National Library of Energy BETA

Sample records for dna double-strand breaks

  1. Microbial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant Defense

    E-Print Network [OSTI]

    of an alternative mediator of pathogen-induced H2AX phosphorylation. In summary, pathogenic microorganisms canMicrobial Pathogens Trigger Host DNA Double-Strand Breaks Whose Abundance Is Reduced by Plant largely unknown. We report that multiple bacterial, fungal and oomycete plant pathogen species induce

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

    SciTech Connect (OSTI)

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

    2009-02-01

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

  3. 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.

    2005-10-01

    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.

  4. Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

    SciTech Connect (OSTI)

    Wang, Chen [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)] [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada); Lees-Miller, Susan P., E-mail: leesmill@ucalgary.ca [Departments of Biochemistry and Molecular Biology and Oncology, and Southern Alberta Cancer Research Institute, University of Calgary, Calgary (Canada)

    2013-07-01

    DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.

  5. The probability of double-strand breaks in giant DNA decreases markedly as the DNA concentration increases

    E-Print Network [OSTI]

    Shimobayashi, Shunsuke F; Mori, Toshiaki; Yoshikawa, Kenichi

    2012-01-01

    DNA double-strand breaks (DSBs) represent a serious source of damage for all living things and thus there have been many quantitative studies of DSBs both in vivo and in vitro. Despite this fact, the processes that lead to their production have not yet been clearly understood, and there is no established theory that can account for the statistics of their production, in particular, the number of DSBs per base pair per unit Gy, here denoted by P1, which is the most important parameter for evaluating the degree of risk posed by DSBs. Here, using the single-molecule observation method with giant DNA molecules (166 kbp), we evaluate the number of DSBs caused by gamma-ray irradiation. We find that P1 is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. A simple model that accounts for the marked decrease of P1 shows that it is necessary to consider the characteristics of giant DNA molecules as semiflexible polymers to interpret the intrinsic mechanism of DSBs.

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

    SciTech Connect (OSTI)

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

    2013-05-07

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

  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)

    2009-07-21

    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. 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.

    2015-01-09

    regions of PAXX1-204 and PAXXV199A/F201A were amplified from the vectors by PCR and cloned into the pcDNA3.1(-) vector (a gift from Dr. V. Bolanos-Garcia) together with GFP or FLAG tags using In-Fusion (Clontech). Vectors were sequenced by the DNA... -treated or treated for 1 hour with 300 µM phleomycin to induce large numbers of DSBs, before being harvested either at this point or after an additional 1-hour recovery period in phleomycin-free medium after three PBS washes. Cells were washed twice in ice-cold PBS...

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

    SciTech Connect (OSTI)

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

    2010-06-29

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

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

    SciTech Connect (OSTI)

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

    2009-07-15

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

  11. 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

    2012-05-12

    motif-containing protein 1 (gene) RING Really interesting new gene domain SCE Sister chromatid exchange xxiii SEM Standard error of the mean shRNA Short hairpin RNA ssDNA single-strand DNA TAE Tris-acetate-EDTA TN Triple...

  12. Exploitation of the genomic double-strand breaks to reduce the reproductive power of microorganisms

    E-Print Network [OSTI]

    Sassi, Giandomenico

    2015-01-01

    It is shown how to take advantage of the frequent occurrence of double-strand breaks in the genome of prokaryotic cells, in order to reduce their high efficient reproductive capability. The analysis examines the physical status of the free ends of each break and considers how this status can interfere with an external physical apparatus, with the aim of undermining the repair processes. We indicate the biological consequences of this interaction and we give an approximate evaluation of the topological and dynamical effects that arise on the genomic material involved. The overall result suggests a significant reduction of the dynamics of the repair.

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

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2013-11-21

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

  14. Euler buckling and nonlinear kinking of double-stranded DNA

    E-Print Network [OSTI]

    Cohen, Adam E.

    physiological conditions: at high curvature, does the DNA bend smoothly, or does it kink like a drinking straw and damage). These aspects of DNA mechanics are likely to influence protein binding and DNA packaging, yet the effect of single-nucleotide mismatches on DNA bending. Our data support a model of linear elastic bending

  15. Sequence-dependent spin-selective tunneling along double-stranded DNA

    E-Print Network [OSTI]

    Guo, Ai-Min

    2012-01-01

    We report spin-selective tunneling of electrons along natural and artificial double-stranded DNA (dsDNA) sandwiched by nonmagnetic leads. The results reveal that the spin polarization strongly depends on the dsDNA sequence and is dominated by its end segment. Both genomic and artificial dsDNA could be efficient spin filters. The spin-filtering effects are sensitive to point mutation which occurs in the end segment. These results are in good agreement with recent experiments and are robust against various types of disorder, and could help for designing DNA-based spintronic devices.

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

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

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

    2015-06-02

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

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

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-05-28

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

  18. Translocation frequency of double-stranded DNA through a solid-state nanopore

    E-Print Network [OSTI]

    Bell, Nicholas A W; Keyser, Ulrich F

    2015-01-01

    Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-stranded DNA translocations through conical quartz nanopores with mean opening diameter 15 nm. We observe an entropic barrier limited, length dependent translocation frequency at 4M LiCl salt concentration and a drift-dominated, length independent translocation frequency at 1M KCl salt concentration. These observations are described by a unifying convection-diffusion equation which includes the contribution of an entropic barrier for polymer entry.

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

    SciTech Connect (OSTI)

    Hud, N.V.

    1995-10-01

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

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

    SciTech Connect (OSTI)

    Simchi, Hamidreza; Esmaeilzadeh, Mahdi Mazidabadi, Hossein

    2014-02-07

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

  1. Bubble dynamics in double stranded DNA : A Rouse chain based approach

    E-Print Network [OSTI]

    Rajarshi Chakrabarti

    2010-10-26

    We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed when the transverse displacement of the chain attains a critical value. This simple model effectively reproduces the autocorrelation function for the tagged base pair in the DNA strand as measured in the seminal single molecule experiment by Altan-Bonnet et. al (Phys. Rev. Lett. 90, 138101 (2003)). Although our model is mathematically similar to the one proposed by Chatterjee et al. (J. Chem. Phys. 127, 155104 (2007)) it goes beyond a single reaction coordinate description by incorporating the chain dynamics through a confined Rouse chain and thus considers the collective nature of the dynamics. Our model also shows that the autocorrelation function is very sensitive to the relaxation times of the normal modes of the chain, which is obvious since the fluctuation dynamics of the bubble has the contribution from the different normal modes of the chain.

  2. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23

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

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

    DOE Patents [OSTI]

    Gray, J.W.; Pinkel, D.

    1991-07-02

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

  4. Torsional regulation of hRPA-induced unwinding of double-stranded DNA

    E-Print Network [OSTI]

    Dekker, Cees

    and mechanism of the unwinding and rewinding reaction through single-molecule experiments. Human RPA (h Department of Cell Biology and Genetics, Cancer Genomic Center and 3 Department of Radiation OncologyDNA. Here, we study the dynamics of human RPA (hRPA) activity on topolog- ically constrained ds

  5. The COP9 signalosome is vital for timely repair of DNA double-strand breaks

    E-Print Network [OSTI]

    Meir, Michal; Galanty, Yaron; Kashani, Lior; Blank, Michael; Khosravi, Rami; Fernández-Ávila, María Jesús; Cruz-García, Andrés; Star, Ayelet; Shochot, Lea; Thomas, Yann; Garrett, Lisa J.; Chamovitz, Daniel A.; Bodine, David M.; Kurz, Thimo; Huertas, Pablo; Ziv, Yael; Shiloh, Yosef

    2015-04-08

    is critical for proper DSB repair, and that loss of this phosphorylation site alone is sufficient to cause a DDR deficiency phenotype in the mouse. This novel branch of the DSB response thus significantly affects genome stability....

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

    DOE Patents [OSTI]

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

    1996-01-09

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

  7. 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

  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,Ã, 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. Suberoylanilide Hydroxyamic Acid Modification of Chromatin Architecture Affects DNA Break Formation and Repair

    SciTech Connect (OSTI)

    Singh, Sheetal; Le Hongan; Shih, S.-J.; Ho, Bay [Department of Radiation Oncology, University of California at Davis, 4501 X St., Sacramento, California 95817 (United States); Vaughan, Andrew T., E-mail: andrew.vaughan@ucdmc.ucdavis.ed [Department of Radiation Oncology, University of California at Davis, 4501 X St., Sacramento, California 95817 (United States); Department of Veterans Affairs, Mather, California 95655 (United States)

    2010-02-01

    Purpose: Chromatin-modifying compounds that inhibit the activity of histone deacetylases have shown potency as radiosensitizers, but the action of these drugs at a molecular level is not clear. Here we investigated the effect of suberoylanilide hydroxyamic acid (SAHA) on DNA breaks and their repair and induction of rearrangements. Methods and Materials: The effect of SAHA on both clonogenic survival and repair was assessed using cell lines SCC-25, MCF7, and TK6. In order to study unique DNA double-strand breaks, anti-CD95 antibody was employed to introduce a DNA double-strand break at a known location within the 11q23 region. The effects of SAHA on DNA cleavage and rearrangements were analyzed by ligation-mediated PCR and inverse PCR, respectively. Results: SAHA acts as radiosensitizer at 1 {mu}M, with dose enhancement factors (DEFs) at 10% survival of: SCC-25 - 1.24 +- 0.05; MCF7 - 1.16 +- 0.09 and TK6 - 1.17 +- 0.05, and it reduced the capacity of SCC-25 cells to repair radiation induced lesions. Additionally, SAHA treatment diffused site-specific fragmentation over at least 1 kbp in TK6 cells. Chromosomal rearrangements produced in TK6 cells exposed to SAHA showed a reduction in microhomology at the breakpoint between 11q23 and partner chromosomes. Conclusions: SAHA shows efficacy as a radiosensitizer at clinically obtainable levels. In its presence, targeted DNA strand breaks occur over an expanded region, indicating increased chromatin access. The rejoining of such breaks is degraded by SAHA when measured as rearrangements at the molecular level and rejoining that contributes to cell survival.

  10. Repair of DNA double strand breaks and radiosensitivity: modulation of DNA repair and radiosensitivity by microRNA-335 and mtPAP

    E-Print Network [OSTI]

    Martin, Nathan

    2014-01-01

    DDR by at least three mechanisms: 1) maintaining ROS homeostasis, 2) mediating apoptotic signals, and 3) producing energy

  11. Synthesis of DNA

    DOE Patents [OSTI]

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

    2008-11-18

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

  12. VOLUME 82, NUMBER 22 P H Y S I C A L R E V I E W L E T T E R S 31 MAY 1999 Bending and Base-Stacking Interactions in Double-Stranded DNA

    E-Print Network [OSTI]

    Zhang, Yang

    is proposed by taking into account the structural properties of realistic dsDNA. Bending energy of the sugar and un- winding instability of DNA. We suggest that the present model, after some revisions, will also

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

    E-Print Network [OSTI]

    Taksu Cheon; Sergey S. Poghosyan

    2015-03-03

    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.

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

    SciTech Connect (OSTI)

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

    2011-06-01

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

  15. Mitigating security issues in the evolving DNA synthesis industry

    E-Print Network [OSTI]

    Turlington, Ralph Donald, III

    2013-01-01

    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, ...

  16. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power AdministrationRobust, High-ThroughputUpcomingmagnetoresistance | ArgonnePrinceton Plasma

  17. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07

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

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

    SciTech Connect (OSTI)

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

    2014-01-17

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

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

    SciTech Connect (OSTI)

    Su, Fengtao [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Mukherjee, Shibani [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Yang, Yanyong [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Mori, Eiichiro [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Bhattacharya, Souparno [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Kobayashi, Junya [Kyoto Univ. (Japan); Yannone, Steven  M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Chen, David  J. [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States); Asaithamby, Aroumougame [Univ. of Texas Southwestern Medical Center, Dallas, TX (United States)

    2014-11-20

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

  20. DNA Duplication Revealed in New Beginnings | Department of Energy

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

    to wrap around and bend approximately 70 base pairs of double stranded DNA (red and blue). When a replication initiator Cdc6 (green) joins ORC, the partial ring is now complete...

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

    SciTech Connect (OSTI)

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

    2014-09-22

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

  2. J.M. Butler -DNA and Biometrics June 24, 2008 http://www.cstl.nist.gov/biotech/strbase/NISTpub.htm 1

    E-Print Network [OSTI]

    Butler Margaret Kline Amy Decker Becky Hill Dave Duewer Jan Redman NIST Human Identity Project Team is Targeted and Probed for Each DNA Marker Examined chromosome cell nucleus Double stranded DNA molecule

  3. Reactive Molecular Dynamics study on the first steps of DNA-damage by free hydroxyl radicals

    E-Print Network [OSTI]

    Abolfath, Ramin M; Brabec, Thomas

    2011-01-01

    We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the randomly distributed clusters of diatomic OH-radicals that are primary products of megavoltage ionizing radiation in water-based systems are the main source of hydrogen-abstraction as well as formation of carbonyl- and hydroxyl-groups in the sugar-moiety that create holes in the sugar-rings. These holes grow up slowly between DNA-bases and DNA-backbone and the damage collectively propagate to DNA single and double strand break.

  4. J.M. Butler DNA Statistics Lockheed Martin BEACON Lecture Series

    E-Print Network [OSTI]

    Lecture Rockville, MD August 19, 2009 NIST Applied Genetics Group Margaret Kline Jan Redman Amy Decker chromosome cell nucleus Double stranded DNA molecule Individual nucleotides 22 pairs + XX or XY ~3 billion

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

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

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

    2015-02-22

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

  6. Mechanochemistry of a Viral DNA Packaging Motor , Jeffrey Moffitt1

    E-Print Network [OSTI]

    Oster, George

    Mechanochemistry of a Viral DNA Packaging Motor Jin Yu1 , Jeffrey Moffitt1 , Craig L. Hetherington1 The pentameric ATPase motor gp16 packages double-stranded DNA into the bacteriophage 29 virus capsid to explain how the packaging motor translocates the DNA in bursts of four 2.5 bp power strokes, while

  7. Flow cytomeric measurement of DNA and incorporated nucleoside analogs

    DOE Patents [OSTI]

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

    1989-01-01

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

  8. Extremely low-frequency electromagnetic fields cause DNA strand breaks in normal Vero cells

    E-Print Network [OSTI]

    Cosmin Teodor Miha; Gabriela Vochita; Florin Brinza; Pincu Rotinberg

    2013-01-23

    Extremely low frequency electromagnetic fields aren't considered as a real carcinogenic agent despite the fact that some studies have showed impairment of the DNA integrity in different cells lines. The aim of this study was evaluation of the late effects of a 100 Hz and 5.6 mT electromagnetic field, applied continuously or discontinuously, on the DNA integrity of Vero cells assessed by alkaline Comet assay and by cell cycle analysis. Normal Vero cells were exposed to extremely low frequency electromagnetic fields (100 Hz, 5.6 mT) for 45 minutes. The Comet assay and cell cycle analysis were performed 48 hours after the treatment. Exposed samples presented an increase of the number of cells with high damaged DNA as compared with non-exposed cells. Quantitative evaluation of the comet assay showed a significantly ($cells. Cell cycle analysis showed an increase of the frequency of the cells in S phase, proving the occurrence of single strand breaks. The most probable mechanism of induction of the registered effects is the production of different types of reactive oxygen species.

  9. J.M. Butler -DNA Quality and Biometrics (Biometric Quality Workshop II)

    E-Print Network [OSTI]

    , 2007 Pete Vallone John Butler Margaret Kline Amy Decker Becky Hill Dave Duewer Jan Redman NIST Human Butler Margaret Kline Amy Decker Becky Hill Dave Duewer Jan Redman NIST Human Identity Project Team · 19 and Probed for Each DNA Marker Examined chromosome cell nucleus Double stranded DNA molecule Individual

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

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

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

    2014-11-20

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

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

    E-Print Network [OSTI]

    Shaikh, Faisal

    2008-10-10

    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 UV Ultraviolet RIE Reactive Ion Etcher CCD Charge Coupled... potential............................... 41 Figure 16 DNA visible under white light (100 bp DNA ladder in 1X TBE buffer) ............................................................................................ 45 Figure 17 Schematic...

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

    SciTech Connect (OSTI)

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

    2009-09-07

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

  13. 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)

    1997-01-01

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

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

    DOE Patents [OSTI]

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

    1997-05-27

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

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

    SciTech Connect (OSTI)

    Roper, Katherine; Coverley, Dawn

    2012-03-10

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

  16. Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study

    E-Print Network [OSTI]

    Ghosh, Soumadwip; Chakrabarti, Rajarshi

    2015-01-01

    The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations we investigate the preferential binding of metal ion such as Na+ and molecular ions such as tetramethyl ammonium (TMA+) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO+) to double stranded DNA. The thermodynamic driving force for a particular molecular ion- DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO+. The ion binding processes are found to be entropically favourable. In addition, the contribution of hy...

  17. 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

  18. From Breaking Bad to Worse: Exploiting Homologous DNA Repair Deficiency in Cancer

    E-Print Network [OSTI]

    Hemann, Michael

    DNA repair deficiencies are common among cancer cells and represent a potential vulnerability that might be exploited by targeting compensatory repair pathways. However, the identification of synthetically lethal combinations ...

  19. DNA translocation through nanopores with salt gradients: The role of osmotic flow

    E-Print Network [OSTI]

    Hatlo, Marius M; van Roij, René

    2010-01-01

    Recent experiments of translocation of double stranded DNA through nanopores [M. Wanunu et al. Nature Nanotech. 5, 160 (2010)] reveal that the DNA capture rate can be significantly influenced by a salt gradient across the pore. We show that osmotic flow combined with electrophoresis can quantitatively explain the experimental data on the capture rate. The osmotic flow is induced by the salt gradient across the nanopore, and can be the dominant mechanism for DNA translocation through nanopores with a salt gradient.

  20. Induction and Persistence of Large ?H2AX Foci by High Linear Energy Transfer Radiation in DNA-Dependent protein kinase–Deficient Cells

    SciTech Connect (OSTI)

    Bracalente, Candelaria; Ibañez, Irene L.; Molinari, Beatriz; Palmieri, Mónica; Kreiner, Andrés; Valda, Alejandro; and others

    2013-11-15

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

  1. Shear Unzipping of DNA

    E-Print Network [OSTI]

    Buddhapriya Chakrabarti; David R. Nelson

    2009-04-09

    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.

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

    SciTech Connect (OSTI)

    Shi, Yun-bo

    1988-03-01

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

  3. Selective chemical labelling of natural T modifications in DNA

    E-Print Network [OSTI]

    Hardisty, Robyn E.; Kawasaki, Fumiko; Sahakyan, Aleksandr B.; Balasubramanian, Shankar

    2015-05-06

    enriched, we carried out experiments exploiting the selective reactions developed for probes 1, 2, and 3. A double-stranded 80-mer bearing two modifications per strand was used as a model for 5-fU (fU-DNA), while an analogous ODN containing 5-fC (f... C-DNA) and a non-modified ODN (GCAT-DNA) were used as controls (Supporting Information, Table S1). These ODNs were subjected to the biotinylation reaction followed by affinity enrichment using streptavidin- coated magnetic beads. fU-DNA was enriched over f...

  4. Hepatitis C virus NS3/4A protein interacts with ATM, impairs DNA repair and enhances sensitivity to ionizing radiation

    SciTech Connect (OSTI)

    Lai, Chao-Kuen; Jeng, King-Song [Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan (China); Machida, Keigo [Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, 2001 Zonal Avenue, Los Angeles, CA 90033 (United States); Cheng, Yi-Sheng [Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan (China); Lai, Michael M.C. [Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan (China); Department of Molecular Microbiology and Immunology, University of Southern California, Keck School of Medicine, 2001 Zonal Avenue, Los Angeles, CA 90033 (United States)], E-mail: michlai@gate.sinica.edu.tw

    2008-01-20

    Hepatitis C virus (HCV) infection is frequently associated with the development of hepatocellular carcinomas and non-Hodgkin's B-cell lymphomas. Nonstructural protein 3 (NS3) of HCV possesses serine protease, nucleoside triphosphatase, and helicase activities, while NS4A functions as a cofactor for the NS3 serine protease. Here, we show that HCV NS3/4A interacts with the ATM (ataxia-telangiectasia mutated), a cellular protein essential for cellular response to irradiation. The expression of NS3/4A caused cytoplasmic translocation of either endogenous or exogenous ATM and delayed dephosphorylation of the phosphorylated ATM and {gamma}-H2AX following ionizing irradiation. As a result, the irradiation-induced {gamma}-H2AX foci persisted longer in the NS3/4A-expressing cells. Furthermore, these cells showed increased comet tail moment in single-cell electrophoresis assay, indicating increased double-strand DNA breaks. The cells harboring an HCV replicon also exhibited cytoplasmic localization of ATM and increased sensitivity to irradiation. These results demonstrate that NS3/4A impairs the efficiency of DNA repair by interacting with ATM and renders the cells more sensitive to DNA damage. This effect may contribute to HCV oncogenesis.

