functionalized Graphene Improves Its Biostability...

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

    Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity. Constraint of DNA on Functionalized Graphene Improves Its Biostability and Specificity....

  15. ap dna endonuclease: Topics by E-print Network

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

    specificity Raines, Ronald T. 2 A DNA and restriction enzyme implementation of Turing Ma (Turing machines; Universal Turing machines; recombinant DNA; nonpalindromic...

  16. adenovirus dna sequences: Topics by E-print Network

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

    description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly...

  17. andribosomal dna sequences: Topics by E-print Network

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

    description of the given DNA string in terms of a smaller set of distinct domain labels. This yields a minimal domain description of a given DNA sequence, significantly...

  18. IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY...

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

    IN VITRO MUTAGENIC AND DNA AND CHROMOSOMAL DAMAGE ACTIVITY BY SURFACTANT DISPERSION OR SOLVENT EXTRACT OF A REFERENCE DIESEL EXHAUST PARTICULATE MATERIAL IN VITRO MUTAGENIC AND DNA...

  19. Electrochemical Branched-DNA Assay for Polymerase Chain Reaction...

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

    Branched-DNA Assay for Polymerase Chain Reaction-Free Detection and Quantification of Oncogenes in Messenger RNA Electrochemical Branched-DNA Assay for Polymerase Chain...

  20. adapting dna microarray: Topics by E-print Network

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

    Gene Expression Analysis & R Tutorial 12;DNA Microarrays An R Tutorial Functional Genomics Qiu, Weigang 3 Research tools known as DNA microarrays are Biology and Medicine...

  1. archived dna microarrays: Topics by E-print Network

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

    Gene Expression Analysis & R Tutorial 12;DNA Microarrays An R Tutorial Functional Genomics Qiu, Weigang 3 Research tools known as DNA microarrays are Biology and Medicine...

  2. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    a nucleotide from the DNA double helix to its active site to access damaged nucleotides. But unlike AGT and most other known DNA nucleotide-flipping proteins, this...

  3. DNA Replication via Entanglement Swapping

    E-Print Network [OSTI]

    Onur Pusuluk; Cemsinan Deliduman

    2011-03-31T23:59:59.000Z

    Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can be considered as hardware and software of living systems that are co-optimized during evolution. We try to model DNA replication in this sense as a multi-body entanglement swapping with a reliable qubit representation of the nucleotides. In our model molecular recognition of a nucleotide triggers an intrabase entanglement corresponding to a superposition state of different tautomer forms. Then, base pairing occurs by swapping intrabase entanglements with interbase entanglements. We examine possible realizations of quantum circuits to be used to obtain intrabase entanglement and swapping protocols to be employed to obtain interbase entanglement. Finally, we discuss possible ways for computational and experimental verification of the model.

  4. Abstract DNA-type systems

    E-Print Network [OSTI]

    Diederik Aerts; Marek Czachor

    2005-12-22T23:59:59.000Z

    An abstract DNA-type system is defined by a set of nonlinear kinetic equations with polynomial nonlinearities that admit soliton solutions associated with helical geometry. The set of equations allows for two different Lax representations: A von Neumann form and a Darboux-covariant Lax pair. We explain why non-Kolmogorovian probability models occurring in soliton kinetics are naturally associated with chemical reactions. The most general known characterization of soliton kinetic equations is given and a class of explicit soliton solutions is discussed. Switching between open and closed states is a generic behaviour of the helices. The effect does not crucially depend on the order of nonlinearity (i.e. types of reactions), a fact that may explain why simplified models possess properties occuring in realistic systems. We explain also why fluctuations based on Darboux transformations will not destroy the dynamics but only switch between a finite number of helical structures.

  5. Double Ended Guillotine Break in a Prismatic Block VHTR Lower Plenum Air Ingress Scenario

    E-Print Network [OSTI]

    Hartley, Jessica

    2012-10-19T23:59:59.000Z

    The double ended guillotine break leading to density-driven air ingress has been identified as a low probability yet high consequence event for Very High Temperature Reactor (VHTR). The lower plenum of the VHTR contains the core support structure...

  6. Physics and learning based computational models for breaking bow waves based on new boundary immersion approaches

    E-Print Network [OSTI]

    Weymouth, Gabriel David

    2008-01-01T23:59:59.000Z

    A ship moving on the free surface produces energetic breaking bow waves which generate spray and air entrainment. Present experimental, analytic, and numerical studies of this problem are costly, inaccurate and not robust. ...

  7. Electroweak symmetry breaking in the era of the Higgs boson discovery

    E-Print Network [OSTI]

    Bertolini, Daniele, Ph. D. Massachusetts Institute of Technology

    2014-01-01T23:59:59.000Z

    In this thesis we study possible deviations from the electroweak symmetry breaking mechanism as predicted by the Standard Model (SM), and we introduce a new framework to analyze hadronic final states at colliders. In the ...

  8. Introduction of Break-Out Session at the International PV Module Quality Assurance Forum (Presentation)

    SciTech Connect (OSTI)

    Kurtz, S.; Wohlgemuth, J.; Yamamichi, M.; Sample, T.

    2011-07-01T23:59:59.000Z

    This presentation outlines review requirements for quality assurance (QA) rating systems, logical design of QA systems, and specific tasks for break-out session 1 of the 2011 International PV Module Quality Assurance Forum.

  9. Design Considerations for Monopile Founded Offshore Wind Turbines Subject to Breaking Waves

    E-Print Network [OSTI]

    Owens, Garrett Reese 1987-

    2012-11-26T23:59:59.000Z

    The majority of offshore wind farms utilize monopile substructures. As these wind farms are typically located in water depths less than 30 meters, the effect of breaking waves on these structures is of great concern to design engineers...

  10. Double Ended Guillotine Break in a Prismatic Block VHTR Lower Plenum Air Ingress Scenario 

    E-Print Network [OSTI]

    Hartley, Jessica

    2012-10-19T23:59:59.000Z

    and is composed of graphite. During an air ingress event, oxidation of the graphite structure under high temperature conditions in an oxygen containing environment could degrade the integrity of the core support structure. Following this large break, air from...

  11. Design Considerations for Monopile Founded Offshore Wind Turbines Subject to Breaking Waves 

    E-Print Network [OSTI]

    Owens, Garrett Reese 1987-

    2012-11-26T23:59:59.000Z

    The majority of offshore wind farms utilize monopile substructures. As these wind farms are typically located in water depths less than 30 meters, the effect of breaking waves on these structures is of great concern to design engineers...

  12. Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA

    E-Print Network [OSTI]

    Richardson, Charles C.

    Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft

  13. SU(3) and Isospin Breaking Effects on B to PPP Amplitudes

    E-Print Network [OSTI]

    Xiao-Gang He; Guan-Nan Li; Dong Xu

    2015-03-05T23:59:59.000Z

    Several modes of $B$ decays into three pseudoscalar octet mesons PPP have been measured. These decays have provided useful information for B decays in the standard model (SM). Some of powerful tools in analyzing B decays are flavor $SU(3)$ and isospin symmetries. Such analyses are usually hampered by $SU(3)$ breaking effects due to a relatively large strange quark mass which breaks SU(3) symmetry down to isospin symmetry. The isospin symmetry also breaks down when up and down quark mass difference is non-zero. It is therefore interesting to find relations which are not sensitive to $SU(3)$ and isospin breaking effects. We find that the relations among several fully-symmetric $B \\to PPP$ decay amplitudes are not affected by first order $SU(3)$ breaking effects due to a non-zero strange quark mass, and also some of them are not affected by first isospin breaking effects. These relations, therefore, hold to good precisions. Measurements for these relations can provide important information about B decays in the SM.