  5. DNA repair: Dynamic defenders against cancer and aging

    SciTech Connect (OSTI)

    Fuss, Jill O.; Cooper, Priscilla K.

    2006-04-01

    You probably weren't thinking about your body's cellular DNA repair systems the last time you sat on the beach in the bright sunshine. Fortunately, however, while you were subjecting your DNA to the harmful effects of ultraviolet light, your cells were busy repairing the damage. The idea that our genetic material could be damaged by the sun was not appreciated in the early days of molecular biology. When Watson and Crick discovered the structure of DNA in 1953 [1], it was assumed that DNA is fundamentally stable since it carries the blueprint of life. However, over 50 years of research have revealed that our DNA is under constant assault by sunlight, oxygen, radiation, various chemicals, and even our own cellular processes. Cleverly, evolution has provided our cells with a diverse set of tools to repair the damage that Mother Nature causes. DNA repair processes restore the normal nucleotide sequence and DNA structure of the genome after damage [2]. These responses are highly varied and exquisitely regulated. DNA repair mechanisms are traditionally characterized by the type of damage repaired. A large variety of chemical modifications can alter normal DNA bases and either lead to mutations or block transcription if not repaired, and three distinct pathways exist to remove base damage. Base excision repair (BER) corrects DNA base alterations that do not distort the overall structure of the DNA helix such as bases damaged by oxidation resulting from normal cellular metabolism. While BER removes single damaged bases, nucleotide excision repair (NER) removes short segments of nucleotides (called oligonucleotides) containing damaged bases. NER responds to any alteration that distorts the DNA helix and is the mechanism responsible for repairing bulky base damage caused by carcinogenic chemicals such as benzo [a]pyrene (found in cigarette smoke and automobile exhaust) as well as covalent linkages between adjacent pyrimidine bases resulting from the ultraviolet (UV) component of sunlight. NER can be divided into two classes based on where the repair occurs. NER occurring in DNA that is not undergoing transcription (i.e., most of the genome) is called global genome repair (GGR or GGNER), while NER taking place in the transcribed strand of active genes is called transcription-coupled repair (TCR or TC-NER). We will explore NER in more detail below. Mismatch repair (MMR) is another type of excision repair that specifically removes mispaired bases resulting from replication errors. DNA damage can also result in breaks in the DNA backbone, in one or both strands. Single-strand breaks (SSBs) are efficiently repaired by a mechanism that shares common features with the later steps in BER. Double-strand breaks (DSBs) are especially devastating since by definition there is no intact complementary strand to serve as a template for repair, and even one unrepaired DSB can be lethal [3]. In cells that have replicated their DNA prior to cell division, the missing information can be supplied by the duplicate copy, or sister chromatid, and DSBs in these cells are faithfully repaired by homologous recombination involving the exchange of strands of DNA between the two copies. However, most cells in the body are non-dividing, and in these cells the major mechanism for repairing DSBs is by non-homologous end joining (NHEJ), which as the name implies involves joining two broken DNA ends together without a requirement for homologous sequence and which therefore has a high potential for loss of genetic information.

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

    DOE Patents [OSTI]

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

    1997-01-01

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

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

    DOE Patents [OSTI]

    Ji, H.; Smith, L.M.

    1997-01-07

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

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

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

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

    2014-04-01

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

  9. 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

    2007-01-01

    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 ...

  10. Effect of salt concentration on the stability of heterogeneous DNA

    E-Print Network [OSTI]

    Amar Singh; Navin Singh

    2015-09-28

    We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution, act as shielding agents thereby reducing the repulsion between these strands. We study several heterogeneous DNA molecules. We calculate the phase diagrams for DNA molecules in thermal as well as in force ensembles using Peyrard-Bishop-Dauxois (PBD) model. The dissociation and the stacking energies are the two most important factors that play an important role in the DNA stability. With suitable modifications in the model parameters we investigate the role of cation concentration on the stability of different heterogeneous DNA molecules. The objective of this work is to understand how these cations modify the strength of different pairs or bases along the strand. The phase diagram for the force ensemble case (a dsDNA is pulled from an end) is compared with the experimental results.

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

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

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

    2014-01-01

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

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

    SciTech Connect (OSTI)

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

    2012-11-01

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

  13. A new type of optical biosensor from DNA wrapped semiconductor graphene ribbons

    E-Print Network [OSTI]

    Anh D. Phan; N. A. Viet

    2012-08-03

    Based on a model of the optical biosensors (Science 311, 508 (2006)) by wrapping a piece of double-stranded DNA around the surface of single-walled carbon nanotubes (SWCNT), we propose a new design model of this sensor, in which the SWCNT is replaced by a semiconductor graphene ribbon (SGR). Using a simple theory of exciton in SGRs, we investigated transition of DNA secondary structure from the native, right-handed B form to the alternate, left-handed Z form. This structural phase transition of DNA is the working principle of this optical biosensor at the sub cellular level from DNA and semiconductor graphene ribbons.

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

    DOE Patents [OSTI]

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

    1998-12-08

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

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

    DOE Patents [OSTI]

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

    1998-01-01

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

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

    SciTech Connect (OSTI)

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

    2014-01-01

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

  17. DNA Sequencing Using capillary Electrophoresis

    SciTech Connect (OSTI)

    Dr. Barry Karger

    2011-05-09

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

  18. 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

    2010-01-06

    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.

  19. Protective effects of pulmonary epithelial lining fluid on oxidative stress and DNA single-strand breaks caused by ultrafine carbon black, ferrous sulphate and organic extract of diesel exhaust particles

    SciTech Connect (OSTI)

    Chuang, Hsiao-Chi [School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan (China) [School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan (China); Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan (China); Cheng, Yi-Ling; Lei, Yu-Chen [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China)] [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Chang, Hui-Hsien [Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China)] [Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Cheng, Tsun-Jen, E-mail: tcheng@ntu.edu.tw [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China) [Institute of Occupational Medicine and Industrial Hygiene, College of Public Health, National Taiwan University, Taipei, Taiwan (China); Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan (China)

    2013-02-01

    Pulmonary epithelial lining fluid (ELF) is the first substance to make contact with inhaled particulate matter (PM) and interacts chemically with PM components. The objective of this study was to determine the role of ELF in oxidative stress, DNA damage and the production of proinflammatory cytokines following physicochemical exposure to PM. Ultrafine carbon black (ufCB, 15 nm; a model carbonaceous core), ferrous sulphate (FeSO{sub 4}; a model transition metal) and a diesel exhaust particle (DEP) extract (a model organic compound) were used to examine the acellular oxidative potential of synthetic ELF and non-ELF systems. We compared the effects of exposure to ufCB, FeSO{sub 4} and DEP extract on human alveolar epithelial Type II (A549) cells to determine the levels of oxidative stress, DNA single-strand breaks and interleukin-8 (IL-8) production in ELF and non-ELF systems. The effects of ufCB and FeSO{sub 4} on the acellular oxidative potential, cellular oxidative stress and DNA single-strand breakage were mitigated significantly by the addition of ELF, whereas there was no decrease following treatment with the DEP extract. There was no significant effect on IL-8 production following exposure to samples that were suspended in ELF/non-ELF systems. The results of the present study indicate that ELF plays an important role in the initial defence against PM in the pulmonary environment. Experimental components, such as ufCB and FeSO{sub 4}, induced the production of oxidative stress and led to DNA single-strand breaks, which were moderately prevented by the addition of ELF. These findings suggest that ELF plays a protective role against PM-driven oxidative stress and DNA damage. -- Highlights: ? To determine the role of ELF in ROS, DNA damage and IL-8 after exposure to PM. ? ufCB, FeSO{sub 4} and DEP extract were used to examine the protective effects of ELF. ? PM-driven oxidative stress and DNA single-strand breakage were mitigated by ELF. ? The findings suggest that ELF has a protective role against PM. ? The synthetic ELF system could reduce the use of animals in PM-driven ROS testing.

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01

    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-

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01

    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-

  2. Insights into DNA-mediated interparticle interactions from a coarse-grained model

    E-Print Network [OSTI]

    Yajun Ding; Jeetain Mittal

    2015-03-05

    DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA- functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

  3. int. j. radiat. biol 2001, vol. 77, no. 2, 155 164 DNA strand break yields after post-high LET irradiation

    E-Print Network [OSTI]

    irradiation incubation with endonuclease-III and evidence for hydroxyl radical clustering J. R. MILLIGAN*, J (DSB) yields after post-high LET irradiation incuba- conditions (Nikjoo et al. 1999), the conclusion DNA in aerobic aqueous solution was irradiated with one of ve radiation types: 137 Cs c-rays (LET

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

    SciTech Connect (OSTI)

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

    2009-06-08

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

  5. Computational Chemistry DOI: 10.1002/anie.200501671

    E-Print Network [OSTI]

    Simons, Jack

    and Environmental Research, Low Dose Radiation Research Program (M.G.), and the Polish State Committee-energy radiation. Recent experiments suggested that single- and double-strand breaks develop in DNA exposed to low acid bases may be formed by trapping low- energy electrons produced in living cells by high

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

    SciTech Connect (OSTI)

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

    2015-06-21

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

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

    E-Print Network [OSTI]

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

    2015-05-19

    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 up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

  8. Breaking Earth Poems

    E-Print Network [OSTI]

    Hernandez, Scott Mcnaul

    2012-01-01

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

  9. Lorentz Breaking and Gravity

    E-Print Network [OSTI]

    R. Bluhm

    2013-07-22

    Gravitational theories with Lorentz violation must account for a number of possible features in order to be consistent theoretically and phenomenologically. A brief summary of these features is given here. They include evasion of a no-go theorem, connections between spontaneous Lorentz breaking and diffeomorphism breaking, the appearance of massless Nambu-Goldstone modes and massive Higgs modes, and the possibility of a Higgs mechanism in gravity.

  10. A novel property of the RecA nucleoprotein filament: activation

    E-Print Network [OSTI]

    Kowalczykowski, Stephen C.

    A novel property of the RecA nucleoprotein filament: activation of double-stranded DNA for strand. Upon binding to single-stranded DNA (ssDNA), RecA protein forms a helical nucleoprotein filament. Normally, this nucleoprotein filament binds double-stranded DNA (dsDNA) and promotes exchange of base pairs

  11. 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

  12. Strong Electroweak Symmetry Breaking

    E-Print Network [OSTI]

    Grinstein, Benjamin

    2011-01-01

    Models of spontaneous breaking of electroweak symmetry by a strong interaction do not have fine tuning/hierarchy problem. They are conceptually elegant and use the only mechanism of spontaneous breaking of a gauge symmetry that is known to occur in nature. The simplest model, minimal technicolor with extended technicolor interactions, is appealing because one can calculate by scaling up from QCD. But it is ruled out on many counts: inappropriately low quark and lepton masses (or excessive FCNC), bad electroweak data fits, light scalar and vector states, etc. However, nature may not choose the minimal model and then we are stuck: except possibly through lattice simulations, we are unable to compute and test the models. In the LHC era it therefore makes sense to abandon specific models (of strong EW breaking) and concentrate on generic features that may indicate discovery. The Technicolor Straw Man is not a model but a parametrized search strategy inspired by a remarkable generic feature of walking technicolor,...

  13. DNA Mixture DNA Mixture

    E-Print Network [OSTI]

    ;Introductions J.M. Butler ­ Wisconsin DNA Mixture Training May 12, 2009 http://www.cstl.nist.gov/biotech.M. Butler ­ Wisconsin DNA Mixture Training May 12, 2009 http://www.cstl.nist.gov/biotech textbook (now in its 2nd Edition) · STRBase website: http://www.cstl.nist.gov/biotech/strbase/ · Family

  14. Strong Electroweak Symmetry Breaking

    E-Print Network [OSTI]

    Benjamin Grinstein

    2011-02-19

    Models of spontaneous breaking of electroweak symmetry by a strong interaction do not have fine tuning/hierarchy problem. They are conceptually elegant and use the only mechanism of spontaneous breaking of a gauge symmetry that is known to occur in nature. The simplest model, minimal technicolor with extended technicolor interactions, is appealing because one can calculate by scaling up from QCD. But it is ruled out on many counts: inappropriately low quark and lepton masses (or excessive FCNC), bad electroweak data fits, light scalar and vector states, etc. However, nature may not choose the minimal model and then we are stuck: except possibly through lattice simulations, we are unable to compute and test the models. In the LHC era it therefore makes sense to abandon specific models (of strong EW breaking) and concentrate on generic features that may indicate discovery. The Technicolor Straw Man is not a model but a parametrized search strategy inspired by a remarkable generic feature of walking technicolor, that technivector mesons are light, narrow and decay readily into electroweak vector mesons and photons. While walking technicolor is popular among practitioners, alternatives exist and the Straw Man may not lead to their discovery.

  15. Reactivity studies of antitumor active dirhodium compounds with DNA oligonucleotides 

    E-Print Network [OSTI]

    Kang, Mijeong

    2007-04-25

    are clearly less stable. Reaction of cis-[Rh2(DAP)(O2CCH3)3(CH3OH)](O2CCH3) (DAP = 1,12- diazaperylene) with 5'-CTCTCAACTTCC produced a major adduct in which DAP group intercalates between 6A and 7A in the double stranded adduct with the rhodium atom...

  16. Alternative Breaks Emergency Contact & Verification of Medical

    E-Print Network [OSTI]

    Tipple, Brett

    Alternative Breaks Emergency Contact & Verification of Medical Insurance Form Participant Name is STRONGLY RECCOMENDED, it is not required for participation in Alternative Breaks. *Please note: All

  17. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    SciTech Connect (OSTI)

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA/sub 3/XA/sub 3/G with the complement dCT/sub 3/YT/sub 3/G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G)centerreverse arrowdot)C base pair become more stable than those containing only A)centerreverse arrowdot)T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I)centerreverse arrowdot)C )succ) I)centerreverse arrowdot) A)succ) I)centerreverse arrowdot)T approx. I)centerreverse arrowdot)G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG))centerreverse arrowdot)d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.

  18. Conserved Steps in Eukaryotic DNA Replication

    E-Print Network [OSTI]

    Blow, J. Julian

    and 50 car- bons of deoxyribose. The 10 carbon of the deoxyribose is linked to one of four different of DNA contains all the information necessary to produce new second strands through complementary base the input of chemical energy to break the hydrogen bonds. This energy is derived from hydrolysis of ATP

  19. Chiral Symmetry Breaking in Graphene

    E-Print Network [OSTI]

    Gordon W. Semenoff

    2011-08-19

    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.

  20. 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)

    2014-07-23

    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.

  1. SUSY Breaking and Light Gauginos

    E-Print Network [OSTI]

    Glennys R. Farrar

    1997-04-13

    Several supersymmetry breaking mechanisms do not produce dimension-3 operators. I show here that this scenario is consistent with present observations and has several significant virtues: i) When there are no dimension-3 SUSY-breaking operators there is no SUSY-CP problem. ii) SUSY-breaking need not occur through gauge singlets, so that the cosmological problems often encountered in hidden sector SUSY-breaking can be avoided. iii) Photino and gluino and $R$-hadron masses are naturally consistent with relic photinos providing the required dark matter density. Requiring spontaneous electroweak symmetry implies that scalar masses are mostly in the $\\sim 100$ GeV range. The gluino and photino are massless at tree level. At 1-loop, the gluino and photino masses at the ew scale are predicted to be $m_{\\gluino}\\sim 10 - 600$ MeV and $m_{\\photino} \\sim 100 - 1400$ MeV. New hadrons with mass $\\sim 1 \\frac{1}{2}$ GeV are predicted and described. The ``extra'' flavor singlet pseudoscalar in the $\\iota(1440)$ region which has been observed in several experiments is naturally interpreted as the mainly-$\\gluino \\gluino$ bound state which gets its mass via the QCD anomaly. Its superpartner, a gluon-gluino bound state, would be the lightest $R$-hadron. For the most interesting portions of parameter space the $R^0$ lifetime is $10^{-6} - 10^{-10}$ sec, so existing searches would not have been sensitive to it. Search strategies and other consequences of the scenario are briefly mentioned.

  2. Complete quantum measurements break entanglement

    E-Print Network [OSTI]

    Juha-Pekka Pellonpää

    2012-06-27

    Complete measurement of a quantum observable (POVM) is a measurement of the maximally refined version of the POVM. Complete measurements give information on multiplicities of measurement outcomes and can be viewed as state preparation procedures. Moreover, any observable can be measured completely. In this Letter, we show that a complete measurement breaks entanglement completely between the system, ancilla and their environment. Finally, consequences to the quantum Zeno effect and complete position measurements are discussed.

  3. Alternative Break Participant Expectations 2014-2015

    E-Print Network [OSTI]

    Tipple, Brett

    Alternative Break Participant Expectations 2014-2015 (These expectations apply for all Participants Social Justice 101 or 201 Training Pay for Alternative Break experience prior to departure and on time and procedures as they apply to the Alternative Break experience. Individuals are expected to remain substance

  4. RENAL SYSTEM DEVELOPMENT IN THE ZEBRAFISH: A BASIC NEPHROGENESIS MODEL

    E-Print Network [OSTI]

    Tank, Jennifer L.

    -diethylaminobenzaldehyde DL distal late dpi days post injection DSB double-stranded break ESRD end-stage renal disease HDR homology directed repair hpf hours post fertilization IM intermediate mesoderm indels insertion or deletion

  5. Hydrogen Atom Loss in Pyrimidine DNA Bases Induced by Low-Energy Electrons: Energetics Predicted by Theory

    E-Print Network [OSTI]

    Simons, Jack

    Hydrogen Atom Loss in Pyrimidine DNA Bases Induced by Low-Energy Electrons: Energetics Predicted In addition to inducing DNA strand breaks, low-energy electrons (LEEs) also have been shown to induce of a hydrogen atom from a DNA base-electron adduct initiates chemical modification of the base, which can cause

  6. Higgs Portal to Visible Supersymmetry Breaking

    E-Print Network [OSTI]

    K. -I. Izawa; Yuichiro Nakai; Takashi Shimomura

    2011-02-28

    We propose a supersymmetric extension of the standard model whose Higgs sector induces a spontaneous supersymmetry breaking by itself. Unlike the minimal extension, the current Higgs mass bound can be evaded even at the tree-level without the help of the soft breaking terms due to the usual hidden sector, as is reminiscent of the next to minimal case. We also have a possibly light pseudo-goldstino in our visible sector in addition to extra Higgs particles, both of which stem from supersymmetry breaking dynamics. In such a setup of visible supersymmetry breaking, we may see a part of supersymmetry breaking dynamics rather directly in future experiments.

  7. History of electroweak symmetry breaking

    E-Print Network [OSTI]

    T. W. B. Kibble

    2015-02-22

    In this talk, I recall the history of the development of the unified electroweak theory, incorporating the symmetry-breaking Higgs mechanism, as I saw it from my standpoint as a member of Abdus Salam's group at Imperial College. I start by describing the state of physics in the years after the Second World War, explain how the goal of a unified gauge theory of weak and electromagnetic interactions emerged, the obstacles encountered, in particular the Goldstone theorem, and how they were overcome, followed by a brief account of more recent history, culminating in the historic discovery of the Higgs boson in 2012.

  8. Breaking Points in Quartic Maps

    E-Print Network [OSTI]

    M. Romera; G. Pastor; M. -F. Danca; A. Martin; A. B. Orue; F. Montoya

    2014-12-18

    Dynamical systems, whether continuous or discrete, are used by physicists in order to study non-linear phenomena. In the case of discrete dynamical systems, one of the most used is the quadratic map depending on a parameter. However, some phenomena can depend alternatively of two values of the same parameter. We use the quadratic map $x_{n+1} =1-ax_{n}^{2} $ when the parameter alternates between two values during the iteration process. In this case, the orbit of the alternate system is the sum of the orbits of two quartic maps. The bifurcation diagrams of these maps present breaking points where abruptly change their evolution.

  9. Progress in Electroweak Symmetry Breaking

    E-Print Network [OSTI]

    Dawson, S

    2015-01-01

    In this talk, I discuss theoretical advances in understanding the properties of the Higgs boson and the implications for models of electroweak symmetry breaking. I begin by reviewing some of the recent progress in Standard Model calculations for Higgs boson production and decay rates, followed by a lightning tour of the use of effective field theories in the search for new physics in the Higgs sector. I end with a discussion of the complementarity of precision Higgs coupling measurements and direct searches for heavy particles for the discovery of Beyond the Standard Model physics in the electroweak sector.

  10. Total-derivative supersymmetry breaking

    SciTech Connect (OSTI)

    Haba, Naoyuki; Uekusa, Nobuhiro

    2010-05-15

    On an interval compactification in supersymmetric theory, boundary conditions for bulk fields must be treated carefully. If they are taken arbitrarily following the requirement that a theory is supersymmetric, the conditions could give redundant constraints on the theory. We construct a supersymmetric action integral on an interval by introducing brane interactions with which total-derivative terms under the supersymmetry transformation become zero due to a cancellation. The variational principle leads equations of motion and also boundary conditions for bulk fields, which determine boundary values of bulk fields. By estimating mass spectrum, spontaneous supersymmetry breaking in this simple setup can be realized in a new framework. This supersymmetry breaking does not induce a massless R axion, which is favorable for phenomenology. It is worth noting that fermions in hyper-multiplet, gauge bosons, and the fifth-dimensional component of gauge bosons can have zero-modes (while the other components are all massive as Kaluza-Klein modes), which fits the gauge-Higgs unification scenarios.

  11. QCD, Symmetry Breaking and the Random Lattice

    E-Print Network [OSTI]

    Saul D. Cohen

    2006-02-15

    According to the Nielsen-Ninomiya No-Go theorem, the doubling of fermions on the lattice cannot be suppressed in a chiral theory. Whereas Wilson and staggered fermions suppress doublers with explicit breaking of chiral symmetry, the random lattice does so by spontaneous chiral symmetry breaking even in the free theory. I present results for meson masses, the chiral condensate and fermionic eigenvalues from simulations of quenched QCD on random lattices in four dimensions, focusing on chiral symmetry breaking.

  12. NREL: Technology Transfer - Popular Mechanics: Scientists Break...

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

    Popular Mechanics: Scientists Break This Virtual Power Grid to Save the Real One July 27, 2015 Popular Mechanics describes how NREL's Energy Systems Integration Facility (ESIF)...

  13. 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

  14. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Nov. 2011, p. 76637668 Vol. 77, No. 21 0099-2240/11/$12.00 doi:10.1128/AEM.00289-11

    E-Print Network [OSTI]

    Bae, Jin-Woo

    . Amplification Methods Bias Metagenomic Libraries of Uncultured Single-Stranded and Double-Stranded DNA Viruses amplified shotgun library (LASL) and multiple displacement amplification (MDA) methods, were applied from different libraries. The resulting taxonomic classifications of the viruses, their functional

  15. J.M. Butler NIST Update for SWGDAM January 8, 2008 http://www.cstl.nist.gov/biotech/strbase/NISTpub.htm 1

    E-Print Network [OSTI]

    and Technology SWGDAM Fredericksburg, VA January 8, 2008 Pete Vallone John Butler Margaret Kline Amy Decker Becky/µL double stranded DNA. We do not know the uncertainty in this conversion. Component 260 nm error at 260nm

  16. P. M. Vallone -NIST Update for CODIS October 30, 2007 http://www.cstl.nist.gov/biotech/strbase/NISTpub.htm 1

    E-Print Network [OSTI]

    Decker Becky Hill Dave Duewer Jan Redman NIST Human Identity Project Team Our Team Mission Statement was estimated Using 1 OD = 50 ng/µL double stranded DNA. We do not know the uncertainty in this conversion

  17. BioMed Central Page 1 of 13

    E-Print Network [OSTI]

    Weller, Jennifer Walsh

    package. 21 ± 13% of the nucleotides in each probe binding site are within a double-stranded structure of a long single-stranded labeled DNA or RNA target molecule to shorter oligonu- cleotide probes

  18. Development and characterization of an in vitro culture system as a physiological model for chronic Hepatitis B infection

    E-Print Network [OSTI]

    Sams, Alexandria V. (Alexandria Victoria)

    2007-01-01

    Human Hepatitis B virus (HBV) is the prototype member of the family Hepadnaviridae that consists of enveloped, partially double stranded DNA viruses that specifically target hepatocytes for viral replication. Although a ...

  19. Studies into host macrophage transcriptional control by the African Swine Fever Virus protein A238L 

    E-Print Network [OSTI]

    Silk, Rhiannon Nicola

    2010-01-01

    African swine fever virus (ASFV) is a large double-stranded DNA virus which causes a lethal haemorrhagic fever in domestic pigs. This virus primarily infects cells from the monocyte/macrophage lineage and its ability to ...

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

    E-Print Network [OSTI]

    Pope, Welkin Hazel

    2005-01-01

    Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10³¹ particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed ...

  1. Gauge symmetry breaking in orbifold model building

    E-Print Network [OSTI]

    Michele Trapletti

    2006-11-02

    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.

  2. Laboratory Directed Research and Development Program. Annual report

    SciTech Connect (OSTI)

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

    1992-12-01

    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.

  3. Laboratory Directed Research and Development Program

    SciTech Connect (OSTI)

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

    1992-12-01

    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.

  4. Advance the DNA computing 

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30

    It has been previously shown that DNA computing can solve those problems currently intractable on even the fastest electronic computers. The algorithm design for DNA computing, however, is not straightforward. A strong background in both the DNA...

  5. Effective field theory for spacetime symmetry breaking

    E-Print Network [OSTI]

    Yoshimasa Hidaka; Toshifumi Noumi; Gary Shiu

    2014-12-17

    We discuss the effective field theory for spacetime symmetry breaking from the local symmetry point of view. By gauging spacetime symmetries, the identification of Nambu-Goldstone (NG) fields and the construction of the effective action are performed based on the breaking pattern of diffeomorphism, local Lorentz, and (an)isotropic Weyl symmetries as well as the internal symmetries including possible central extensions in nonrelativistic systems. Such a local picture distinguishes, e.g., whether the symmetry breaking condensations have spins and provides a correct identification of the physical NG fields, while the standard coset construction based on global symmetry breaking does not. We illustrate that the local picture becomes important in particular when we take into account massive modes associated with symmetry breaking, whose masses are not necessarily high. We also revisit the coset construction for spacetime symmetry breaking. Based on the relation between the Maurer-Cartan one form and connections for spacetime symmetries, we classify the physical meanings of the inverse Higgs constraints by the coordinate dimension of broken symmetries. Inverse Higgs constraints for spacetime symmetries with a higher dimension remove the redundant NG fields, whereas those for dimensionless symmetries can be further classified by the local symmetry breaking pattern.

  6. DNA Engine Thermal Cycler

    E-Print Network [OSTI]

    Raizada, Manish N.

    ® Peltier Thermal Cycler PTC-0200 DNA Engine Cycler Operations Manual Version 4.0 #12;ii Tech Support: 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .vi The DNA Engine® Peltier Thermal Cycler Introduction

  7. Long Wave Breaking Effects on Fringing Reefs 

    E-Print Network [OSTI]

    Goertz, John 1985-

    2012-12-12

    Modeling of wave energy transformation and breaking on fringing reefs is inherently difficult due to the unique topography of reefs. Prior methods of determining dissipation are based on empirical data from gently sloping beaches and offer only bulk...

  8. Breaking Parity Symmetry Using Extra Dimensions

    E-Print Network [OSTI]

    R. N. Mohapatra; A. Pérez-Lorenzana

    1999-11-17

    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.

  9. siRNA-Like Double-Stranded RNAs Are Specifically Protected Against Degradation in Human Cell Extract

    E-Print Network [OSTI]

    Walter, Nils G.

    -access article distributed under the terms of the Creative Commons Attribution License, which permits are credited. Funding: This work was supported by a Camille Dreyfus Teacher-Scholar award and NIH grant GM

  10. Mechanism for Damage to DNA by Low-Energy Electrons Robyn Barrios, Piotr Skurski, and Jack Simons*

    E-Print Network [OSTI]

    Simons, Jack

    Mechanism for Damage to DNA by Low-Energy Electrons Robyn Barrios, Piotr Skurski, and Jack Simons electronic structure calculations on a portion of DNA, the results of which provide support for a mechanism that produces single-strand breaks (SSBs) with low-energy electrons. This mechanism involves attaching a low

  11. DNA Topology: Fundamentals

    E-Print Network [OSTI]

    Mirkin, Sergei

    in Genome Functioning . Biological Role of Alternative DNA Structures Figure 1 A hypothetical circular DNA. 1ENCYCLOPEDIA OF LIFE SCIENCES / & 2001 Nature Publishing Group / www.els.net #12;topological

  12. Winter Break Trip 2014 New York City

    E-Print Network [OSTI]

    Hutcheon, James M.

    Winter Break Trip 2014 New York City Tentative Trip Information December 13-19, 2014 Saturday Park & Ride Service" o These buses are NOT on the New York City Metro system. · Transportation in the City o Buying a New York Metro card is highly encouraged. o Price for a ride is $2.75 o The cost

  13. 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

  14. DNA Sequencing apparatus

    DOE Patents [OSTI]

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

    1992-01-01

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

  15. Breaking a Pocket of Resistance in the Fight Against Cancer

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

    Breaking a Pocket of Resistance in the Fight Against Cancer Breaking a Pocket of Resistance in the Fight Against Cancer Print Thursday, 12 December 2013 11:55 ras protein The new...

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

    E-Print Network [OSTI]

    Black, Alan W; Taylor, Paul A

    1997-01-01

    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 ...

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

    DOE Patents [OSTI]

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

    2002-01-01

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

  18. 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...

  19. Collective neutrino oscillations and spontaneous symmetry breaking

    E-Print Network [OSTI]

    Duan, Huaiyu

    2015-01-01

    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...

  20. A Fourth Chiral Generation And Susy Breaking

    E-Print Network [OSTI]

    Akin Wingerter

    2011-05-30

    We revisit four generations within the context of supersymmetry. We compute the perturbativity limits for the fourth generation Yukawa couplings and show that if the masses of the fourth generation lie within reasonable limits of their present experimental lower bounds, it is possible to have perturbativity only up to scales around 1000 TeV, i.e. the current experimental bounds and perturbative unification are mutually exclusive. Such low scales are ideally suited to incorporate gauge mediated supersymmetry breaking, where the mediation scale can be as low as 10-20 TeV. The minimal messenger model, however, is highly constrained. Lack of electroweak symmetry breaking rules out a large part of the parameter space, and in the remaining part, the fourth generation stau is tachyonic.

  1. Symmetry Breaking in Neuroevolution: A Technical Report

    E-Print Network [OSTI]

    Urfalioglu, Onay

    2011-01-01

    Artificial Neural Networks (ANN) comprise important symmetry properties, which can influence the performance of Monte Carlo methods in Neuroevolution. The problem of the symmetries is also known as the competing conventions problem or simply as the permutation problem. In the literature, symmetries are mainly addressed in Genetic Algoritm based approaches. However, investigations in this direction based on other Evolutionary Algorithms (EA) are rare or missing. Furthermore, there are different and contradictionary reports on the efficacy of symmetry breaking. By using a novel viewpoint, we offer a possible explanation for this issue. As a result, we show that a strategy which is invariant to the global optimum can only be successfull on certain problems, whereas it must fail to improve the global convergence on others. We introduce the \\emph{Minimum Global Optimum Proximity} principle as a generalized and adaptive strategy to symmetry breaking, which depends on the location of the global optimum. We apply the...

  2. Textural break foundation wall construction modules

    DOE Patents [OSTI]

    Phillips, Steven J. (Kennewick, WA)

    1990-01-01

    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.

  3. Alternative Breaks Alcohol and Drug Policy 2014-2015

    E-Print Network [OSTI]

    Tipple, Brett

    Alternative Breaks Alcohol and Drug Policy 2014-2015 In order to promote personal development order and stability on Alternative Break trips, the following standards concerning drug and alcohol use have been set and will be enforced on all Alternative Break trips: 1. Use, possession or distribution

  4. Inhibition of Hsp27 Radiosensitizes Head-and-Neck Cancer by Modulating Deoxyribonucleic Acid Repair

    SciTech Connect (OSTI)

    Guttmann, David M.; Hart, Lori; Du, Kevin; Seletsky, Andrew; Koumenis, Constantinos

    2013-09-01

    Purpose: To present a novel method of tumor radiosensitization through Hsp27 knockdown using locked nucleic acid (LNA) and to investigate the role of Hsp27 in DNA double strand break (DSB) repair. Methods and Materials: Clonogenic survival assays, immunoblotting, the proximity ligation assay, and ?H2AX foci analysis were conducted in SQ20B and FaDu human head-and-neck cancer cell lines treated with Hsp27 LNA and Hsp27 short hairpin RNA (shRNA). Additionally, nude mice with FaDu flank tumors were treated with fractionated radiation therapy after pretreatment with Hsp27 LNA and monitored for tumor growth. Results: Hsp27 LNA and Hsp27 shRNA radiosensitized head-and-neck cancer cell lines in an Hsp27-dependent manner. Ataxia-Telangectasia Mutated-mediated DNA repair signaling was impaired in irradiated cells with Hsp27 knockdown. ATM kinase inhibition abrogated the radiosensitizing effect of Hsp27. Furthermore, Hsp27 LNA and shRNA both attenuated DNA repair kinetics after radiation, and Hsp27 was found to colocalize with ATM in both untreated and irradiated cells. Last, combined radiation and Hsp27 LNA treatment in tumor xenografts in nude mice suppressed tumor growth compared with either treatment alone. Conclusions: These results support a radiosensitizing property of Hsp27 LNA in vitro and in vivo, implicate Hsp27 in double strand break repair, and suggest that Hsp27 LNA might eventually serve as an effective clinical agent in the radiotherapy of head-and-neck cancer.

  5. Introduction: DNA Electrophoresis Fralin Life Science

    E-Print Network [OSTI]

    Hopkins, William A.

    .................................... 12 Student Pre-Lab Activity: What is DNA? DNA extraction from strawberry ..... Teacher guide: DNA extraction from strawberry.................................. 14 Student guide: DNA extraction from strawberry.................................. 16

  6. Acoustic Emission from Breaking Bamboo Chopstick

    E-Print Network [OSTI]

    Sun-Ting Tsai; Panpan Huang; Li-Min Wang; Zhengning Yang; Chin-De Chang; Tzay-Ming Hong

    2015-09-02

    The acoustic emission from breaking a bamboo chopstick or a bundle of spaghetti is found to exhibit similar behavior as the famous seismic laws of Gutenberg-Richter, Omori, and Bath. By use of a force-sensitive detector, we establish a positive correlation between the sound intensity and the magnitude of tremor. We also succeed at deriving these power laws analytically without invoking the concept of phase transition or self-organized criticality. In essence, geometry is more important than mechanics at rendering the statistical behavior of this crackling sound.

  7. Breaking Barriers in Polymer Additive Manufacturing

    SciTech Connect (OSTI)

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

    2015-01-01

    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.

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

    DOE Patents [OSTI]

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

    2002-01-01

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

  9. Chip breaking system for automated machine tool

    DOE Patents [OSTI]

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

    1987-01-01

    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.

  10. Becky Hill Green Mountain DNA Conference LT-DNA Analysis

    E-Print Network [OSTI]

    Becky Hill ­ Green Mountain DNA Conference LT-DNA Analysis July 26, 2010 http of the Chief Medical Examiner, NYC Green Mountain DNA Conference Burlington, VT July 26, 2010 Low Template (LT generally aim for 0.5-2 ng 100 pg template 5 pg template #12;Becky Hill ­ Green Mountain DNA Conference LT

  11. Three-dimensional Invasion of Human Glioblastoma Cells Remains Unchanged by X-ray and Carbon Ion Irradiation In Vitro

    SciTech Connect (OSTI)

    Eke, Iris; Storch, Katja; Kaestner, Ina; Vehlow, Anne; Faethe, Christina; Mueller-Klieser, Wolfgang; Taucher-Scholz, Gisela; Temme, Achim; Schackert, Gabriele; Department of Radiation Oncology, Medical Faculty Carl Gustav Carus, Dresden University of Technology, Dresden

    2012-11-15

    Purpose: Cell invasion represents one of the major determinants that treatment has failed for patients suffering from glioblastoma. Contrary findings have been reported for cell migration upon exposure to ionizing radiation. Here, the migration and invasion capability of glioblastoma cells on and in collagen type I were evaluated upon irradiation with X-rays or carbon ions. Methods and Materials: Migration on and invasion in collagen type I were evaluated in four established human glioblastoma cell lines exposed to either X-rays or carbon ions. Furthermore, clonogenic radiation survival, proliferation (5-bromo-2-deoxyuridine positivity), DNA double-strand breaks ({gamma}H2AX/53BP1-positive foci), and expression of invasion-relevant proteins (eg, {beta}1 integrin, FAK, MMP2, and MMP9) were explored. Migration and invasion assays for primary glioblastoma cells also were carried out with X-ray irradiation. Results: Neither X-ray nor carbon ion irradiation affected glioblastoma cell migration and invasion, a finding similarly observed in primary glioblastoma cells. Intriguingly, irradiated cells migrated unhampered, despite DNA double-strand breaks and reduced proliferation. Clonogenic radiation survival was increased when cells had contact with extracellular matrix. Specific inhibition of the {beta}1 integrin or proliferation-associated signaling molecules revealed a critical function of JNK, PI3K, and p38 MAPK in glioblastoma cell invasion. Conclusions: These findings indicate that X-rays and carbon ion irradiation effectively reduce proliferation and clonogenic survival without modifying the migration and invasion ability of glioblastoma cells in a collagen type I environment. Addition of targeted agents against members of the MAPK and PI3K signaling axis to conventional chemoradiation therapy seems potentially useful to optimize glioblastoma therapy.

  12. Three-Dimensional Simulations of Deep-Water Breaking Waves

    E-Print Network [OSTI]

    Brucker, Kyle A; Dommermuth, Douglas G; Adams, Paul

    2014-01-01

    The formulation of a canonical deep-water breaking wave problem is introduced, and the results of a set of three-dimensional numerical simulations for deep-water breaking waves are presented. In this paper fully nonlinear progressive waves are generated by applying a normal stress to the free surface. Precise control of the forcing allows for a systematic study of four types of deep-water breaking waves, characterized herein as weak plunging, plunging, strong plunging, and very strong plunging.

  13. Alternative Breaks: A Study on Risk Management and Safety Policies

    E-Print Network [OSTI]

    Ong, Alyssa

    2013-04-01

    74 | JOURNAL OF undergraduate research Alternative Breaks: A Study on Risk Management and Safety Policies Alyssa Ong Safety and liability issues have always been a concern of the Alternative Breaks program at the University of Kansas.... To promote participant safety and to protect the program from litigation, this research was done to gain a deeper understanding of what other University’s Alternative Breaks programs have been doing. This research was done specifically to find out...

  14. How Do Low-Energy (0.1-2 eV) Electrons Cause DNA-Strand

    E-Print Network [OSTI]

    Simons, Jack

    How Do Low-Energy (0.1-2 eV) Electrons Cause DNA-Strand Breaks? JACK SIMONS* Chemistry Department by which very low-energy (0.1-2 eV) free electrons attach to DNA and cause strong (ca. 4 eV) covalent bonds of electrons in the above energy range to base * orbitals is more likely than attachment elsewhere and (ii

  15. Dynamical electroweak symmetry breaking and the top quark

    SciTech Connect (OSTI)

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

    1997-01-01

    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. Multiplex analysis of DNA

    DOE Patents [OSTI]

    Church, George M. (Boston, MA); Kieffer-Higgins, Stephen (Dorchester, MA)

    1992-01-01

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

  17. Wave breaking and setup over fringing reefs Zhenhua Huang

    E-Print Network [OSTI]

    Wave breaking and setup over fringing reefs Zhenhua Huang Principal investigator at Earth Observatory of Singapore Nanyang Technological University Abstract Wave breaking over coral reefs can induce wave setup and near-shore currents, which have significant impacts on near-shore circulations

  18. The hidden X-ray breaks in afterglow light curves

    SciTech Connect (OSTI)

    Curran, P. A.; Wijers, R. A. M. J.; Horst, A. J. van der; Starling, R. L. C.