  14. Molecular Imaging of the ATM Kinase Activity

    SciTech Connect (OSTI)

    Williams, Terence M. [Department of Radiation Oncology, Ohio State University, Columbus, Ohio (United States); Nyati, Shyam [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Center for Molecular Imaging, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Ross, Brian D. [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Department of Radiology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Rehemtulla, Alnawaz, E-mail: alnawaz@umich.edu [Department of Radiation Oncology, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Center for Molecular Imaging, University of Michigan Medical Center, Ann Arbor, Michigan (United States); Department of Radiology, University of Michigan Medical Center, Ann Arbor, Michigan (United States)

    2013-08-01T23:59:59.000Z

    Purpose: Ataxia telangiectasia mutated (ATM) is a serine/threonine kinase critical to the cellular DNA-damage response, including from DNA double-strand breaks. ATM activation results in the initiation of a complex cascade of events including DNA damage repair, cell cycle checkpoint control, and survival. We sought to create a bioluminescent reporter that dynamically and noninvasively measures ATM kinase activity in living cells and subjects. Methods and Materials: Using the split luciferase technology, we constructed a hybrid cDNA, ATM-reporter (ATMR), coding for a protein that quantitatively reports on changes in ATM kinase activity through changes in bioluminescence. Results: Treatment of ATMR-expressing cells with ATM inhibitors resulted in a dose-dependent increase in bioluminescence activity. In contrast, induction of ATM kinase activity upon irradiation resulted in a decrease in reporter activity that correlated with ATM and Chk2 activation by immunoblotting in a time-dependent fashion. Nuclear targeting improved ATMR sensitivity to both ATM inhibitors and radiation, whereas a mutant ATMR (lacking the target phosphorylation site) displayed a muted response. Treatment with ATM inhibitors and small interfering (si)RNA-targeted knockdown of ATM confirm the specificity of the reporter. Using reporter expressing xenografted tumors demonstrated the ability of ATMR to report in ATM activity in mouse models that correlated in a time-dependent fashion with changes in Chk2 activity. Conclusions: We describe the development and validation of a novel, specific, noninvasive bioluminescent reporter that enables monitoring of ATM activity in real time, in vitro and in vivo. Potential applications of this reporter include the identification and development of novel ATM inhibitors or ATM-interacting partners through high-throughput screens and in vivo pharmacokinetic/pharmacodynamic studies of ATM inhibitors in preclinical models.

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

    DOE Patents [OSTI]

    Hammond, Mark L. (Angier, NC); Jett, James H. (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Marrone, Babetta L. (Los Alamos, NM); Martin, John C. (Los Alamos, NM)

    1996-01-01T23:59:59.000Z

    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.

  16. Assessing the Risk of Mercury in Drinking Water after UV Lamp Breaks Page 1 Assessing the Risk of Mercury in Drinking Water after UV Lamp Breaks

    E-Print Network [OSTI]

    energy through temperature and pressure to drive the mercury into a vapor phase. Mercury is a heavy metal, and is regulated in drinking water by the EPA through the Safe Drinking Water Act (SDWA). If an on-line lamp break historically the U.S. has been skeptical to implement UV into drinking water systems, many areas of Europe

  17. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C. (Los Alamos, NM); Kuske, Cheryl R. (Los Alamos, NM); Mullen, Kenneth I. (Los Alamos, NM)

    2002-01-01T23:59:59.000Z

    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.

  18. , btzhang}@bi.snu.ac.kr Boosted DNA Computing for Evolutionary Graphical Structure Learning

    E-Print Network [OSTI]

    PLM (Probabilistic Library Model PLM PLM DNA bead seperation PCR (Polymerase Chain Reaction) PLM PLM DNA DNA PLM PLM PLM PLM DNA PLM PLM evolutionary graph structure PLM DNA &$$) Jc`" '& Bc" %6 #12

  19. DNA looping: the consequences and its control

    E-Print Network [OSTI]

    Leonor Saiz; Jose M. G. Vilar

    2006-09-26T23:59:59.000Z

    The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of DNA looping in its natural context and how they propagate to the cellular behavior through gene regulation. The results of connecting the molecular properties with cellular physiology indicate that looping of DNA in vivo is much more complex and easier than predicted from current models and reveals a wealth of previously unappreciated details.

  20. 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

    2013-06-25T23:59:59.000Z

    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.

  1. The unholy trinity: taxonomy, species delimitation and DNA barcoding

    E-Print Network [OSTI]

    DeSalle, Rob

    The unholy trinity: taxonomy, species delimitation and DNA barcoding Rob DeSalle*, Mary G. Egan are clarified and resolved, before the use of DNA as a tool for taxonomy and species delimitation can framework for interweaving classical taxonomy with the goals of `DNA barcoding'. Keywords: DNA barcoding

  2. DNA ARRAY DECODING FROM NONLINEAR MEASUREMENTS BY BELIEF PROPAGATION

    E-Print Network [OSTI]

    DNA ARRAY DECODING FROM NONLINEAR MEASUREMENTS BY BELIEF PROPAGATION Mona A. Sheikh, Shriram Compressed Sensing (CS) and demonstrate its utility in DNA array decoding. In a CS DNA microarray, the array spots identify DNA sequences that are shared between multiple organisms, thereby reduc- ing the number

  3. DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications

    E-Print Network [OSTI]

    Weiss, Sharon

    DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications Jenifer L. Lawrie for improving the sensitivity of label-free optical biosensors based on in-situ synthesis of DNA probes within was utilized as the sensor structure. Synthesis of DNA probe, as well as sensing of target DNA, was verified

  4. DNA Deformation Energy as an Indirect Recognition Mechanism in

    E-Print Network [OSTI]

    Lathrop, Richard H.

    DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions Kimberly A. Senear Abstract--Proteins that bind to specific locations in genomic DNA control many basic cellular. Deformation energy, which models the energy required to bend DNA from its native shape to its shape when bound

  5. DNA Translocation Governed by Interactions with Solid-State Nanopores

    E-Print Network [OSTI]

    Meller, Amit

    DNA Translocation Governed by Interactions with Solid-State Nanopores Meni Wanunu, Jason Sutin, Ben dynamics of individual DNA molecules through solid-state nanopores in the diameter range 2.7­5 nm. Our with DNA length by two power laws: for short DNA molecules, in the range 150­3500 bp, we find an exponent

  6. DNA Compression Challenge Revisited: a Dynamic Programming Approach

    E-Print Network [OSTI]

    Lonardi, Stefano

    DNA Compression Challenge Revisited: a Dynamic Programming Approach Behshad Behzadi and Fabrice Le Fessant LIX, Ecole Polytechnique, Paris, FRANCE June 21 2005 B. Behzadi, F. Le Fessant (LIX) DNA Compression June 21 2005 1 / 38 #12;Outline 1 DNA Compression Challenge 2 Tools and Methods 3 DNA Compression

  7. DNA Computing: A Research University of Western Ontario

    E-Print Network [OSTI]

    Kari, Lila

    31 DNA Computing: A Research Snapshot Lila Kari University of Western Ontario Kalpana Mahalingam ........................................... 31-6 31.5 DNA Memory ................................................... 31-8 Nested Primer Molecular Memory · Organic DNA Memory · Design of DNA Sequences 31.6 Computation in Living Cells

  8. Deoxyribose oxidation chemistry and endogenous DNA adducts

    E-Print Network [OSTI]

    Zhou, Xinfeng

    2006-01-01T23:59:59.000Z

    Endogenous and exogenous oxidants react with cellular macromolecules to generate a variety of electrophiles that react with DNA produce cytotoxic and mutagenic adducts. One source of such electrophiles is deoxyribose in ...

  9. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08T23:59:59.000Z

    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

  10. Linear Thermodynamics of Rodlike DNA Filtration

    E-Print Network [OSTI]

    Li, Zirui

    Linear thermodynamics transportation theory is employed to study filtration of rodlike DNA molecules. Using the repeated nanoarray consisting of alternate deep and shallow regions, it is demonstrated that the complex ...

  11. 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...

  12. The Initiation of Bacterial DNA Replication

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

    that the ATP-DnaA active site is in a closed configuration, which allows it to bind nucleotides using conserved residues from neighboring AAA+ protomers. The precise geometry of...

  13. RecA acts in trans to allow replication of damaged DNA by DNA polymerase V

    E-Print Network [OSTI]

    Cox, Michael M.