    2008-05-22

    Gamma-Ray Burst (GRB) afterglow observations in the Swift era have a perceived lack of achromatic jet breaks compared to the BeppoSAX, or pre-Swift era. Specifically, relatively few breaks, consistent with jet breaks, are observed in the X-ray light curves of these bursts. If these breaks are truly missing, it has serious consequences for the interpretation of GRB jet collimation and energy requirements, and the use of GRBs as standard candles.Here we address the issue of X-ray breaks which are possibly 'hidden' and hence the light curves are misinterpreted as being single power-laws. We show how a number of precedents, including GRB 990510 and GRB 060206, exist for such hidden breaks and how, even with the well sampled light curves of the Swift era, these breaks may be left misidentified. We do so by synthesising X-ray light curves and finding general trends via Monte Carlo analysis. Furthermore, in light of these simulations, we discuss how to best identify achromatic breaks in afterglow light curves via multi-wavelength analysis.

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

    SciTech Connect (OSTI)

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

    2008-01-18

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

  20. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

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

    2013-08-18

    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.

  1. 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

    2013-01-01

    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.

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

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25

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

  3. 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, ...

  4. Research article Development and usage of a NIST standard reference material

    E-Print Network [OSTI]

    quantitation of human DNA§ P.M. Vallone *, M.C. Kline, D.L. Duewer, A.E. Decker, J.W. Redman, J.C. Travis, M.0 at 260 nm equals 50 ng/mL of double stranded DNA. In addition, an interlaboratory study has been

  5. Subscriber access provided by STANFORD UNIV GREEN LIBR Analytical Chemistry is published by the American Chemical Society. 1155 Sixteenth

    E-Print Network [OSTI]

    Barron, Annelise E.

    in the electropherogram, both single- and double-stranded. Using these protocols and a panel of 11 p53 mutant DNA samples with 32P-labeled (radioactive) primers, thermal denaturation, and cooling of the resulting dsDNA to form

  6. www.landesbioscience.com GM Crops and Food: Biotechnology in Agriculture and the Food Chain 1 GM Crops and Food: Biotechnology in Agriculture and the Food Chain 3:4, 1-5; October/November/December 2012; 2012 Landes Bioscience

    E-Print Network [OSTI]

    is a strong constitutive pro- moter, generating high levels of gene expression in dicotyledon- ous plants fam- ily. CaMV was one of first plant DNA viruses to be studied, and its double-stranded circular DNA. The regulatory elements of CaMV have been used since the 1980s to express novel genes in plants;2 specifically

  7. nature physics | VOL 5 | JUNE 2009 | www.nature.com/naturephysics 373 Attack of the cyberspider

    E-Print Network [OSTI]

    Antal, Tibor

    technology always seems another decade away, receding into the future almost as fast as we chase it. So far technology. The more immediate transforming technology is emerging from techniques for controlling to be called `molecular cybernetics'. Double-stranded DNA may be the basis of life, but single-stranded DNA may

  8. Direct Gauge Mediation of Uplifted Metastable Supersymmetry Breaking in Supergravity

    E-Print Network [OSTI]

    Nobuhito Maru

    2010-08-11

    We propose a direct gauge mediation model based on an uplifted metastable SUSY breaking coupled to supergravity. A constant superpotential plays an essential role to fix the moduli as well as breaking SUSY and R-symmetry and the cancellation of the cosmological constant. Gaugino masses are generated at leading order of SUSY breaking scale, and comparable to the sfermion masses as in the ordinary gauge mediation. Landau pole problem for QCD coupling can be easily solved since more than half of messengers become superheavy, which are heavier than the GUT scale.

  9. Chiral symmetry breaking with no bilinear condensate revisited

    E-Print Network [OSTI]

    Kanazawa, Takuya

    2015-01-01

    While chiral symmetry breaking in the QCD vacuum is attributed to nonzero chiral condensate, an alternative symmetry breaking pattern with no chiral condensate is also possible, as pointed out by Stern. We study the $\\theta$ dependence of this unorthodox phase on the basis of chiral perturbation theory. Physical observables such as energy density, topological susceptibility, non-local chiral order parameter and meson masses are computed analytically in the epsilon-regime. At nonzero $\\theta$ we find an exotic phase that breaks vectorial flavor symmetries in a way analogous to the Aoki phase in lattice QCD.

  10. 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)

    2006-05-26

    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.

  11. 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

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

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

    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...

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

    E-Print Network [OSTI]

    Abatzoglou, John T; Magnusdottir, Gudrun

    2007-01-01

    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.

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

    E-Print Network [OSTI]

    Burdman, Gustavo; Nomura, Yasunori

    2003-01-01

    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

  15. LANL breaks ground on key sediment control project

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

    project LANL breaks ground on key sediment control project Called "grade-control" structures, the approximately 2 million features are up to eight feet high and made of rocks...

  16. 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 ...

  17. Symmetry-Breaking Orbital Anisotropy Observed for Detwinned Ba...

    Office of Scientific and Technical Information (OSTI)

    Observed for Detwinned Ba(Fe (1-X) Co (X) ) (2) As (2) Above the Spin Density Wave Transition Citation Details In-Document Search Title: Symmetry-Breaking Orbital...

  18. BUBBLE ENTRAINMENT AND LIQUID-BUBBLE INTERACTION UNDER UNSTEADY BREAKING

    E-Print Network [OSTI]

    Kirby, James T.

    BUBBLE ENTRAINMENT AND LIQUID-BUBBLE INTERACTION UNDER UNSTEADY BREAKING WAVES BY MORTEZA DERAKHTI Momentum Exchange . . . . . . . . . . . . . . . . . . . . . 11 2.3 Bubble Entrainment Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 4.1 Bubble Entrainment And Transport . . . . . . . . . . . . . . . . . . . 27 4.1.1 3D free

  19. Strength distributions and symmetry breaking in coupled microwave billiards

    E-Print Network [OSTI]

    B. Dietz. T. Guhr; H. L. Harney; A. Richter

    2006-06-14

    Flat microwave cavities can be used to experimentally simulate quantum mechanical systems. By coupling two such cavities, we study the equivalent to the symmetry breaking in quantum mechanics. As the coupling is tunable, we can measure resonance strength distributions as a function of the symmetry breaking. We analyze the data employing a qualitative model based on Random Matrix Theory (RMT) and show that the results derived from the strength distribution are consistent with those previously obtained from spectral statistics.

  20. Lorentz symmetry breaking effects on relativistic EPR correlations

    E-Print Network [OSTI]

    Belich, H; Bakke, K

    2015-01-01

    Lorentz symmetry breaking effects on relativistic EPR (Einstein-Podolsky-Rosen) correlations are discussed. From the modified Maxwell theory coupled to gravity, we establish a possible scenario of the Lorentz symmetry violation and write an effective metric for the Minkowski spacetime. Then, we obtain the Wigner rotation angle via the Fermi-Walker transport of spinors and consider the WKB ((Wentzel-Kramers-Brillouin) approximation in order to study the influence of Lorentz symmetry breaking effects on the relativistic EPR correlations.

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

    E-Print Network [OSTI]

    Wirosoetisno, Djoko

    ships to oil rigs, repair vessels for offshore wind farms, rescue vessels, and coast guard vessels with structures. We aim to progress nonlinear and breaking wave interactions on offshore structures, in particular

  2. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01

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

  3. DNA waves and water

    E-Print Network [OSTI]

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

    2010-12-23

    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.

  4. RARAF Publications This list does not include papers given at scientific meetings unless published in

    E-Print Network [OSTI]

    .L., Meltzer, P., Trent, J.M. and Fornace, Jr, A.J. Differential responses of stress genes to low dose Research Award lecture: Telomeres and Double-strand Breaks ­ All's Well That Ends Well. Radiat. Res. 169: 1, C. and Bond, V.P. Dose- dependence of fast neutron RBE for lens opacification in mice. Radiat. Res

  5. 1.E+01 1.E+02 1.E+03 1.E+04 1.E+05 1.E+06 1.E+07 1.E+08 Concentration(c/L)

    E-Print Network [OSTI]

    . The D10 scale is a measure of absorbance and is traceable to the unit 1. The conventional conversion the slow conversion of double-stranded DNA (dsDNA) to single-stranded (ssDNA). The conventional conversion factor for dsDNA is 50 ng/µL per absorbance unit while that for ssDNA is 37 ng/uL. There was no evidence

  6. 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

    1997-01-01

    dsRNA banding patterns, (Az9O-33-, Tx93-449+, Ca9l-17"+, Tx93-529+, and Tx93-314+'-) were examined in repeated greenhouse pathogenicity trials from 1995 to 1996 to determine if a specific set of dsRNA fragments were associated with hypovirulence and...

  7. Symmetry Breaking and the Geometry of Reduced Density Matrices

    E-Print Network [OSTI]

    V. Zauner; D. Draxler; Y. Lee; L. Vanderstraeten; J. Haegeman; F. Verstraete

    2015-03-03

    The concept of symmetry breaking and the emergence of corresponding local order parameters constitute the pillars of modern day many body physics. The theory of quantum entanglement is currently leading to a paradigm shift in understanding quantum correlations in many body systems and in this work we show how symmetry breaking can be understood from this wavefunction centered point of view. We demonstrate that the existence of symmetry breaking is a consequence of the geometric structure of the convex set of reduced density matrices of all possible many body wavefunctions. The surfaces of those convex bodies exhibit non-analytic behavior in the form of ruled surfaces, which turn out to be the defining signatures for the emergence of symmetry breaking and of an associated order parameter. We illustrate this by plotting the convex sets arising in the context of three paradigmatic examples of many body systems exhibiting symmetry breaking: the quantum Ising model in transverse magnetic field, exhibiting a second order quantum phase transition; the classical Ising model at finite temperature in two dimensions, which orders below a critical temperature $T_c$; and a system of free bosons at finite temperature in three dimensions, exhibiting the phenomenon of Bose-Einstein condensation together with an associated order parameter $\\langle\\psi\\rangle$. Remarkably, these convex sets look all very much alike. We believe that this wavefunction based way of looking at phase transitions demystifies the emergence of order parameters and provides a unique novel tool for studying exotic quantum phenomena.

  8. DNA | Open Energy Information

    Open Energy Info (EERE)

    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 Data Center Home Page on QA:QA J-E-1 SECTION J APPENDIX E LISTStar EnergyLawler,CoalConcordiaConsumerLEDSEnergyDMS Company Ltd Jump to:DNA Jump

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

    E-Print Network [OSTI]

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

    2015-01-01

    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.

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

    SciTech Connect (OSTI)

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

    1992-01-01

    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.

  11. Lorentz symmetry breaking as a quantum field theory regulator

    E-Print Network [OSTI]

    Visser, Matt

    2009-01-01

    Perturbative expansions of relativistic quantum field theories typically contain ultraviolet 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. We shall explore the features of a Lorentz symmetry breaking regulator in a simple polynomial scalar field theory, and discuss its implications. We shall quantify just "how much" Lorentz symmetry breaking is required to fully regulate the 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 [arXiv:0901.3775 [hep-th

  12. 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

    1997-04-01

    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.

  13. Slamming of a breaking wave on a wall

    E-Print Network [OSTI]

    Shu, Jian-Jun

    2014-01-01

    This paper is intended to study impact forces of breaking waves on a rigid wall based on a nonlinear potential-flow theory. This is a model problem for some technologically important design issues such as the impact of breaking waves on ships, coastal and offshore structures. We are interested in the short-time successive triggering of nonlinear effects using a small-time expansion. The analytical solutions for the impact force on a rigid wall and the free-surface profile are derived.

  14. DISS. ETH NO. 19459 Synchronization and Symmetry Breaking

    E-Print Network [OSTI]

    Waldmann, Uwe

    DISS. ETH NO. 19459 Synchronization and Symmetry Breaking in Distributed Systems A dissertation of the system's resources becomes a fascinating and challenging task. This dissertation treats of several such coordination problems arising in distributed systems. In the clock synchronization problem, devices carry

  15. Winter Break Trip 2014 New York City & Washington DC

    E-Print Network [OSTI]

    Hutcheon, James M.

    Winter Break Trip 2014 New York City & Washington DC Tentative Trip Information December 13/Meadowlands 575 Park Plaza Drive Secaucus, NJ 07094 (201) 422-9480 Hotel is located 3 miles west of New York City for departure at 5pm. · Public Transportation to and from the city o Bus stop is at NW E ST & NW New Jersey Ave

  16. How does a thermal binary crystal break under shear?

    E-Print Network [OSTI]

    Tobias Horn; Hartmut Löwen

    2014-11-21

    When exposed to strong shearing, the particles in a crystal will rearrange and ultimately, the crystal will break by forming large nonaffine defects. Even for the initial stage of this process, only little effort has been devoted to the understanding of the breaking process on the scale of the individual particle size for thermalized mixed crystals. Here, we explore the shear-induced breaking for an equimolar two-dimensional binary model crystal with a high interaction asymmetry between the two different species such that the initial crystal has an intersecting square sublattice of the two constituents. Using Brownian dynamics computer simulations, we show that the combination of shear and thermal fluctuations leads to a characteristic hierarchical breaking scenario where initially, the more strongly coupled particles are thermally distorted, paving the way for the weakly coupled particles to escape from their cage. This in turn leads to mobile defects which may finally merge, proliferating a cascade of defects, which triggers the final breakage of the crystal. This scenario is in marked contrast to the breakage of one-component crystals close to melting. Moreover, we explore the orientational dependence of the initial shear direction relative to the crystal orientation and compare this to the usual melting scenario without shear. Our results are verifiable in real-space experiments of superparamagnetic colloidal mixtures at a pending air-water interface in an external magnetic field where the shear can be induced by an external laser field.

  17. Static potential from spontaneous breaking of scale symmetry

    E-Print Network [OSTI]

    Patricio Gaete; Eduardo Guendelman; Euro Spallucci

    2007-04-11

    We determine the static potential for a heavy quark-antiquark pair from the spontaneous symmetry breaking of scale invariance in a non-Abelian gauge theory. Our calculation is done within the framework of the gauge-invariant, path-dependent, variables formalism. The result satisfies the 't Hooft basic criterion for achieving confinement.

  18. Towards breaking temperature equilibrium in multi-component Eulerian schemes

    SciTech Connect (OSTI)

    Grove, John W [Los Alamos National Laboratory; Masser, Thomas [Los Alamos National Laboratory

    2009-01-01

    We investigate the effects ofthermal equilibrium on hydrodynamic flows and describe models for breaking the assumption ofa single temperature for a mixture of components in a cell. A computational study comparing pressure-temperature equilibrium simulations of two dimensional implosions with explicit front tracking is described as well as implementation and J-D calculations for non-equilibrium temperature methods.

  19. The far-UV break in quasar energy distributions: dust?

    E-Print Network [OSTI]

    L. Binette; Y. Krongold; S. Haro-Corzo; A. Andersen

    2006-11-01

    A prominent continuum steepening is observed in quasar energy distributions near 1100A. We review possible interpretations for the origin of the so-called far-UV break, putting emphasis on those that favor the emergence of an upturn in the extreme-UV.

  20. Monochromatic and random wave breaking at blocking points

    E-Print Network [OSTI]

    Kirby, James T.

    ; published 4 July 2002. [1] In this paper we study the energy dissipation due to current-limited waveMonochromatic and random wave breaking at blocking points Arun Chawla Center for Coastal and Land and Technology, Portland, Oregon, USA James T. Kirby Center for Applied Coastal Research, University of Delaware

  1. Complete Genome Sequence of Pseudomonas Aeruginosa Phage vB_PaeM_CEB_DP1

    E-Print Network [OSTI]

    Pires, Diana P.

    vB_PaeM_CEB_DP1 is a Pseudomonas aeruginosa bacteriophage (phage) belonging to the Pbunalikevirus genus of the Myoviridae family of phages. It was isolated from hospital sewage. vB_PaeM_CEB_DP1 is a double-stranded DNA ...

  2. Development and Usage of a NIST Standard Reference Material for Real Time PCR Quantitation of Human DNANational Institute of Standards and Technology

    E-Print Network [OSTI]

    : petev@nist.gov Peter M. Vallone, Margaret C. Kline, David L. Duewer, Amy E. Decker, Janette W. Redman an absorbance of 1.0 at 260 nm equals 50 ng/µL of double stranded DNA. In addition, an interlaboratory study has

  3. Posttranscriptional gene silencing in nuclei Paul Hoffera

    E-Print Network [OSTI]

    Pikaard, Craig

    (1). RNAi can be divided into two major categories: transcriptional gene silencing (TGS) and posttranscriptional gene silencing (PTGS). Both TGS and PTGS depend on small interfering RNAs (siRNA) or microRNAs (miRNA) that are produced from double-stranded RNA (dsRNA) precursors. TGS occurs in nuclei via DNA methylation and histone

  4. 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

  5. Nucleotide cleaving agents and method

    DOE Patents [OSTI]

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

    2000-01-01

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

  6. Small RNA analysis using the Genome SequencerTM The Genome SequencerTM FLX System from 454 Life SciencesTM and Roche Applied Science is a

    E-Print Network [OSTI]

    Cai, Long

    collection of molecules with several important biological functions. Genome Sequencer technology is ideally Genome Sequencer FLX DNA library preparation protocol. The Genome Sequencer process­specific A and B molecules.The resulting double-stranded library is transferred to the emulsion PCR (emPCRTM) step for clonal

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

    E-Print Network [OSTI]

    Ortiz, Michael

    2003-01-01

    -50, Pasadena, CA 91125, USA. Fax: +1-626-449-6359. E-mail address: ortiz@aero.caltech.edu (M. Ortiz). 1 A virus years, the structure of the portal motor which translocates double-stranded DNA into the capsid

  8. New Insights into the Mechanism Underlying the Synergistic Action of Ionizing Radiation With Platinum Chemotherapeutic Drugs: The Role of Low-Energy Electrons

    SciTech Connect (OSTI)

    Rezaee, Mohammad, E-mail: Mohammad.Rezaee@USherbrooke.ca; Hunting, Darel John; Sanche, Léon

    2013-11-15

    Purpose: To investigate the efficiencies of platinum chemotherapeutic drugs (Pt-drugs) in the sensitization of DNA to the direct effects of ionizing radiation and to determine the role of low-energy electrons (LEEs) in this process. Methods and Materials: Complexes of supercoiled plasmid DNA covalently bound to either cisplatin, carboplatin, or oxaliplatin were prepared in different molar ratios. Solid films of DNA and DNA modified by Pt-drugs were irradiated with either 10-KeV or 10-eV electrons. Damages to DNA were quantified by gel electrophoresis, and the yields for damage formation were obtained from exposure–response curves. Results: The presence of an average of 2 Pt-drug–DNA adducts (Pt-adducts) in 3199-bp plasmid DNA increases the probability of a double-strand break by factors of 3.1, 2.5, and 2.4 for carboplatin, cisplatin, and oxaliplatin, respectively. Electrons with energies of 10 eV and 10 KeV interact with Pt-adducts to preferentially enhance the formation of cluster lesions. The maximum increase in radiosensitivity per Pt-adduct is found at ratios up to 3.1 × 10{sup ?4} Pt-adducts per nucleotide, which is equivalent to an average of 2 adducts per plasmid. Carboplatin and oxaliplatin show higher efficiencies than cisplatin in the radiosensitization of DNA. Because carboplatin and cisplatin give rise to identical reactive species that attach to DNA, carboplatin must be considered as a better radiosensitizer for equal numbers of Pt-adducts. Conclusion: Platinum chemotherapeutic drugs preferentially enhance the formation of cluster damage to DNA induced by the direct effect of ionizing radiation, and LEEs are the main species responsible for such an enhancement via the formation of electron resonances.

  9. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10

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

  10. Normalized cDNA libraries

    DOE Patents [OSTI]

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

    1997-01-01

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

  11. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, S.K.

    1998-03-24

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

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

    E-Print Network [OSTI]

    Belden, Jesse (Jesse Levi)

    2009-01-01

    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 ...

  13. 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...

  14. 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) ...

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

    E-Print Network [OSTI]

    Qian, Tingting

    2010-07-14

    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...

  16. Breaking Up (Hydrogen) No Longer As Hard To Do | Department of...

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

    Breaking Up (Hydrogen) No Longer As Hard To Do Breaking Up (Hydrogen) No Longer As Hard To Do December 29, 2011 - 1:12pm Addthis Researchers at Argonne National Lab have recently...

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

    E-Print Network [OSTI]

    McDonald, Angus Kai

    2005-01-01

    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 ...