    , Michael M. Cox2 , Roger Woodgate3 & Myron F. Goodman1 The DNA polymerase V (pol V) and RecA proteins

  14. Carbon Nanotube DNA Sensor and Sensing Mechanism

    E-Print Network [OSTI]

    Le Roy, Robert J.

    nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label for direct label-free detection of DNA hybridization in a biocompatible buffer solution. We also carried out is a field effect device, which has a typical on-current of 3-6 µA at 10 mV source- drain bias and an on-off

  15. Method for in vitro recombination

    DOE Patents [OSTI]

    Gibson, Daniel Glenn; Smith, Hamilton O

    2013-05-07T23:59:59.000Z

    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. Regulation of DNA repair by parkin

    SciTech Connect (OSTI)

    Kao, Shyan-Yuan, E-mail: shyan-yuan_kao@meei.harvard.edu [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)] [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)

    2009-05-01T23:59:59.000Z

    Mutation of parkin is one of the most prevalent causes of autosomal recessive Parkinson's disease (PD). Parkin is an E3 ubiquitin ligase that acts on a variety of substrates, resulting in polyubiquitination and degradation by the proteasome or monoubiquitination and regulation of biological activity. However, the cellular functions of parkin that relate to its pathological involvement in PD are not well understood. Here we show that parkin is essential for optimal repair of DNA damage. Parkin-deficient cells exhibit reduced DNA excision repair that can be restored by transfection of wild-type parkin, but not by transfection of a pathological parkin mutant. Parkin also protects against DNA damage-induced cell death, an activity that is largely lost in the pathological mutant. Moreover, parkin interacts with the proliferating cell nuclear antigen (PCNA), a protein that coordinates DNA excision repair. These results suggest that parkin promotes DNA repair and protects against genotoxicity, and implicate DNA damage as a potential pathogenic mechanism in PD.

  17. DNA Polymerase-Mediated DNA Synthesis on a TNA Template John C. Chaput, Justin K. Ichida, and Jack W. Szostak*

    E-Print Network [OSTI]

    Heller, Eric

    DNA Polymerase-Mediated DNA Synthesis on a TNA Template John C. Chaput, Justin K. Ichida, and Jack TNA is capable of antiparallel, Watson-Crick base-pairing with complementary DNA, RNA, and TNA oligo- nucleotides.2 This property is remarkable, given that the TNA repeat unit is one atom shorter than that of DNA

  18. The evolution of the break preclusion concept for nuclear power plants in Germany

    SciTech Connect (OSTI)

    Schulz, H. [Gesellschaft fuer Anlagen- und Reaktorsicherheit, Koeln (Germany)

    1997-04-01T23:59:59.000Z

    In the updating of the Guidelines for PWR`s of the {open_quotes}Reaktor-Sicherheitskommission{close_quotes} (RSK) in 1981 the requirements on the design have been changed with respect to the postulated leaks and breaks in the primary pressure boundary. The major change was a revision in the requirements for pipe whip protection. As a logical consequence of the {open_quotes}concept of basic safety{close_quotes} a guillotine type break or any other break type resulting in a large opening is not postulated any longer for the calculation of reaction and jet forces. As an upper limit for a leak an area of 0, 1 A (A = open cross section of the pipe) is postulated. This decision was based on a general assessment of the present PWR system design in Germany. Since then a number of piping systems have been requalified in the older nuclear power plants to comply with the break preclusion concept. Also a number of extensions of the concept have been developed to cover also leak-assumptions for branch pipes. Furthermore due considerations have been given to other aspects which could contribute to a leak development in the primary circuit, like vessel penetrations, manhole covers, flanges, etc. Now the break preclusion concept originally applied to the main piping has been developed into an integrated concept for the whole pressure boundary within the containment and will be applied also in the periodic safety review of present nuclear power plants.

  19. Effects of $?$-cluster breaking on 3$?$ cluster structures in $^{12}$C

    E-Print Network [OSTI]

    Tadahiro Suhara; Yoshiko Kanada-En'yo

    2015-02-17T23:59:59.000Z

    To clarify the effects of $\\alpha$-cluster breaking on 3$\\alpha$ cluster structures in $^{12}$C, we investigate $^{12}$C using a hybrid model that combines the Brink-Bloch cluster model with the $p_{3/2}$ subshell closure wave function. We have found that $\\alpha$-cluster breaking caused by spin-orbit force significantly changes cluster structures of excited $0^{+}$ states through orthogonality to lower states. Spatially developed cluster components of the $0^{+}_{2}$ state are reduced. The $0^{+}_{3}$ state changes from a vibration mode in the bending motion of three $\\alpha$ clusters to a chain-like 3$\\alpha$ structure having an open triangle configuration. As a result of these structure changes of $0^{+}$ states, the band assignment for the $2^{+}_{2}$ state is changed by the $\\alpha$-cluster breaking effect. Namely, in model calculations without the $\\alpha$-cluster breaking effect, the $0^{+}_{2}$ state is assigned to be the band-head of the $2^{+}_{2}$ state. However, when we incorporate $\\alpha$-cluster breaking caused by the spin-orbit force, the $0^{+}_{3}$ state is regarded as the band-head of the $2^{+}_{2}$ state.

  20. Gaugino Condensation, S-Duality and Supersymmetry Breaking in Supergravity Models

    E-Print Network [OSTI]

    Z. Lalak; A. Niemeyer; H. P. Nilles

    1995-04-07T23:59:59.000Z

    The status of the gaugino condensation as the source of supersymmetry breaking is reexamined. It is argued that one cannot have stable minima with broken supersymmetry in models where the dilaton is coupled only linearly to the gaugino condensate. We show that the problems of the gaugino condensate mechanism can be solved by considering nonstandard gauge kinetic functions, created by nonperturbative effects. As an example we use the principle of S-duality to modify the coupling of the gaugino condensate to effective supergravity (superstring) Lagrangians. We show that such an approach can solve the problem of the runaway dilaton and lead to satisfactory supersymmetry breaking in models with a {\\em single} gaugino condensate. We exhibit a general property of theories containing a symmetry acting on the dilaton and also shed some light on the question whether it is generically the auxiliary field of the modulus $T$, which dominates supersymmetry breaking.

  1. Building a market for small wind: The break-even turnkey cost of residential wind systems in the United States

    E-Print Network [OSTI]

    Edwards, Jennifer L.; Wiser, Ryan; Bolinger, Mark; Forsyth, Trudy

    2004-01-01T23:59:59.000Z

    Break-Even Turnkey Cost of Residential Wind Systems in theaggregate installed cost of a small wind system that couldand wind resource class, (2) significant cost reductions

  2. Wave breaking phenomenon of lower-hybrid oscillations induced by a background inhomogeneous magnetic field

    SciTech Connect (OSTI)

    Maity, Chandan; Chakrabarti, Nikhil [Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064 (India); Sengupta, Sudip [Institute for Plasma Research, Bhat, Gandhinagar 382428 (India)

    2012-10-15T23:59:59.000Z

    In a fluid description, we study space-time evolution of lower hybrid modes in a cold quasi-neutral homogeneous plasma in presence of a background inhomogeneous magnetic field. Within a linear analysis, a dispersion relation with inhomogeneous magnetic field shows 'phase mixing' of such oscillations. A manifestation of 'phase mixing' is shown in 'mode coupling.' By using Lagrangian variables, an exact solution is presented in parametric form of this nonlinear time dependent problem. It is demonstrated that initially excited lower hybrid modes always break via phase mixing phenomenon in presence of an inhomogeneous magnetic field. Breaking of such oscillations is revealed by the appearance of spikes in the plasma density profile.

  3. Semiclassical treatment of symmetry breaking and bifurcations in a non-integrable potential

    E-Print Network [OSTI]

    M. V. Koliesnik; Ya. D. Krivenko-Emetov; A. G. Magner; K. Arita; M. Brack

    2014-11-10T23:59:59.000Z

    We have derived an analytical trace formula for the level density of the H\\'enon-Heiles potential using the improved stationary phase method, based on extensions of Gutzwiller's semiclassical path integral approach. This trace formula has the correct limit to the standard Gutzwiller trace formula for the isolated periodic orbits far from all (critical) symmetry-breaking points. It continuously joins all critical points at which an enhancement of the semiclassical amplitudes occurs. We found a good agreement between the semi- classical and the quantum oscillating level densities for the gross shell structures and for the energy shell corrections, solving the symmetry breaking problem at small energies.