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

    E-Print Network [OSTI]

    Hendrickson, Kelli L

    2005-01-01

    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 ...

  19. Topics in Forensic DNA Analysis &

    E-Print Network [OSTI]

    chemistry from the University of Virginia. His dissertation research, which was conducted at the FBI Academy guest of the FBI's Scientific Working Group on DNA Analysis Methods (SWGDAM) and a member

  20. The Environmental Impact of Lyman-break Galaxies

    E-Print Network [OSTI]

    Elizabeth J. Tasker; Greg L. Bryan

    2006-04-11

    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.

  1. Nanodiamond dust and the far-ultraviolet quasar break

    E-Print Network [OSTI]

    Binette, L; Morisset, C; Haro-Corzo, S; De Diego, J A; Mutschke, H; Andersen, A C

    2005-01-01

    We explore the possibility that the steepening observed shortward of 1000A in the energy distribution of quasars may result from absorption by dust, being either intrinsic to the quasar environment or intergalactic. We find that a dust extinction curve consisting of nanodiamonds, composed of terrestrial cubic diamonds or with surface impurities as found in carbonaceous chondrite meteorites, such as Allende, is successful in reproducing the sharp break observed. The intergalactic dust model is partially successful in explaining the shape of the composite energy distribution, but must be discarded in the end, as the amount of crystalline dust required is unreasonable and would imply an improbable fine tuning among the dust formation processes. The alternative intrinsic dust model requires a mixture of both cubic diamonds and Allende nanodiamonds and provide a better fit of the UV break. The gas column densities implied are of the order 10^{20} cm^{-2} assuming solar metallicity for carbon and full depletion of ...

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

    E-Print Network [OSTI]

    Dario Cannone; Jinn-Ouk Gong; Gianmassimo Tasinato

    2015-05-29

    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.

  3. Spectral breaks of Alfvenic turbulence in a collisionless plasma

    E-Print Network [OSTI]

    Boldyrev, Stanislav; Xia, Qian; Zhdankin, Vladimir

    2015-01-01

    Recent observations reveal that magnetic turbulence in the nearly colisionless solar wind plasma extends to scales smaller than the plasma microscales, such as ion gyroradius and ion inertial length. Measured breaks in the spectra of magnetic and density fluctuations at high frequencies are thought to be related to the transition from large-scale hydromagnetic to small-scale kinetic turbulence. The scales of such transitions and the responsible physical mechanisms are not well understood however. In the present work we emphasize the crucial role of the plasma parameters in the transition to kinetic turbulence, such as the ion and electron plasma beta, the electron to ion temperature ratio, the degree of obliquity of turbulent fluctuations. We then propose an explanation for the spectral breaks reported in recent observations.

  4. Experimental evidence of replica symmetry breaking in random lasers

    E-Print Network [OSTI]

    Ghofraniha, N; Di Maria, F; Barbarella, G; Gigli, G; Leuzzi, L; Conti, C

    2014-01-01

    Spin-glass theory is one of the leading paradigms of complex physics and describes condensed matter, neural networks and biological systems, ultracold atoms, random photonics, and many other research fields. According to this theory, identical systems under identical conditions may reach different states and provide different values for observable quantities. This effect is known as Replica Symmetry Breaking and is revealed by the shape of the probability distribution function of an order parameter named the Parisi overlap. However, a direct experimental evidence in any field of research is still missing. Here we investigate pulse-to-pulse fluctuations in random lasers, we introduce and measure the analogue of the Parisi overlap in independent experimental realizations of the same disordered sample, and we find that the distribution function yields evidence of a transition to a glassy light phase compatible with a replica symmetry breaking.

  5. Quantum Walk Search with Time-Reversal Symmetry Breaking

    E-Print Network [OSTI]

    Thomas G. Wong

    2015-07-15

    We formulate Grover's unstructured search algorithm as a chiral quantum walk, where transitioning in one direction has a phase conjugate to transitioning in the opposite direction. For small phases, this breaking of time-reversal symmetry is too small to significantly affect the evolution: the system still approximately evolves in its ground and first excited states, rotating to the marked vertex in time $\\pi \\sqrt{N} / 2$. Increasing the phase does not change the runtime, but rather changes the support for the 2D subspace, so the system evolves in its first and second excited states, or its second and third excited states, and so forth. Apart from the critical phases corresponding to these transitions in the support, which become more frequent as the phase grows, this reveals that our model of quantum search is robust against time-reversal symmetry breaking.

  6. $\\mathcal{PT}$-Symmetry-Breaking Chaos in Optomechanics

    E-Print Network [OSTI]

    Lü, Xin-You; Ma, Jin-Yong; Wu, Ying

    2015-01-01

    We demonstrate a $\\mathcal{PT}$-symmetry-breaking chaos in optomechanical system (OMS), which features an ultralow driving threshold. In principle, this chaos will emerge once a driving laser is applied to the cavity mode and lasts for a period of time. The driving strength is inversely proportional to the starting time of chaos. This originally comes from the dynamical enhancement of nonlinearity by field localization in $\\mathcal{PT}$-symmetry-breaking phase ($\\mathcal{PT}$BP). Moreover, this chaos is switchable by tuning the system parameters so that a $\\mathcal{PT}$-symmetry phase transition occurs. This work may fundamentally broaden the regimes of cavity optomechanics and nonlinear optics. It offers the prospect of exploring ultralow-power-laser triggered chaos and its potential applications in secret communication.

  7. Sequestered uplifting and the pattern of soft supersymmetry breaking terms

    E-Print Network [OSTI]

    Kwang Sik Jeong

    2007-12-17

    We examine the pattern of soft supersymmetry breaking terms in moduli stabilization, where an uplifting potential is provided by spontaneously broken supersymmetry in a generic sequestered sector. From stationary conditions, we derive the relation between moduli F-term vacuum expectation values which does not depend on the details of sequestered uplifting. This moduli F-term relation is crucial for identifying the dominant source of soft terms of visible fields.

  8. Electroweak symmetry breaking by strong dynamics and the collider phenomenology

    SciTech Connect (OSTI)

    Timothy L. Barklow et al.

    2002-12-23

    We discuss the possible signatures in the electroweak symmetry breaking sector by new strong dynamics at future hadron colliders such as the Tevatron upgrade, the LHC and VLHC, and e{sup +}e{sup -} linear colliders. Examples include a heavy Higgs-like scalar resonance, a heavy Technicolor-like vector resonance and pseudo-Goldstone states, non-resonance signatures via enhanced gauge-boson scattering and fermion compositeness.

  9. Statistical estimation of water distribution system pipe break risk 

    E-Print Network [OSTI]

    Yamijala, Shridhar

    2009-05-15

    of support or bedding. 5) Soil movement: Subsidence due to mining, filled land etc. Differential consolidation or geological changes. Changes in water table or soil moisture content. Extremes of climate such as frost heave or clay shrinkage. Loss....021 and 0.014 for pit cast iron and sandspun cast iron pipes respectively, when they employed a similar modeling approach on other datasets. 16 The Shamir and Howard models are one of the first attempts to statistically analyze break records...

  10. Finsler-like structures from Lorentz-breaking classical particles

    E-Print Network [OSTI]

    Neil Russell

    2015-01-11

    A method is presented for deducing classical point-particle Lagrange functions corresponding to a class of quartic dispersion relations. Applying this to particles violating Lorentz symmetry in the minimal Standard-Model Extension leads to a variety of novel lagrangians in flat spacetime. Morphisms in these classical systems are studied that echo invariance under field redefinitions in the quantized theory. The Lagrange functions found offer new possibilities for understanding Lorentz-breaking effects by exploring parallels with Finsler-like geometries.

  11. 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 Data Center Home Page on Delicious RankADVANCED MANUFACTURINGEnergyPlan | Department ofSUPPLEMENTSwitzerland 2012 ProgramSynergyBreak-Out

  12. Upper tropospheric drying and the ``transition to break'' in the Indian summer monsoon during 1999

    E-Print Network [OSTI]

    Roca, Rémy

    level convergence. A rapid shift occurs in divergence field during transition with convergence replacing to transition in to a break phase from an active monsoon phase. 1.1. Active and Break Spells [3] Infra RedUpper tropospheric drying and the ``transition to break'' in the Indian summer monsoon during 1999

  13. The Szilard engine revisited: Entropy, macroscopic randomness, and symmetry breaking phase transitions

    E-Print Network [OSTI]

    Parrondo, Juan M.R.

    The Szilard engine revisited: Entropy, macroscopic randomness, and symmetry breaking phase 2001 The role of symmetry breaking phase transitions in the Szilard engine is analyzed. It is shown that symmetry breaking is the only necessary ingredient for the engine to work. To support this idea, we show

  14. Under consideration for publication in J. Fluid Mech. 1 Dam breaking seiches

    E-Print Network [OSTI]

    Balmforth, Neil

    Under consideration for publication in J. Fluid Mech. 1 Dam breaking seiches N. J. Balmforth1, J the break of a moraine dam by catastrophic erosional incision initiated by overtopping with a displacement confirm that dams can be broken by a catastrophic incision. However, the displacement wave does not break

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

    SciTech Connect (OSTI)

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

    1992-12-31

    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.

  16. Peccei-Quinn Symmetry from Dynamical Supersymmetry Breaking

    E-Print Network [OSTI]

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

    2015-01-01

    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.

  17. Peccei-Quinn Symmetry from Dynamical Supersymmetry Breaking

    E-Print Network [OSTI]

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

    2015-05-27

    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.

  18. Supersymmetric Custodial Higgs Triplets and the Breaking of Universality

    E-Print Network [OSTI]

    Mateo Garcia-Pepin; Stefania Gori; Mariano Quiros; Roberto Vega; Roberto Vega-Morales; Tien-Tien Yu

    2014-12-21

    Higgs triplet models are known to have difficulties obtaining agreement with electroweak precision data and in particular constraints on the $\\rho$ parameter. Either a global $SU(2)_L \\otimes SU(2)_R$ symmetry has to be imposed on the scalar potential at the electroweak scale, as done in the well-known Georgi-Machacek (GM) model, or the triplet vacuum expectation values must be very small. We construct a supersymmetric model that can satisfy constraints on the $\\rho$ parameter, even if these two conditions are not fulfilled. We supersymmetrize the GM model by imposing the $SU(2)_L \\otimes SU(2)_R$ symmetry at a scale $\\mathcal M$, which we argue should be at or above the messenger scale, where supersymmetry breaking is transmitted to the observable sector. We show that scales $\\mathcal M$ well above 100 TeV and sizable contributions from the triplets to electroweak symmetry breaking can be comfortably accommodated. We discuss the main phenomenological properties of the model and demonstrate that the departure from custodial symmetry at the electroweak scale, due to radiative breaking, can show up at the LHC as a deviation in the `universal' relation for the Higgs couplings to $WW$ and $ZZ$. As a by-product of supersymmetry, we also show that one can easily obtain both large tree-level \\emph{and} one loop corrections to the Higgs mass. This allows for stops that can be significantly lighter and with smaller mixing than those needed in the MSSM.

  19. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    SciTech Connect (OSTI)

    Henrique Barreta, Marcos; Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS ; Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de; Ferreira, Rogerio; Oliveira, Joao Francisco de; Goncalves, Paulo Bayard Dias; Bordignon, Vilceu

    2012-10-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  20. Characterization of nanoparticle-DNA conjugate and control of DNA conformation on particle surface

    E-Print Network [OSTI]

    Park, Sunho, 1976-

    2009-01-01

    Nano-science has exploited the hybridization and de-hybridization phenomena of DNA which are one of its fundamental functions. In particular, conjugates of gold nanoparticles and DNA (Au NP-DNA) have been extensively ...

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

    E-Print Network [OSTI]

    Woodruff, Rachel Van Etten

    2008-01-01

    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 ...

  2. Magnetic tweezers to studyMagnetic tweezers to studyMagnetic tweezers to studyMagnetic tweezers to study DNA motorsDNA motorsDNA motorsDNA motors

    E-Print Network [OSTI]

    Ritort, Felix

    to study DNA motorsDNA motorsDNA motorsDNA motors MariaMariaMariaMaria MañosasMañosasMañosasMañosas Ritort) · Applications: 1. Tracking DNA motors: (i) Helicases (ii) Annealing motor 2. Studying a multiprotein system: DNA hexamers (Dong et al, JBC 1995) Tracking DNA motors: (i) Helicases #12;Passive: helicase behaves

  3. The Structure of DNA within Cationic Lipid/DNA Complexes

    E-Print Network [OSTI]

    Braun, Chad S.; Jas, Gouri S.; Choosakoonriang, Sirirat; Koe, Gary S.; Smith, Janet G.; Middaugh, C. Russell

    2003-02-01

    hexagonal phase of cationic liposome-DNA complexes related to DNA release and delivery. Science. 281:78–81. Koppel, D. E. 1972. Analysis of macromolecular polydispersity in inten- sity correlation spectroscopy: the method of cumulants. J. Chem. Phys. 57:4814..., DOTAP, 1,2-dioleoyl-sn-glycero-3-phosphatidyletha- nolamine, and cholesterol were purchased from Avanti Polar Lipids (Alabaster, AL). Poly(dG) Æ poly(dC) (4 kbp), poly(dA) Æ poly(dT) (;229 bp), poly(dGdC) Æ poly(dGdC) (724 bp), and poly(dAdT) Æ poly(d...

  4. Downregulation of SWI/SNF chromatin remodeling factor subunits modulates cisplatin cytotoxicity

    SciTech Connect (OSTI)

    Kothandapani, Anbarasi; Gopalakrishnan, Kathirvel; Kahali, Bhaskar; Reisman, David; Patrick, Steve M.

    2012-10-01

    Chromatin remodeling complex SWI/SNF plays important roles in many cellular processes including transcription, proliferation, differentiation and DNA repair. In this report, we investigated the role of SWI/SNF catalytic subunits Brg1 and Brm in the cellular response to cisplatin in lung cancer and head/neck cancer cells. Stable knockdown of Brg1 and Brm enhanced cellular sensitivity to cisplatin. Repair kinetics of cisplatin DNA adducts revealed that downregulation of Brg1 and Brm impeded the repair of both intrastrand adducts and interstrand crosslinks (ICLs). Cisplatin ICL-induced DNA double strand break repair was also decreased in Brg1 and Brm depleted cells. Altered checkpoint activation with enhanced apoptosis as well as impaired chromatin relaxation was observed in Brg1 and Brm deficient cells. Downregulation of Brg1 and Brm did not affect the recruitment of DNA damage recognition factor XPC to cisplatin DNA lesions, but affected ERCC1 recruitment, which is involved in the later stages of DNA repair. Based on these results, we propose that SWI/SNF chromatin remodeling complex modulates cisplatin cytotoxicity by facilitating efficient repair of the cisplatin DNA lesions. -- Highlights: Black-Right-Pointing-Pointer Stable knockdown of Brg1 and Brm enhances cellular sensitivity to cisplatin. Black-Right-Pointing-Pointer Downregulation of Brg1 and Brm impedes the repair of cisplatin intrastrand adducts and interstrand crosslinks. Black-Right-Pointing-Pointer Brg1 and Brm deficiency results in impaired chromatin relaxation, altered checkpoint activation as well as enhanced apoptosis. Black-Right-Pointing-Pointer Downregulation of Brg1 and Brm affects recruitment of ERCC1, but not XPC to cisplatin DNA lesions.

  5. Nanodiamond dust and the far-ultraviolet quasar break

    E-Print Network [OSTI]

    L. Binette; G. Magris C.; Y. Krongold; C. Morisset; S. Haro-Corzo; J. A. de Diego; H. Mutschke; A. C. Andersen

    2005-05-29

    We explore the possibility that the steepening observed shortward of 1000A in the energy distribution of quasars may result from absorption by dust, being either intrinsic to the quasar environment or intergalactic. We find that a dust extinction curve consisting of nanodiamonds, composed of terrestrial cubic diamonds or with surface impurities as found in carbonaceous chondrite meteorites, such as Allende, is successful in reproducing the sharp break observed. The intergalactic dust model is partially successful in explaining the shape of the composite energy distribution, but must be discarded in the end, as the amount of crystalline dust required is unreasonable and would imply an improbable fine tuning among the dust formation processes. The alternative intrinsic dust model requires a mixture of both cubic diamonds and Allende nanodiamonds and provide a better fit of the UV break. The gas column densities implied are of the order 10^{20} cm^{-2} assuming solar metallicity for carbon and full depletion of carbon into dust. The absorption only occurs in the ultraviolet and is totally negligible in the visible. The minimum dust mass required is of the order ~ 0.003 r_{pc}^{2}M_o, where r_{pc} is the distance in parsec between the dust screen and the continuum source. The intrinsic dust model reproduces the flux {\\it rise} observed around 660A in key quasar spectra quite well. We present indirect evidence of a shallow continuum break near 670A (18.5 eV), which would be intrinsic to the quasar continuum.

  6. Revolving D-branes and Spontaneous Gauge Symmetry Breaking

    E-Print Network [OSTI]

    Satoshi Iso; Noriaki Kitazawa

    2015-10-07

    We propose a new mechanism of spontaneous gauge symmetry breaking in the world-volume theory of revolving D-branes around a fixed point of orbifolds. In this paper, we consider a simple model of the T6/Z3 orbifold on which we put D3-branes, D7-branes and their anti-branes. The configuration breaks supersymmetry, but the R-R tadpole cancellation conditions are satisfied. A set of three D3-branes at an orbifold fixed point can separate from the point, but when they move perpendicular to the anti-D7-branes put on the fixed point, they are forced to be pulled back due to an attractive interaction between the D3 and anti-D7 branes. In order to stabilize the separation of the D3-branes at nonzero distance, we consider revolution of the D3-branes around the fixed point. Then the gauge symmetry on D3-branes is spontaneously broken, and the rank of the gauge group is reduced. The distance can be set at our will by appropriately choosing the angular momentum of the revolving D3-branes, which should be determined by the initial condition of the cosmological evolution of D-brane configurations. The distance corresponds to the vacuum expectation values of brane moduli fields in the world-volume theory and, if it is written as M/Ms^2 in terms of the string scale Ms, the scale of gauge symmetry breaking is given by M. Angular momentum conservation of revolving D3-branes assures the stability of the scale M against Ms.

  7. PT symmetry and spontaneous symmetry breaking in a microwave billiard

    E-Print Network [OSTI]

    S. Bittner; B. Dietz; U. Guenther; H. L. Harney; M. Miski-Oglu; A. Richter; F. Schaefer

    2011-12-02

    We demonstrate the presence of parity-time (PT) symmetry for the non-Hermitian two-state Hamiltonian of a dissipative microwave billiard in the vicinity of an exceptional point (EP). The shape of the billiard depends on two parameters. The Hamiltonian is determined from the measured resonance spectrum on a fine grid in the parameter plane. After applying a purely imaginary diagonal shift to the Hamiltonian, its eigenvalues are either real or complex conjugate on a curve, which passes through the EP. An appropriate basis choice reveals its PT symmetry. Spontaneous symmetry breaking occurs at the EP.

  8. Comparison of symmetry breaking in the canonical and microcanonical ensembles

    SciTech Connect (OSTI)

    Arthur Weldon, H. (Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (US))

    1989-07-01

    High temperature field theories have always been formulated in the canonical ensemble (i.e., fixed {ital T}). Here the same theories are investigated in the microcanonical ensemble (i.e., fixed total energy {ital E}). To incorporate spontaneous symmetry breaking a microcanonical analogue of the effective potential is developed. There is a critical value of the energy {ital E}{sub {ital c}} which separates the broken from the unbroken phase. Explicit one loop calculations in the two ensembles allow for detailed comparisons and lead to agreement in the limit {ital VT}{sup 3}{r arrow}{infinity}. {copyright} 1989 Academic Press, Inc.

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

    SciTech Connect (OSTI)

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

    1997-04-01

    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.

  10. Breaking a Pocket of Resistance in the Fight Against Cancer

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room News PublicationsAudits &Bradbury Science Museum - Science onBranding &Breaking a

  11. Breaking the ties that bind: New hope for biomass fuels

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room News PublicationsAudits &Bradbury Science Museum - Science onBranding &Breaking aNew

  12. Breaking the Fuel Cell Cost Barrier | 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 Data Center Home Page on Delicious Rank EERE:FinancingPetroleum Based Fuels Researchof Energy|Make6,Energy1Breaking the Fuel Cell Cost

  13. Breaking the Biological Barriers to Cellulosic Ethanol, June 2006 |

    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 Data Center Home Page on Delicious Rank EERE: Alternative FuelsofProgram:Y-12Power, IncBio CentersBreaking Up (Hydrogen) No Longer As Hard To

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

    E-Print Network [OSTI]

    McCann, Andrew

    2015-01-01

    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.