  4. Frequency-doubled scattering of symmetry-breaking surface-state electrons on liquid Helium

    E-Print Network [OSTI]

    Miao Zhang; Wenzhi Jia; Lianfu Wei

    2013-03-18T23:59:59.000Z

    Any systems with symmetry-breaking eigenstates can effectively radiate photons with doubled frequency of the incident light, which is known as the second harmonic generation. Here, we study the second-order nonlinear effects with the system of surface-state electrons on liquid Helium. Due to the symmetry-breaking eigenstates, we show that a Rabi oscillation between two levels of the surface-state electrons can be realized beyond the usual resonant driving. Consequently, an electromagnetic field with the doubled frequency of the applied driving could be effectively radiated. This can be regarded as a frequency-doubled fluorescence, and interestingly, it works in the unusual Terahertz range.

  5. Symmetry breaking patterns and collective modes of spin-one color superconductors

    E-Print Network [OSTI]

    Tomas Brauner; Jin-yi Pang; Qun Wang

    2009-09-23T23:59:59.000Z

    Spin-one color superconductor is a viable candidate phase of dense matter in the interiors of compact stars. Its low-energy excitations will influence the transport properties of such matter and thus have impact on late-stage evolution of neutron stars. It also provides a good example of spontaneous symmetry breaking with rich breaking patterns. In this contribution, we reanalyze the phase diagram of a spin-one color superconductor and point out that a part of it is occupied by noninert states, which have been neglected in literature so far. We classify the collective Nambu--Goldstone modes, which are essential to the transport phenomena.

  6. The concepts of leak before break and absolute reliability of NPP equipment and piping

    SciTech Connect (OSTI)

    Getman, A.F.; Komarov, O.V.; Sokov, L.M. [and others

    1997-04-01T23:59:59.000Z

    This paper describes the absolute reliability (AR) concept for ensuring safe operation of nuclear plant equipment and piping. The AR of a pipeline or component is defined as the level of reliability when the probability of an instantaneous double-ended break is near zero. AR analysis has been applied to Russian RBMK and VVER type reactors. It is proposed that analyses required for application of the leak before break concept should be included in AR implementation. The basic principles, methods, and approaches that provide the basis for implementing the AR concept are described.

  7. Role of space-time foam in breaking supersymmetry via the Barbero-Immirzi parameter

    SciTech Connect (OSTI)

    Ellis, John; Mavromatos, Nick E. [Theoretical Particle Physics and Cosmology Group, Department of Physics, King's College London, Strand, London WC2R 2LS, UK and Theory Division, Physics Department, CERN, CH-1211 Geneva 23 (Switzerland)

    2011-10-15T23:59:59.000Z

    We discuss how: (i) a dilaton/axion superfield can play the role of a Barbero-Immirzi field in four-dimensional conformal quantum supergravity theories, (ii) a fermionic component of such a dilaton/axion superfield may play the role of a Goldstino in the low-energy effective action obtained from a superstring theory with F-type global supersymmetry breaking, (iii) this global supersymmetry breaking is communicated to the gravitational sector via the supergravity coupling of the Goldstino, and (iv) such a scenario may be realized explicitly in a D-foam model with D-particle defects fluctuating stochastically.

  8. Multicritical Symmetry Breaking and Naturalness of Slow Nambu-Goldstone Bosons

    E-Print Network [OSTI]

    Tom Griffin; Kevin T. Grosvenor; Petr Horava; Ziqi Yan

    2013-09-02T23:59:59.000Z

    We investigate spontaneous global symmetry breaking in the absence of Lorentz invariance, and study technical Naturalness of Nambu-Goldstone (NG) modes whose dispersion relation exhibits a hierarchy of multicritical phenomena with Lifshitz scaling and dynamical exponents $z>1$. For example, we find NG modes with a technically natural quadratic dispersion relation which do not break time reversal symmetry and are associated with a single broken symmetry generator, not a pair. The mechanism is protected by an enhanced `polynomial shift' symmetry in the free-field limit.

  9. 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)

    1998-01-01T23:59:59.000Z

    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.

  10. DNA nanotechnology: understanding and optimisation through simulation

    E-Print Network [OSTI]

    Thomas E. Ouldridge

    2014-11-07T23:59:59.000Z

    DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended `overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.

  11. Unraveling siRNA Unzipping Kinetics with Graphene

    E-Print Network [OSTI]

    Santosh Mogurampelly; Swati Panigrahi; Dhananjay Bhattacharyya; A. K. Sood; Prabal K. Maiti

    2012-07-19T23:59:59.000Z

    Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (t) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping.

  12. Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate

    SciTech Connect (OSTI)

    Changela, Anita; DiGate, Russell J.; Mondragon, Alfonso (NWU); (Phil. Col. Pharmacy)

    2010-03-05T23:59:59.000Z

    Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5{prime} phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.

  13. Conditions for positioning of nucleosomes on DNA

    E-Print Network [OSTI]

    Michael Sheinman; Ho-Ryun Chung

    2015-04-29T23:59:59.000Z

    Positioning of nucleosomes along eukaryotic genomes plays an important role in their organization and regulation. There are many different factors affecting the location of nucleosomes. Some can be viewed as preferential binding of a single nucleosome to different locations along the DNA and some as interactions between neighboring nucleosomes. In this study we analyzed how well nucleosomes are positioned along the DNA as a function of strength of the preferential binding, correlation length of the binding energy landscape, interactions between neighboring nucleosomes and others relevant system properties. We analyze different scenarios: designed energy landscapes and generically disordered ones and derive conditions for good positioning. Using analytic and numerical approaches we find that, even if the binding preferences are very weak, synergistic interplay between the interactions and the binding preferences is essential for a good positioning of nucleosomes, especially on correlated energy landscapes. Analyzing empirical energy landscape, we discuss relevance of our theoretical results to positioning of nucleosomes on DNA \\emph{in vivo.}

  14. 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)

    2011-01-18T23:59:59.000Z

    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.

  15. Breaking News Export Control Certification on I-129 Required 21 Feb. 2011

    E-Print Network [OSTI]

    Scharer, John E.

    Breaking News Export Control Certification on I-129 Required 21 Feb. 2011 Effective 21 February-129 regarding compliance with the deemed export licensing requirements of the export control as the UW-Madison Export Control Officer, Tom Demke, to provide clear instructions and a form to ensure our

  16. NHMFL Breaks the 100 Tesla Barrier Gregory S. Boebinger, National High Magnetic Field Laboratory

    E-Print Network [OSTI]

    Weston, Ken

    NHMFL Breaks the 100 Tesla Barrier Gregory S. Boebinger, National High Magnetic Field Laboratory. 109no. 31 12404-12407 On March 22nd 2012, the NHMFL ­ Pulsed Field Facility broke the 100T tesla barrier, setting a world record of 100.75 tesla for a non-destructive magnet. By using advanced

  17. Facebook, Twitter and Google Plus for Breaking News: Is there a winner? Miles Osborne

    E-Print Network [OSTI]

    Osborne, Miles

    Facebook, Twitter and Google Plus for Breaking News: Is there a winner? Miles Osborne School Media have be- gun to carry news. Here we examine how Facebook, Google Plus and Twitter report Facebook or Google Plus. Face- book and Google Plus largely repost newswire stories and their main research

  18. All Your Face Are Belong to Us: Breaking Facebook's Social Authentication

    E-Print Network [OSTI]

    Yang, Junfeng

    All Your Face Are Belong to Us: Breaking Facebook's Social Authentication Iasonas Polakis FORTH adversaries from compromising accounts using stolen credentials. Facebook has recently released a two can obtain the information needed to solve the chal- lenges presented by Facebook. We implement

  19. Multiple Structural Breaks in India's GDP: Evidence from India's Service Sector

    E-Print Network [OSTI]

    Bandyopadhyay, Antar

    of economists and policy makers. India was designated as an agricultural country with a highest share1 Multiple Structural Breaks in India's GDP: Evidence from India's Service Sector Purba Roy Choudhury1 Abstract: This paper takes a comprehensive investigation into India's service sector, the main

  20. Assessing the catastrophic break up of Briksdalsbreen, Norway,1 associated with rapid climate change.2

    E-Print Network [OSTI]

    Southampton, University of

    about the potential influence of rapid climate change13 on the stability of major ice sheets retreat of Greenland's tidewater glaciers.32 33 Introduction34 The response of glaciers to climate change1 Assessing the catastrophic break up of Briksdalsbreen, Norway,1 associated with rapid climate