  15. Intermediate-break LOCA analyses for the AP600 design

    SciTech Connect (OSTI)

    Boyack, B.E.; Lime, J.F.

    1995-07-01

    A postulated double-ended guillotine break of a direct-vessel-injection line in an AP600 plant has been analyzed. This event is characterized as an intermediate break loss-of-coolant accident (IBLOCA). Most of the insights regarding the response of the AP600 safety systems to the postulated accident are derived from calculations performed with the TRAC-PFl/MOD2 code. However, complementary insights derived from a scaled experiment conducted in the ROSA facility, as well as insights based upon calculations by other codes, are also presented. The key processes occurring in an AP600 during a IBLOCA are primary coolant system depressurization, inventory depletion, inventory replacement via emergency core coolant injection, continuous core cooling, and long-term decay heat rejection to the atmosphere. Based upon the calculated and experimental results, the AP600 will not experience a core heat up and will reach a safe shutdown state using only safety-class equipment. Only the early part of the long-term cooling period initiated by In-containment Refueling Water Storage Tank injection was evaluated Thus, the observation that the core is continuously cooled should be verified for the latter phase of the long-term cooling period, the interval when sump injection and containment cooling processes are important.

  16. CP breaking in $S(3)$ flavoured Higgs model

    E-Print Network [OSTI]

    E. Barradas-Guevara; O. Félix-Beltrán; E. Rodríguez-Jáuregui

    2015-07-18

    We analyze the Higgs sector of the minimal $S(3)$-invariant extension of the Standard Model including CP violation arising from the spontaneous breaking of the electroweak symmetry. This extended Higgs sector includes three $SU(2)$ doublets Higgs fields with complex vev's provide an interesting scenario to analyze the Higgs masses spectrum, trilinear self-couplings and CP violation. We present how the spontaneous electroweak symmetry breaking coming from three $S(3)$ Higgs fields gives an interesting scenario with nine physical Higgs and three Goldstone bosons when spontaneous CP violation arises from the Higgs field $S(3)$ singlet $H_S$. Furthermore, numerical analysis of the Higgs masses and trilinear self-couplings is presented, particularly we find a physical solution for the scenario in which spontaneous CPB is provided by the single field $H_S$. The scalar Higgs $H_4^0$ is identified whose mass is 125 GeV and $\\lambda_{H_{4}^0 H_{4}^0 H_{4}^0} \\sim \\lambda_{h^0 h^0 h^0}^{SM}$ in good agreement with the latest experimental results.

  17. Spontaneous Symmetry Breaking in Presence of Electric and Magnetic Charges

    E-Print Network [OSTI]

    Pushpa; P. S. Bisht; O. P. S. Negi

    2010-11-17

    Starting with the definition of quaternion gauge theory, we have undertaken the study of SU(2)_{e}\\times SU(2)_{m}\\times U(1)_{e}\\times U(1)_{m} in terms of the simultaneous existence of electric and magnetic charges along with their Yang - Mills counterparts. As such, we have developed the gauge theory in terms of four coupling constants associated with four - gauge symmetry SU(2)_{e}\\times SU(2)_{m}\\times U(1)_{e}\\times U(1)_{m}. Accordingly, we have made an attempt to obtain the abelian and non - Abelian gauge structures for the particles carrying simultaneously the electric and magnetic charges (namely dyons). Starting from the Lagrangian density of two SU(2)\\times U(1) gauge theories responsible for the existence of electric and magnetic charges, we have discussed the consistent theory of spontaneous symmetry breaking and Higgs mechanism in order to generate the masses. From the symmetry breaking, we have generated the two electromagnetic fields, the two massive vector W^{\\pm} and Z^{0} bosons fields and the Higgs scalar fields.

  18. Brane World as a Result of Spontaneous Symmetry Breaking

    E-Print Network [OSTI]

    Boris E. Meierovich

    2009-10-09

    The theories of brane world and multidimensional gravity are widely discussed in the literature in connection with problems of evolution of early Universe, including dark matter and energy. A natural physical concept is that a distinguished surface in the space-time manifold is a topological defect appeared as a result of a phase transition with spontaneous symmetry breaking. The macroscopic theory of phase transitions allows considering the brane world concept self-consistently, even without the knowledge of the nature of physical vacuum. Gravitational properties of topological defects (cosmic strings, monopoles,...) in extra dimensions are studied in General Relativity considering the order parameter as a vector and a multiplet in a plane target space of scalar fields. The common results and differences of these two approaches are analyzed and demonstrated in detail. Among the variety of regular solutions, there are those having brane features, including solutions with multiple branes, as well as the ones of potential interest from the standpoint of the dark matter and hierarchy problems. Regular configurations have a growing gravitational potential and are able to trap the matter on the brane. If the energy of spontaneous symmetry breaking is high, the attracting potential can have several points of minimum. Identical in the uniform bulk spin-less particles, being trapped within the separate points of minimum, acquire different masses and appear to an observer on brane as different particles with integer spins.

  19. Flavour symmetry breaking in the kaon parton distribution amplitude

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

    none,

    2014-11-01

    We compute the kaon's valence-quark (twist-two parton) distribution amplitude (PDA) by projecting its Poincaré-covariant Bethe–Salpeter wave-function onto the light-front. At a scale ? = 2 GeV, the PDA is a broad, concave and asymmetric function, whose peak is shifted 12–16% away from its position in QCD's conformal limit. These features are a clear expression of SU(3)-flavour-symmetry breaking. They show that the heavier quark in the kaon carries more of the bound-state's momentum than the lighter quark and also that emergent phenomena in QCD modulate the magnitude of flavour-symmetry breaking: it is markedly smaller than one might expect based on themore »difference between light-quark current masses. Our results add to a body of evidence which indicates that at any energy scale accessible with existing or foreseeable facilities, a reliable guide to the interpretation of experiment requires the use of such nonperturbatively broadened PDAs in leading-order, leading-twist formulae for hard exclusive processes instead of the asymptotic PDA associated with QCD's conformal limit. We illustrate this via the ratio of kaon and pion electromagnetic form factors: using our nonperturbative PDAs in the appropriate formulae, FK/F?=1.23 at spacelike-Q2=17 GeV2, which compares satisfactorily with the value of 0.92(5) inferred in e+e- annihilation at s=17 GeV2.« less

  20. Revolving D-branes and Spontaneous Gauge Symmetry Breaking

    E-Print Network [OSTI]

    Iso, Satoshi

    2015-01-01

    We propose a new mechanism of spontaneous gauge symmetry breaking in the world-volume theory of revolving D-branes around a fixed point of orbifolds. In this paper, we consider a simple model of the T6/Z3 orbifold on which we put D3-branes, D7-branes and their anti-branes. The configuration breaks supersymmetry, but the R-R tadpole cancellation conditions are satisfied. A set of three D3-branes at an orbifold fixed point can separate from the point, but when they move perpendicular to the anti-D7-branes put on the fixed point, they are forced to be pulled back due to an attractive interaction between the D3 and anti-D7 branes. In order to stabilize the separation of the D3-branes at nonzero distance, we consider revolution of the D3-branes around the fixed point. Then the gauge symmetry on D3-branes is spontaneously broken, and the rank of the gauge group is reduced. The distance can be set at our will by appropriately choosing the angular momentum of the revolving D3-branes, which should be determined by the...

  1. The Initiation of Bacterial DNA Replication

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

    for this system. Instead, DnaA forms an open right-handed helix. In addition, the architecture indicates that this AAA+ superhelix will wrap coils of the DNA around its exterior,...

  2. Micropatterned cell arrays for detecting DNA damage

    E-Print Network [OSTI]

    Mittal, Sukant

    2008-01-01

    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 ...

  3. Towards Privacy Preserving of Forensic DNA Databases 

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14

    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...

  4. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

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

    1991-01-01

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

  5. The Future of Forensic DNA

    E-Print Network [OSTI]

    History and Mission · National Institute of Standards and Technology (NIST) was created in 1901The Future of Forensic DNA John M. Butler, PhD National Institute of Standards and Technology.S. Department of Commerce with a mission to develop and promote measurement, standards, and technology

  6. Origami DNA model Mountain fold

    E-Print Network [OSTI]

    Csürös, Miklós

    Origami DNA model Mountain fold Solid lines are "mountains" and are to be folded away from you with the peak pointing towards you. 1. Fold all solid lines going lengthwise down the page into "mountain folds fold 2. Fold all dashed lines going lengthwise down the page into "valley folds". Mountain folds along

  7. The Future of Forensic DNA

    E-Print Network [OSTI]

    ;Checks and Controls on DNA Results Community FBI Quality Assurance Standards (and interlaboratory studies Washington D.C. Dulles Airport Reagan National Airport BWI Airport NIST FBI Lab Baltimore, MD Richmond, VA Materials (SRMs) Helps meet FBI QAS and ISO 17025 requirements Traceable standards to ensure accurate

  8. DNA Mixture Interpretation & Statistical Analysis

    E-Print Network [OSTI]

    of Standards and Technology Gaithersburg, Maryland John M. Butler CIB Forensic Science Center Training Seminar Mixture Workshop This workshop is for analysts, technical reviewers and technical leaders performing) National recommendations of the technical UK DNA working group on mixture interpretation for the NDNAD

  9. DNA sequencing protocols BN Danforth

    E-Print Network [OSTI]

    Danforth, Bryan Nicholas

    in the degradation of DNA. (7) Spin the tubes down at the end to remove condensation from tops of tubes. B. Extraction and RNA digestion. NOTE: We now skip the Rnase step. You will need: Phenol and gently invert several times. This step removes the phenol from the previous extraction. Spin

  10. Biological Physics of DNA Typeset by FoilTEX 1

    E-Print Network [OSTI]

    Potsdam, Universität

    fragments to ssDNA Labelling: eg radioact probe fragm & Xray film http;Packaging of DNA in bacteria 11 #12;DNA melting 12 #12;Polymerase chain reaction Heating dsDNA sample 2

  11. DNA extraction techniques for DNA barcoding of minute gall-inhabiting wasps

    E-Print Network [OSTI]

    extraction methods were compared to determine their efficacy in isolating DNA. Success of each methodDNA extraction techniques for DNA barcoding of minute gall-inhabiting wasps GUDRUN DITTRICH, South Africa Abstract DNA extraction from minute hymenopterans and their larvae is difficult

  12. 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 mismatches with the complements of all the other members in the set. These "DNA word" sets are denoted as nbm. To achieve good discrimination between each DNA word in each set generated using the template-map strategy

  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; Bukczynska, Patricia; Jackson, Susan; Haput, Ygal; Cullinane, Carleen; McArthur, Grant A.; Solomon, Benjamin

    2014-02-01

    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. Probe and method for DNA detection

    DOE Patents [OSTI]

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

    2013-07-02

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

  15. MATERIALS AND METHODS 1) DNA extraction

    E-Print Network [OSTI]

    Collins, Gary S.

    MATERIALS AND METHODS 1) DNA extraction · DNA was extracted from the ileo-cecal nodes of 475 Holstein cows from two herds using the Qiagen DNA extraction kit (Valencia, CA). 2) Map detection · Map was extracted from ileo-cecal nodes using Ambion's MagMAX Total Nucleic Acid Isolation kit (Austin, TX

  16. 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)

    1991-07-01

    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.

  17. 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)

    2012-02-20

    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.

  18. Mechanisms of radiation-induced neoplastic cell transformation

    SciTech Connect (OSTI)

    Yang, T.C.H.; Tobias, C.A.

    1984-04-01

    Studies with cultured mammalian cells demonstrated clearly that radiation can transform cells directly and can enhance the cell transformation by oncogenic DNA viruses. In general, high-LET heavy-ion radiation can be more effective than X and gamma rays in inducing neoplastic cell transformation. Various experimental results indicate that radiation-induced DNA damage, most likely double-strand breaks, is important for both the initiation of cell transformation and for the enhancement of viral transformation. Some of the transformation and enhancement lesions can be repaired properly in the cell, and the amount of irrepairable lesions produced by a given dose depends on the quality of radiation. An inhibition of repair processes with chemical agents can increase the transformation frequency of cells exposed to radiation and/or oncogenic viruses, suggesting that repair mechanisms may play an important role in the radiation transformation. The progression of radiation-transformed cells appears to be a long and complicated process that can be modulated by some nonmutagenic chemical agents, e.g., DMSO. Normal cells can inhibit the expression of transforming properties of tumorigenic cells through an as yet unknown mechanism. The progression and expression of transformation may involve some epigenetic changes in the irradiated cells. 38 references, 15 figures, 1 table.

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

    SciTech Connect (OSTI)

    Martin, Olga A.; Anderson, Robin L.; Russell, Prudence A.; Ashley Cox, R.; Ivashkevich, Alesia; Swierczak, Agnieszka; Doherty, Judy P.; Jacobs, Daphne H.M.; Smith, Jai; Siva, Shankar; Daly, Patricia E.; Ball, David L.; and others

    2014-02-01

    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.

  20. Lorentz Symmetry Breaking in $\\mathcal{N} =2$ Superspace

    E-Print Network [OSTI]

    Faizal, Mir

    2015-01-01

    In this paper, we will study the deformation of a three dimensional theory with $\\mathcal{N} =2$ supersymmetry. This theory will be deformed by the presence of a constant vector field. This deformation will break the Lorentz symmetry. So, we will analyse this theory using $\\mathcal{N} =2$ aether superspace. The $\\mathcal{N} =2$ aether superspace will be obtained from a deformation of the usual $\\mathcal{N} =2$ superspace. This will be done by deforming the generators of the three dimensional $\\mathcal{N} =2$ supersymmetry. After analysing this deformed superalgebra, we will derive an explicit expression for the superspace propagators in this deformed superspace. Finally, we will use these propagators for performing perturbative calculations.

  1. Chiral Symmetry Breaking in Bent-Core Liquid Crystals

    E-Print Network [OSTI]

    Lech Longa; Grzegorz Paj?k; Thomas Wydro

    2009-02-04

    By molecular modeling we demonstrate that the nematic long-range order discovered in bent-core liquid crystal systems should reveal further spatially homogeneous phases. Two of them are identified as a tetrahedratic nematic ($N_T$) phase with $D_{2d}$ symmetry and a chiral tetrahedratic nematic ($N_T^*$) phase with $D_2$ symmetry. These new phases were found for a lattice model with quadrupolar and octupolar anisotropic interactions using Mean Field theory and Monte Carlo simulations. The phase diagrams exhibit tetrahedratic ($T$), $N_T$ and $N_T^*$ phases, in addition to ordinary isotropic ($I$), uniaxial nematic ($N_U$) and biaxial nematic ($N_B$) phases. To our knowledge, this is the first molecular model with spontaneous chiral symmetry breaking in non-layered systems.

  2. Glassy slowdown and replica-symmetry-breaking instantons

    E-Print Network [OSTI]

    Allan Adams; Tarek Anous; Jaehoon Lee; Sho Yaida

    2015-03-30

    Glass-forming liquids exhibit a dramatic dynamical slowdown as the temperature is lowered. This can be attributed to relaxation proceeding via large structural rearrangements whose characteristic size increases as the system cools. These cooperative rearrangements are well modeled by instantons in a replica effective field theory, with the size of the dominant instanton encoding the liquid's cavity point-to-set correlation length. Varying the parameters of the effective theory corresponds to varying the statistics of the underlying free-energy landscape. We demonstrate that, for a wide range of parameters, replica-symmetry-breaking instantons dominate. The detailed structure of the dominant instanton provides a rich window into point-to-set correlations and glassy dynamics.

  3. Impact of an oblique breaking wave on a wall

    E-Print Network [OSTI]

    Shu, Jian-Jun

    2014-01-01

    The intention of this paper is to study impact force of an oblique-angled slamming wave acting on a rigid wall. In the present study the analytical approach is pursued based on a technique proposed by the author. A nonlinear theory in the context of potential flow is presented for determining accurately the free-surface profiles immediately after an oblique breaking wave impingement on the rigid vertical wall that suddenly starts from rest. The small-time expansion is taken as far as necessary to include the accelerating effect. The analytical solutions for the free-surface elevation are derived up to the third order. The results derived in this paper are of particular interest to the marine and offshore engineering industries, which will find the information useful for the design of ships, coastal and offshore.

  4. Single particles accelerate final stages of capillary break up

    E-Print Network [OSTI]

    Lindner, Anke; Wagner, Christian

    2015-01-01

    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.

  5. Single particles accelerate final stages of capillary break up

    E-Print Network [OSTI]

    Anke Lindner; Jorge Eduardo Fiscina; Christian Wagner

    2015-06-12

    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.

  6. A Symmetry Breaking Model for X Chromosome Inactivation

    E-Print Network [OSTI]

    M. Nicodemi; A. Prisco

    2008-01-17

    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.

  7. Multilepton signals of gauge mediated supersymmetry breaking at the LHC

    E-Print Network [OSTI]

    D'Hondt, Jorgen; Fuks, Benjamin; Mariotti, Alberto; Mawatari, Kentarou; Petersson, Christoffer; Redigolo, Diego

    2014-01-01

    We investigate multilepton LHC signals arising from electroweak processes involving sleptons. We consider the framework of general gauge mediated supersymmetry breaking, focusing on models where the low mass region of the superpartner spectrum consists of the three generations of charged sleptons and the nearly massless gravitino. We demonstrate how such models can provide an explanation for the anomalous four lepton events recently observed by the CMS collaboration, while satisfying other existing experimental constraints. The best fit to the CMS data is obtained for a selectron/smuon mass of around 145 GeV and a stau mass of around 90 GeV. These models also give rise to final states with more than four leptons, offering alternative channels in which they can be probed and we estimate the corresponding production rates at the LHC.

  8. Micropropulsion and microrheology in complex fluids via symmetry breaking

    E-Print Network [OSTI]

    Pak, On Shun; Brandt, Luca; Lauga, Eric; 10.1063/1.4758811

    2013-01-01

    Many biological fluids have polymeric microstructures and display non-Newtonian rheology. We take advantage of such nonlinear fluid behavior and combine it with geometrical symmetry-breaking to design a novel small-scale propeller able to move only in complex fluids. Its propulsion characteristics are explored numerically in an Oldroyd-B fluid for finite Deborah numbers while the small Deborah number limit is investigated analytically using a second-order fluid model. We then derive expressions relating the propulsion speed to the rheological properties of the complex fluid, allowing thus to infer the normal stress coefficients in the fluid from the locomotion of the propeller. Our simple mechanism can therefore be used either as a non-Newtonian micro-propeller or as a micro-rheometer.

  9. Gauge Invariance and Symmetry Breaking by Topology and Energy Gap

    E-Print Network [OSTI]

    Heissenberg, Carlo

    2015-01-01

    For the description of observables and states of a quantum system, it may be convenient to use a canonical Weyl algebra of which only a subalgebra $\\mathcal A$, with a non-trivial center $\\mathcal Z$, describes observables, the other Weyl operators playing the role of intertwiners between inequivalent representations of $\\mathcal A$. In particular, this gives rise to a gauge symmetry described by the action of $\\mathcal Z$. A distinguished case is when the center of the observables arises from the fundamental group of the manifold of the positions of the quantum system. Symmetries which do not commute with the topological invariants represented by elements of $\\mathcal Z$ are then spontaneously broken in each irreducible representation of the observable algebra, compatibly with an energy gap; such a breaking exhibits a mechanism radically different from Goldstone and Higgs mechanisms. This is clearly displayed by the quantum particle on a circle, the Bloch electron and the two body problem.

  10. Lorentz Symmetry Breaking in $\\mathcal{N} =2$ Superspace

    E-Print Network [OSTI]

    Mir Faizal; Prince A. Ganai

    2015-09-09

    In this paper, we will study the deformation of a three dimensional theory with $\\mathcal{N} =2$ supersymmetry. This theory will be deformed by the presence of a constant vector field. This deformation will break the Lorentz symmetry. So, we will analyse this theory using $\\mathcal{N} =2$ aether superspace. The $\\mathcal{N} =2$ aether superspace will be obtained from a deformation of the usual $\\mathcal{N} =2$ superspace. This will be done by deforming the generators of the three dimensional $\\mathcal{N} =2$ supersymmetry. After analysing this deformed superalgebra, we will derive an explicit expression for the superspace propagators in this deformed superspace. Finally, we will use these propagators for performing perturbative calculations.

  11. Flavour symmetry breaking in the kaon parton distribution amplitude

    SciTech Connect (OSTI)

    Shi, Chao [Nanjing Univ. (China). Key Lab. of Modern Acoustics and Dept. of Physics.; Chang, Lei [Univ. of Adelaide, Adelaide (Australia). School of Chemistry and Physics.; Roberts, Craig D. [Argonne National Lab., Argonne, IL (United States). Physics Div.; Schmidt, Sebastian M. [Forschungszentrum Julich and JARA, Julich (Germany). Inst. for Advanced Simulation.; Tandy, Peter C. [Kent State Univ., Kent, OH (United States). Center for Nuclear Research.; Zong, Hong -shi [Nanjing Univ. (China). Key Lab. of Modern Acoustics; Institute of Theoretical Physics, Beijing (China). State Key Lab. of Theoretical Physics; Nuclear Physics and Cosmology, Nanjing (China). Joint Center for Particle.

    2014-11-01

    We compute the kaon's valence-quark (twist-two parton) distribution amplitude (PDA) by projecting its Poincaré-covariant Bethe–Salpeter wave-function onto the light-front. At a scale ? = 2 GeV, the PDA is a broad, concave and asymmetric function, whose peak is shifted 12–16% away from its position in QCD's conformal limit. These features are a clear expression of SU(3)-flavour-symmetry breaking. They show that the heavier quark in the kaon carries more of the bound-state's momentum than the lighter quark and also that emergent phenomena in QCD modulate the magnitude of flavour-symmetry breaking: it is markedly smaller than one might expect based on the difference between light-quark current masses. Our results add to a body of evidence which indicates that at any energy scale accessible with existing or foreseeable facilities, a reliable guide to the interpretation of experiment requires the use of such nonperturbatively broadened PDAs in leading-order, leading-twist formulae for hard exclusive processes instead of the asymptotic PDA associated with QCD's conformal limit. We illustrate this via the ratio of kaon and pion electromagnetic form factors: using our nonperturbative PDAs in the appropriate formulae, FK/F?=1.23 at spacelike-Q2=17 GeV2, which compares satisfactorily with the value of 0.92(5) inferred in e+e- annihilation at s=17 GeV2.

  12. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

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

    2002-01-01

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

  13. RNA sequencing for the study of splicing

    E-Print Network [OSTI]

    Gonza?lez-Porta, Mar

    2014-10-07

    segments in the DNA. In their experiments, they hybridised adenoviral mRNAs with complemen- tary single stranded DNA fragments, and following observation with electron microscopy (EM), they detected alternate double stranded and single stranded stretches... [Saltzman et al., 2011]. Overall, the above mentioned processes guarantee that splicing occurs in an ac- curate albeit flexible fashion. The accuracy of splicing is further increased by the many rearrangements that are required before the actual intron...

  14. Electromagnetic Signals from Bacterial DNA

    E-Print Network [OSTI]

    A. Widom; J. Swain; Y. N. Srivastava; S. Sivasubramanian

    2012-02-09

    Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although is is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals hold true for muck lower frequencies. In E. coli bacteria such electromagnetic signals can be generated by electric transitions between energy levels describing electrons moving around DNA loops. The electromagnetic signals between different bacteria within a community is a "wireless" version of intercellular communication found in bacterial communities connected by "nanowires". The wireless broadcasts can in principle be of both the AM and FM variety due to the magnetic flux periodicity in electron energy spectra in bacterial DNA orbital motions.

  15. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01

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

  16. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-13

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

  17. Symmetry Breaking Synchrony Breaking

    E-Print Network [OSTI]

    Darcy, Isabel K.

    Joints on Staffa near Mull ­ p. 9/4 #12;Columns along Snake River ­ p. 10/4 #12;Irish Giants Causeway ­ p/4 #12;Mud Plains ­ p. 3/4 #12;Leopard Spots ­ p. 4/4 #12;Sand Dunes in Namibian Desert ­ p. 5/4 #12 translation in one direction Sand dunes, zebra Spots: states centered at lattice points mud plains, leopard

  18. Instant uplifted inflation: A solution for a tension between inflation and SUSY breaking scale

    E-Print Network [OSTI]

    Yusuke Yamada

    2013-06-04

    The Hubble parameter during the inflationary era must be smaller than the gravitino mass if the moduli are stabilized by the Kachru-Kallosh-Linde-Trivedi mechanism. This condition represents the difficulty to combine the low scale SUSY breaking and the high scale inflation. We propose a simple mechanism which can naturally separate the inflation scale from the SUSY breaking scale today.

  19. Large-Scale Flow Response to the Breaking of Mountain Gravity Waves

    E-Print Network [OSTI]

    Lott, Francois

    Large-Scale Flow Response to the Breaking of Mountain Gravity Waves François Lott, LMD, Ecole and synoptic impacts of mountain gravity waves breaking observations Some diagnostics tools Parameterization in weather prediction and climate models 3) Interaction between a front and an idealised mountain massive

  20. 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.

    2009-12-01

    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.

  1. Huliq:Breaking News Submit News Login Linear Nanotubes Offer Path To High-Performance Electronics

    E-Print Network [OSTI]

    Rogers, John A.

    Huliq:Breaking News Submit News Login Linear Nanotubes Offer Path To High-Performance Electronics.MoSys.com Page 1 of 2Linear nanotubes offer path to high-performance electronics | Huliq: Breaking News 3/28/2007http://www.huliq.com/16423/linear-nanotubes-offer-path-to-high-performance-electronics #12;compared

  2. 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

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

    E-Print Network [OSTI]

    Bapat, Bhas

    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-UP OF MOLECULES USING SOFT X-RAYS RRCAT INDORE, JUNE 2012 3 / 27 #12;INTRODUCTION MOLECULES A molecule may

  4. Short communication A new breaking wave height direct estimator from video imagery

    E-Print Network [OSTI]

    Short communication A new breaking wave height direct estimator from video imagery Rafael Almar a, laborious and limited to short term and localized field observations car- ried out on an energetic bathymetry through depth- inversion algorithms, where wave celerities or a proxy for wave breaking energy

  5. 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

    2014-01-01

    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 ...

  6. 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)

    1992-01-01

    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.

  7. Scales of Fermion Mass Generation and Electroweak Symmetry Breaking

    E-Print Network [OSTI]

    Duane A. Dicus; Hong-Jian He

    2005-06-11

    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 $\

  8. Path integrals and symmetry breaking for optimal control theory

    E-Print Network [OSTI]

    H. J. Kappen

    2005-10-07

    This paper considers linear-quadratic control of a non-linear dynamical system subject to arbitrary cost. I show that for this class of stochastic control problems the non-linear Hamilton-Jacobi-Bellman equation can be transformed into a linear equation. The transformation is similar to the transformation used to relate the classical Hamilton-Jacobi equation to the Schr\\"odinger equation. As a result of the linearity, the usual backward computation can be replaced by a forward diffusion process, that can be computed by stochastic integration or by the evaluation of a path integral. It is shown, how in the deterministic limit the PMP formalism is recovered. The significance of the path integral approach is that it forms the basis for a number of efficient computational methods, such as MC sampling, the Laplace approximation and the variational approximation. We show the effectiveness of the first two methods in number of examples. Examples are given that show the qualitative difference between stochastic and deterministic control and the occurrence of symmetry breaking as a function of the noise.

  9. Lyman-break galaxies are they young spheroids?

    E-Print Network [OSTI]

    Matteucci, F

    2002-01-01

    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.

  10. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

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

    2005-11-01

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

  11. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

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

  12. DNA

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost Ground8 GasDEVELOPMENTS E P I IT h it cdrives

  13. DNA

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

    blueprint of a bacterium's "molecular machinery," showing how bacterial immune systems fight off the viruses that infect them. By tracking down how bacterial defense systems work,...

  14. Base Excision by Thymine DNA Glycosylase Mediates DNA-Directed Cytotoxicity of 5-Fluorouracil 

    E-Print Network [OSTI]

    Selfridge J.; Schar P.; Lettieri T.; Schuermann D.; Saito Y.; Focke F.; Kunz C.

    2009-04-01

    5-Fluorouracil (5-FU), a chemotherapeutic drug commonly used in cancer treatment, imbalances nucleotide pools, thereby favoring misincorporation of uracil and 5-FU into genomic DNA. The processing of these bases by DNA repair activities was proposed...

  15. 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 (13), or the virus capsid itself (14­16), either upon addition of spermine (Spm4þ ) or in a monovalent

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

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01

    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,

  17. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

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

    2013-07-16

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

  18. DNA: The Strand that Connects Us All

    SciTech Connect (OSTI)

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

    2011-03-29

    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.

  19. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

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

    1992-05-12

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

  20. 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 ...

  1. Odd-Parity Superconductivity in the Vicinity of Inversion Symmetry Breaking in Spin-Orbit-Coupled Systems

    E-Print Network [OSTI]

    Kozii, Vladyslav

    We study superconductivity in spin-orbit-coupled systems in the vicinity of inversion symmetry breaking. We find that, because of the presence of spin-orbit coupling, fluctuations of the incipient parity-breaking order ...

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

    SciTech Connect (OSTI)

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

    2013-05-14

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

  3. 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

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

    E-Print Network [OSTI]

    Nielsen, Rasmus

    Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible reported the successful extraction of ancient DNA (aDNA) from both frozen and nonfrozen sediments (even sediments up to 3300 years old at 2 cave sites in the North Island of New Zealand. These sites are ideal

  5. Dellaporta DNA Extraction Citation: Stephen L. Dellaporta,Jonathan Wood , James B. Hicks. A plant DNA

    E-Print Network [OSTI]

    Wurtele, Eve Syrkin

    1 Dellaporta DNA Extraction Citation: Stephen L. Dellaporta,Jonathan Wood , James B. Hicks. A plant supernatant and lightly dry DNA pellets by inverting the tubes on paper towels for 10 min. #12;4 12. Redissolve each DNA pellet with 0.7 mL EB2. May need to let sit overnight at 4°C if having trouble dissolving

  6. Particle-Hole Symmetry Breaking in the Pseudogap State of Bi2201

    SciTech Connect (OSTI)

    Hashimoto, M.; /SIMES, Stanford /Stanford U., Geballe Lab. /LBNL, ALS; He, R.-H.; /aff SIMES, Stanford /Stanford U., Geballe Lab.; Tanaka, K.; /aff SIMES, Stanford /Stanford U., Geballe Lab. /LBNL, ALS /Osaka U.; Testaud, J.P.; /SIMES, Stanford /Stanford U., Geballe Lab. /LBNL, ALS; Meevasana1, W.; Moore, R.G.; Lu, D.H.; /SIMES, Stanford /Stanford U., Geballe Lab.; Yao, H.; /SIMES, Stanford; Yoshida, Y.; Eisaki, H.; /AIST, Tsukuba; Devereaux, T.P.; /SIMES, Stanford /Stanford U., Geballe Lab.; Hussain, Z.; /LBNL, ALS; Shen, Z.-X.; /SIMES, Stanford /Stanford U., Geballe Lab.

    2011-08-19

    In conventional superconductors, a gap exists in the energy absorption spectrum only below the transition temperature (T{sub c}), corresponding to the energy price to pay for breaking a Cooper pair of electrons. In high-T{sub c} cuprate superconductors above T{sub c}, an energy gap called the pseudogap exists, and is controversially attributed either to pre-formed superconducting pairs, which would exhibit particle-hole symmetry, or to competing phases which would typically break it. Scanning tunnelling microscopy (STM) studies suggest that the pseudogap stems from lattice translational symmetry breaking and is associated with a different characteristic spectrum for adding or removing electrons (particle-hole asymmetry). However, no signature of either spatial or energy symmetry breaking of the pseudogap has previously been observed by angle-resolved photoemission spectroscopy (ARPES). Here we report ARPES data from Bi2201 which reveals both particle-hole symmetry breaking and dramatic spectral broadening indicative of spatial symmetry breaking without long range order, upon crossing through T* into the pseudogap state. This symmetry breaking is found in the dominant region of the momentum space for the pseudogap, around the so-called anti-node near the Brillouin zone boundary. Our finding supports the STM conclusion that the pseudogap state is a broken-symmetry state that is distinct from homogeneous superconductivity.

  7. Garcinol, a Histone Acetyltransferase Inhibitor, Radiosensitizes Cancer Cells by Inhibiting Non-Homologous End Joining

    SciTech Connect (OSTI)

    Oike, Takahiro; Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo; Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma ; Ogiwara, Hideaki; Torikai, Kohta; Nakano, Takashi; Yokota, Jun; Kohno, Takashi

    2012-11-01

    Purpose: Non-homologous end joining (NHEJ), a major pathway used to repair DNA double-strand breaks (DSBs) generated by ionizing radiation (IR), requires chromatin remodeling at DSB sites through the acetylation of histones by histone acetyltransferases (HATs). However, the effect of compounds with HAT inhibitory activities on the DNA damage response (DDR), including the NHEJ and cell cycle checkpoint, as well as on the radiosensitivity of cancer cells, remains largely unclear. Here, we investigated whether garcinol, a HAT inhibitor found in the rinds of Garcinia indica fruit (called mangosteens), has effects on DDR, and whether it can be used for radiosensitization. Methods and Materials: The following assays were used to examine the effect of garcinol on the inhibition of DSB repair, including the following: a conventional neutral comet assay; a cell-based assay recently developed by us, in which NHEJ repair of DSBs on chromosomal DNA was evaluated; the micrococcal nuclease sensitivity assay; and immunoblotting for autophosphorylation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs). We assessed the effect of garcinol on the cell cycle checkpoint after IR treatment by analyzing the phosphorylation levels of checkpoint kinases CHK1 and CHK2 and histone H3, and by cell cycle profile analysis using flow cytometry. The radiosensitizing effect of garcinol was assessed by a clonogenic survival assay, whereas its effects on apoptosis and senescence were examined by annexin V and senescence-associated {beta}-galactosidase (SA-{beta}-Gal) staining, respectively. Results: We found that garcinol inhibits DSB repair, including NHEJ, without affecting cell cycle checkpoint. Garcinol radiosensitized A549 lung and HeLa cervical carcinoma cells with dose enhancement ratios (at 10% surviving fraction) of 1.6 and 1.5, respectively. Cellular senescence induced by IR was enhanced by garcinol. Conclusion: These results suggest that garcinol is a radiosensitizer that inhibits NHEJ and facilitates senescence without impairing activation of the cell cycle checkpoint.

  8. The effects of similarity breaking on the intracluster medium

    E-Print Network [OSTI]

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

    2002-03-28

    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.

  9. Moduli stabilization, F-term uplifting and soft supersymmetry breaking terms

    E-Print Network [OSTI]

    Hiroyuki Abe; Tetsutaro Higaki; Tatsuo Kobayashi; Yuji Omura

    2007-01-21

    We study moduli stabilization with F-term uplifting. As a source of uplifting F-term, we consider spontaneous supersymmetry breaking models, e.g. the Polonyi model and the Intriligator-Seiberg-Shih model. We analyze potential minima by requiring almost vanishing vacuum energy and evaluate the size of modulus F-term. We also study soft SUSY breaking terms. In our scenario, the mirage mediation is dominant in gaugino masses. Scalar masses can be comparable with gaugino masses or much heavier, depending on couplings with spontaneous supersymmetry breaking sector.

  10. Allostery through protein-induced DNA bubbles

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

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

    2015-03-12

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

  11. DNA Nanomechanical Switches under Folding Kinetics Control

    E-Print Network [OSTI]

    Meller, Amit

    DNA Nanomechanical Switches under Folding Kinetics Control Virgile Viasnoff,, Amit Meller operate at equilibrium under changes in solution composition. We propose an alternative DNA switch design after heat denaturation drives the switch to its lowest energy conformation, while rapid cooling (>100

  12. 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)

    2014-10-28

    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.

  13. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-10-18

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

  14. Prospects & Overviews Integrating DNA barcode data and

    E-Print Network [OSTI]

    DeSalle, Rob

    , and description Paul Z. Goldstein and Rob DeSalleà DNA barcodes, like traditional sources of taxonomic information interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance

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

    SciTech Connect (OSTI)

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

    2010-06-21

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

  16. Elastic and Proton Dynamics of the DNA

    E-Print Network [OSTI]

    V. L. Golo

    2008-03-28

    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.

  17. Programmable DNA-mediated multitasking processor

    E-Print Network [OSTI]

    Shu, Jian-Jun; Yong, Kian-Yan; Shao, Fangwei; Lee, Kee Jin

    2015-01-01

    Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.

  18. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

    Sessler, A.M.; Dawson, J.

    1993-12-14

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

  19. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

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

    2006-06-06

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

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

    SciTech Connect (OSTI)

    Geard, Charles R.

    2014-12-12

    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.

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

    SciTech Connect (OSTI)

    Niklas, Martin; Abdollahi, Amir; Akselrod, Mark S.; Debus, Jürgen; Jäkel, Oliver; and others

    2013-12-01

    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.

  2. Particulate Carrier Systems for Mucosal DNA Vaccine Delivery

    E-Print Network [OSTI]

    Borchard, Gerrit

    2006-10-26

    Streptomyces griseus Stop solution: 1M KOH In humans: degradation by lysozyme Incubation with chitosanase (1) GPEN 2006 Free DNA chitoplexes Incubation with chitosanase, 37?C Intact DNA ? Degraded chitosan Intact DNA ? Extraction with phenol: chloroform... Streptomyces griseus Stop solution: 1M KOH In humans: degradation by lysozyme Incubation with chitosanase (1) GPEN 2006 Free DNA chitoplexes Incubation with chitosanase, 37?C Intact DNA ? Degraded chitosan Intact DNA ? Extraction with phenol: chloroform...

  3. Wave breaking over sloping beaches using a coupled boundary integral-level set method

    SciTech Connect (OSTI)

    Garzon, M.; Adalsteinsson, D.; Gray, L.; Sethian, J.A.

    2003-12-08

    We present a numerical method for tracking breaking waves over sloping beaches. We use a fully non-linear potential model for in-compressible, irrotational and inviscid flow, and consider the effects of beach topography on breaking waves. The algorithm uses a Boundary Element Method (BEM) to compute the velocity at the interface, coupled to a Narrow Band Level Set Method to track the evolving air/water interface, and an associated extension equation to update the velocity potential both on and off the interface. The formulation of the algorithm is applicable to two and three dimensional breaking waves; in this paper, we concentrate on two-dimensional results showing wave breaking and rollup, and perform numerical convergence studies and comparison with previous techniques.

  4. TRAC-PD2 modeling of LOFT and PWR small cold-leg breaks

    SciTech Connect (OSTI)

    Knight, T.D.; Willcutt, G.J.E. Jr.; Lime, J.F.

    1981-01-01

    The Transient Reactor Analysis Code (TRAC) is being developed at the Los Alamos National Laboratory to provide advanced best-estimate predictions of postulated accidents in light-water reactors. TRAC-PD2, the latest publicly released version of the code, is currently being tested against small-break and other transients in experimental facilities; it is also being used to analyze postulated accidents in commercial power reactors. Calculated results for LOFT small-break experiments are compared to data, and the results from two small-break calculations for two different reactor systems are presented. It is concluded that TRAC-PD2 is useful for the analysis of cold-leg small-break accidents.

  5. Design Considerations for Monopile Founded Offshore Wind Turbines Subject to Breaking Waves 

    E-Print Network [OSTI]

    Owens, Garrett Reese 1987-

    2012-11-26

    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...

  6. Largest Federally Owned Wind Farm Breaks Ground at U.S. Weapons...

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

    Largest Federally Owned ... Largest Federally Owned Wind Farm Breaks Ground at U.S. Weapons Facility Posted: August 13, 2013 - 12:01pm WASHINGTON - Building on President Obama's...

  7. 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.

    2011-07-01

    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.

  8. Nonequilibrium superconducting thin films with sub-gap and pair-breaking photon illumination

    E-Print Network [OSTI]

    Guruswamy, T.; Goldie, D. J.; Withington, S.

    2015-04-08

    We calculate nonequilibrium quasiparticle and phonon distributions for a number of widely-used low transition temperature thin-film superconductors under constant, uniform illumination by sub-gap probe and pair-breaking signal photons simultaneously...

  9. Photo of the Week: Record-Breaking Solar Cells | Department of...

    Broader source: Energy.gov (indexed) [DOE]

    Solar Junction, in partnership with NREL, has developed solar cells that reach a record-breaking 44 percent efficiency -- meaning that more than 40 percent of the sunlight the...

  10. Polar Kerr Effect and Time Reversal Symmetry Breaking in Bilayer Graphene

    E-Print Network [OSTI]

    Nandkishore, Rahul Mahajan

    The unique sensitivity of optical response to different types of symmetry breaking can be used to detect and identify spontaneously ordered many-body states in bilayer graphene. We predict a strong response at optical ...

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

    E-Print Network [OSTI]

    Weymouth, Gabriel David

    2008-01-01

    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. ...

  12. The Nature of the Far-UV Break in the Energy Distribution of Quasars

    E-Print Network [OSTI]

    L. Binette; S. Haro-Corzo; Y. Krongold; A. C. Andersen

    2007-06-13

    A prominent continuum steepening is observed in quasar energy distributions near 1100A. We review possible interpretations for the physical origin of this so-called far-UV break.

  13. Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations...

    Office of Scientific and Technical Information (OSTI)

    Conference: Microfluidics: Kinetics of Hybridized DNA With Fluid Flow Variations. Citation Details In-Document Search Title: Microfluidics: Kinetics of Hybridized DNA With Fluid...

  14. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

    Bridges DNA Base and Nucleotide Excision Repair Pathways Print Alkyltransferase proteins (AGT) protect cells from the biological effects of DNA damage caused by the addition...

  15. 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...

  16. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

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

  17. Simulation of a small break loss of coolant accident conducted at the BETHSY Integral Test Facility 

    E-Print Network [OSTI]

    Bott, Charles Patrick

    1992-01-01

    systems where the interaction mechanisms themselves are complex and contain uncertainties. Early analysis of reactor accidents concentrated on severe accident scenarios in- volving large piping ruptures in the coolant system. These were seen... as the design basis accident for the systems, since, if the system could survive such a, scenario and maintain fuel cladding integrity, any smaller piping break would be a less severe ac- cident of one already evaluated. The duration of these large break loss...

  18. Spontaneous breaking of SU(3) to finite family symmetries: a pedestrian's approach

    E-Print Network [OSTI]

    Christoph Luhn

    2011-01-12

    Non-Abelian discrete family symmetries play a pivotal role in the formulation of models with tri-bimaximal lepton mixing. We discuss how to obtain symmetries such as A4, semidirect product of Z7 and Z3, and Delta(27) from an underlying SU(3) gauge symmetry. Higher irreducible representations are required to achieve the spontaneous breaking of the continuous group. We present methods of identifying the required vacuum alignments and discuss in detail the symmetry breaking potentials.

  19. On the local properties of highly nonlinear unsteady gravity water waves. Part 2. Dynamics and onset of breaking

    E-Print Network [OSTI]

    Barthelemy, X; Peirson, W L; Fedele, F; Allis, M; Dias, F

    2015-01-01

    We revisit the classical, but as yet unresolved problem of predicting the breaking onset of 2D and 3D irrotational gravity water waves. This study focuses on domains with flat bottom topography and conditions ranging from deep to intermediate depth (depth to wavelength ratio between 1 and 0.2). Using a fully-nonlinear boundary element model, our initial calculations investigated geometric, kinematic and energetic differences between maximally recurrent and marginally breaking waves in focusing wave groups. Maximallyrecurrent waves are clearly separated from marginally-breaking waves by their energy fluxes localized near the crest region. Specifically, tracking the local ratio of energy flux velocity to crest speed at the crest of the tallest wave in the evolving group provides a robust breaking onset threshold parameter. Warning of imminent breaking onset was found to depend on the strength of breaking, but was detectable only up to half a carrier wave period prior to a breaking event.

  20. Career Break Record of Contact Days Staff on a career break may, by agreement with their Head of School/Unit, undertake a number of days'

    E-Print Network [OSTI]

    Brierley, Andrew

    with their Head of School/Unit, undertake a number of days' paid work during their career break ("contact days"). The type of work undertaken is a matter of agreement between the member of staff and the Head of School/Unit: _________________________________________________________________ Staff ID/NI Number/ Date of Birth:_________________________________________ School/Unit

  1. Gel Electrophoresis of Gold-DNA Nanoconjugates

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

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

    2007-01-01

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

  2. Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

    E-Print Network [OSTI]

    Yuan-Yan Wu; Zhong-Liang Zhang; Jin-Si Zhang; Xiao-Long Zhu; Zhi-Jie Tan

    2015-07-10

    Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Cobalt Hexammine ion (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive.However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become internal binding into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit external binding to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.

  3. 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)

    2002-01-01

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

  4. Nanopores formed by DNA origami: a review

    E-Print Network [OSTI]

    Bell, Nicholas A. W.; Keyser, Ulrich F.

    2014-06-10

    , coated with hydrophobic moieties, into a lipid bilayer. Recent work in these two branches is now discussed. Hybrid nanopores formed by trapping DNA origami onto a solid state nanopore The combination of DNA origami and solid state nanopores was first... (1982) Nucleic acid junctions and lattices. J. Theor. Biol. 99, 237–47. 28 Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440, 297– 302. 29 Kuzyk A, Schreiber R, Fan Z, Pardatscher G, Roller E-M, Högele A, Simmel FC...

  5. Characterization of GSTA3 Gene Products in Multiple Species and Demonstration of their Conservation in Divergent Species 

    E-Print Network [OSTI]

    Peer, Shawna Marie

    2015-05-12

    of all species investigated including those used as reference ……………………………………….. 51 7 Double stranded DNA sequences of the putative amplicons of GSTA1 and GSTA3 with primer binding sites for primers used... in qRT-PCR highlighted to demonstrate the primers’ specificity for GSTA3 ……………………….. 56 !ix LIST OF TABLES TABLE Page 1 Critical amino acids (AA) for 3-ketosteroid isomerase activity of GSTA3....... 13 2 PCR primer...

  6. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08

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

  7. Casting inorganic structures with DNA molds

    E-Print Network [OSTI]

    Sun, Wei

    We report a general strategy for designing and synthesizing inorganic nanostructures with arbitrarily prescribed three-dimensional shapes. Computationally designed DNA strands self-assemble into a stiff “nanomold” that ...

  8. Deoxyribose oxidation chemistry and endogenous DNA adducts

    E-Print Network [OSTI]

    Zhou, Xinfeng

    2006-01-01

    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. Ubiquitylation, neddylation and the DNA damage response

    E-Print Network [OSTI]

    Brown, Jessica S.; Jackson, Stephen P.

    2015-04-01

    , collectively termed the DNA damage response (DDR), requires the recruitment and subsequent post-translational modification (PTM) of a complex network of proteins. Ubiquitin and the ubiquitin-like protein (UBL) SUMO have established roles in regulating...

  10. NIJ-Funded Research in Forensic DNA

    E-Print Network [OSTI]

    Standards Funding from the FBI S&T Branch through NIST Information Access Division httpDNA) · Technology Evaluation and Development ­ Rapid multiplex PCR protocols* (PCR: 3 hr to FBI

  11. Intriguing DNA Editor Has a Structural Trigger

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

    "plug in" very specific snippets of DNA coding for a variety of reasons. For example, microbes could be re-engineered to consume specific environmental toxins or to produce better...

  12. 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 ...

  13. Extracting biological knowledge from DNA sequences

    SciTech Connect (OSTI)

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

    1996-12-31

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

  14. 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

  15. Synopsis: Repulsion Helps Virus Pack DNA APS/Joan Tycko

    E-Print Network [OSTI]

    Smith, Douglas E.

    Synopsis: Repulsion Helps Virus Pack DNA APS/Joan Tycko Repulsive DNA-DNA Interactions Accelerate, and Douglas E. Smith Phys. Rev. Lett. 112, 248101 (2014) Published June 17, 2014 Featured in Physics Editors reported in Physical Review Letters show that, surprisingly, switching the DNA self-interaction from

  16. DNA Concentration By UV Spectrophotometry Measure Absorption

    E-Print Network [OSTI]

    Aris, John P.

    DNA Concentration By UV Spectrophotometry Measure Absorption: 1. Dilute DNA to 0.5 to 50 µg/ml in TE buffer or dH2O. Plan to use a quartz cuvette or a UV-transparent plastic (disposable) cuvette (1 2. Measure absorption at 260 nm (A260). Start by zeroing instrument with TE buffer or dH2O alone

  17. Overview of DNA Programs at NIST

    E-Print Network [OSTI]

    .nist.gov/mml/bmd/genetics/applied_genetics_pubs.cfm Pete Vallone Erica Butts DNA Biometrics Team Funding from the FBI S&T Branch through NIST Information http://www.cstl.nist.gov/strbase/NISTpub.htm +FBI-funding (DNA biometrics) Workshops 0 0 0 1 2 7 9 6 11) measurement calibration Required under FBI Quality Assurance Standard 9.5.5 for labs connected to the national

  18. 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

  19. Denaturation of DNA at high salt concentrations

    E-Print Network [OSTI]

    Maity, Arghya; Singh, Navin

    2015-01-01

    Cations present in the solution are important for the stability of two negative strands of DNA molecules. Experimental as well as theoretical results show that the DNA molecule is more stable as the concentration of salt (or cations) increases. It is known that the two strands of DNA molecule carry negative charge due to phosphate group along the strands. These cations act as a shielding particles to the two like charge strands. Recently, in an experiment it is shown that there is a critical value in the concentration of salts (or cations) that can stabilize the helical structure of DNA. If one add more salt in the solution beyond this critical value, the stability of the DNA molecule will disrupt. In this work we study the stability of DNA molecules at higher concentrations. How the stability at higher concentration can be explained through some theoretical calculations is the aim of this manuscript. We consider the PBD model with proper modifications that can explain the negative stability of the molecule a...

  20. Denaturation of DNA at high salt concentrations

    E-Print Network [OSTI]

    Arghya Maity; Amar Singh; Navin Singh

    2015-08-19

    Cations present in the solution are important for the stability of two negative strands of DNA molecules. Experimental as well as theoretical results show that the DNA molecule is more stable as the concentration of salt (or cations) increases. It is known that the two strands of DNA molecule carry negative charge due to phosphate group along the strands. These cations act as a shielding particles to the two like charge strands. Recently, in an experiment it is shown that there is a critical value in the concentration of salts (or cations) that can stabilize the helical structure of DNA. If one add more salt in the solution beyond this critical value, the stability of the DNA molecule will disrupt. In this work we study the stability of DNA molecules at higher concentrations. How the stability at higher concentration can be explained through some theoretical calculations is the aim of this manuscript. We consider the PBD model with proper modifications that can explain the negative stability of the molecule at higher concentration. Our findings are in close match with the experimental results.

  1. Effects of $?$-cluster breaking on 3$?$ cluster structures in $^{12}$C

    E-Print Network [OSTI]

    Tadahiro Suhara; Yoshiko Kanada-En'yo

    2015-02-17

    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.

  2. SU(3) breaking effects in hyperon beta decay from lattice QCD

    E-Print Network [OSTI]

    Shoichi Sasaki; Takeshi Yamazaki

    2006-10-13

    We present results of an exploratory study of flavor SU(3) breaking effects in hyperon beta decays using domain wall fermions. From phenomenological point of view, the significance of this subject is twofold: (1) to extract the element $V_{us}$ of the Cabibbo-Kabayashi-Maskawa mixing matrix from the $\\Delta S=1$ decay process, and (2) to provide vital information to analysis of the strange quark fraction of the proton spin with the polarized deep inelastic scattering data. In this study, we explore the $\\Xi^0 \\to \\Sigma^+$ beta decay, which is highly sensitive to the SU(3) breaking since this decay corresponds to the direct analogue of neutron beta decay under an exchange between the down quark and the strange quark. We expose the SU(3) breaking effect on $g_A/g_V=g_1(0)/f_1(0)$ up to the first order in breaking. The second-class form factors $g_2$ and $f_3$, of which non-zero values are the direct signals of the SU(3) breaking effect, are also measured. Finally, we estimate $f_1(0)$ up to the second-order correction and then evaluate $|V_{us}|$ combined with the KTeV experiment.

  3. Optical observations of GRB 060124 afterglow: A case for an injection break

    E-Print Network [OSTI]

    Kuntal Misra; D. Bhattacharya; D. K. Sahu; Ram Sagar; G. C. Anupama; A. J. Castro-Tirado; S. S. Guziy; B. C. Bhatt

    2007-01-15

    We present broad band optical afterglow observations of a long duration GRB 060124 using the 1.04-m Sampurnanand Telescope at ARIES, Nainital and the 2.01-m HCT at IAO, Hanle, including the earliest ground based observations in R band for this GRB. We determine the decay slope of the light curve at different bands and examine the reality of a proposed jet break. We use data from our observations as well as others reported in the literature to construct light curves in different bands and make power law fits to them. The spectral slope of the afterglow emission in the optical band is estimated. Our first R-band observations were taken $\\sim 0.038$~d after burst. We find that all available optical data after this epoch are well fit by a single power law, with a temporal flux decay index $\\alpha\\sim 0.94$. We do not find any evidence of a jet break within our data, which extend till $\\sim 2$~d after the burst. The X-ray light curve, however, shows a distinct break around 0.6 day. We attribute this break to a steepening of the electron energy spectrum at high energies. We conclude that the above measurements are consistent with the picture of a standard fireball evolution with no jet break within $t\\sim 2$~days after the burst. This sets a lower limit of $3\\times 10^{50}$~erg to the total energy released in the explosion.

  4. The evolution of the break preclusion concept for nuclear power plants in Germany

    SciTech Connect (OSTI)

    Schulz, H.

    1997-04-01

    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.

  5. G-quadruplex recognition and isolation with small molecules

    E-Print Network [OSTI]

    Müller, Sebastian

    2011-01-11

    azodicarboxylate DDR DNA damage response DMEM Dulbecco’s modified eagles medium DMSO dimethyl sulfoxide DNA deoxyribonucleic acid Dr. doctor ds-DNA double-stranded DNA equiv. equivalent(s) EDTA ethylenediaminetetraacetate e.g. exempli gratia EBr ethidium bromide Et... OAc ethyl acetate EtOH ethanol FACS fluorescence-activated cell sorting FAM 6-carboxyfluorescein FANCJ Fanconi anemia group J protein FCS fetal calf serum FRET Fo¨rster resonance energy transfer g gram G guanine GFP green fluorescent protein GI50 half...

  6. Method for in vitro recombination

    SciTech Connect (OSTI)

    Gibson, Daniel Glenn; Smith, Hamilton O

    2013-05-07

    The present invention relates to an in vitro method, using isolated protein reagents, for joining two double-stranded (ds) DNA molecules of interest, wherein the distal region of the first DNA molecule and the proximal region of the second DNA molecule share a region of sequence identity. The method allows the joining of a number of DNA fragments, in a predetermined order and orientation, without the use of restriction enzymes. It can be used, e.g., to join synthetically produced sub-fragments of a gene or genome of interest.

  7. Universal power law for the energy spectrum of breaking Riemann waves

    E-Print Network [OSTI]

    Dmitry Pelinovsky; Efim Pelinovsky; Elena Kartashova; Tatjana Talipova; Ayrat Giniyatullin

    2013-06-30

    The universal power law for the spectrum of one-dimensional breaking Riemann waves is justified for the simple wave equation. The spectrum of spatial amplitudes at the breaking time $t = t_b$ has an asymptotic decay of $k^{-4/3}$, with corresponding energy spectrum decaying as $k^{-8/3}$. This spectrum is formed by the singularity of the form $(x-x_b)^{1/3}$ in the wave shape at the breaking time. This result remains valid for arbitrary nonlinear wave speed. In addition, we demonstrate numerically that the universal power law is observed for long time in the range of small wave numbers if small dissipation or dispersion is accounted in the viscous Burgers or Korteweg-de Vries equations.

  8. More on cosmological constraints on spontaneous R-symmetry breaking models

    SciTech Connect (OSTI)

    Hamada, Yuta; Kobayashi, Tatsuo [Department of Physics, Kyoto University, Kyoto, 606-8502 (Japan); Kamada, Kohei [Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, D-22607 (Germany); Ookouchi, Yutaka, E-mail: hamada@gauge.scphys.kyoto-u.ac.jp, E-mail: kohei.kamada@epfl.ch, E-mail: kobayash@gauge.scphys.kyoto-u.ac.jp, E-mail: yutaka.ookouchi@artsci.kyushu-u.ac.jp [Faculty of Arts and Science, Kyushu University, Fukuoka, 819–0395 (Japan)

    2014-01-01

    We study the spontaneous R-symmetry breaking model and investigate the cosmological constraints on this model due to the pseudo Nambu-Goldstone boson, R-axion. We consider the R-axion which has relatively heavy mass in order to complement our previous work. In this regime, model parameters, R-axions mass and R-symmetry breaking scale, are constrained by Big Bang Nucleosynthesis and overproduction of the gravitino produced from R-axion decay and thermal plasma. We find that the allowed parameter space is very small for high reheating temperature. For low reheating temperature, the U(1){sub R} breaking scale f{sub a} is constrained as f{sub a} < 10{sup 12?14} GeV regardless of the value of R-axion mass.

  9. 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

    2004-01-01

    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

  10. 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

    2004-01-01

    L ABORATORY Building a Market for Small Wind: The Break-Evenemployer. BUILDING A MARKET FOR SMALL WIND: T HE B REAK -E

  11. The influence of pairing correlations on the isospin symmetry breaking corrections of superallowed Fermi beta decays

    SciTech Connect (OSTI)

    Cal Latin-Small-Letter-Dotless-I k, A. E.; Gerceklioglu, M.; Selam, C.

    2013-05-15

    Within the framework of quasi-particle random phase approximation, the isospin breaking correction of superallowed 0{sup +} {yields} 0{sup +} beta decay and unitarity of Cabibbo-Kobayashi-Maskawa mixing matrix have been investigated. The broken isotopic symmetry of nuclear part of Hamiltonian has been restored by Pyatov's method. The isospin symmetry breaking correction with pairing correlations has been compared with the previous results without pairing. The effect of pairing interactions has been examined for nine superallowed Fermi beta decays; their parent nuclei are {sup 26}Al, {sup 34}Cl, {sup 38}K, {sup 42}Sc, {sup 46}V, {sup 50}Mn, {sup 54}Co, {sup 62}Ga, {sup 74}Rb.

  12. 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

    2014-11-10

    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.

  13. Symmetry breaking patterns and collective modes of spin-one color superconductors

    E-Print Network [OSTI]

    Tomas Brauner; Jin-yi Pang; Qun Wang

    2009-09-23

    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.

  14. 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)

    2012-10-15

    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.

  15. Spontaneous symmetry breaking in a two-doublet lattice Higgs model

    E-Print Network [OSTI]

    Randy Lewis; R. M. Woloshyn

    2010-09-01

    An SU(2) lattice gauge theory with two doublets of complex scalar fields is considered. All continuous symmetries are identified and, using the nonperturbative methods of lattice field theory, the phase diagram is mapped out by direct numerical simulation. Two-doublet models contain phase transitions that separate qualitatively distinct regions of the parameter space. In some regions global symmetries are spontaneously broken. For some special choices of the model parameters, the symmetry-breaking order parameter is calculated. The pattern of symmetry breaking is verified further through observation of Goldstone bosons.

  16. Multicritical Symmetry Breaking and Naturalness of Slow Nambu-Goldstone Bosons

    E-Print Network [OSTI]

    Tom Griffin; Kevin T. Grosvenor; Petr Horava; Ziqi Yan

    2013-09-02

    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.

  17. From Decay to Complete Breaking: Pulling the Strings in SU(2) Yang-Mills Theory

    SciTech Connect (OSTI)

    Pepe, M.; Wiese, U.-J.

    2009-05-15

    We study (2Q+1) strings connecting two static charges Q in (2+1)D SU(2) Yang-Mills theory. While the fundamental (2) string between two charges Q=(1/2) is unbreakable, the adjoint (3) string connecting two charges Q=1 can break. When a (4) string is stretched beyond a critical length, it decays into a (2) string by gluon pair creation. When a (5) string is stretched, it first decays into a (3) string, which eventually breaks completely. The energy of the screened charges at the ends of a string is well described by a phenomenological constituent gluon model.

  18. Mass Formulas Derived by Symmetry Breaking and Prediction of Masses on Heavy Flavor Hadrons

    E-Print Network [OSTI]

    Yi-Fang Chang

    2008-03-02

    The base is the Lagrangian of symmetry and its dynamical breaking or Higgs breaking. When the soliton-like solutions of the scalar field equations are substituted into the spinor field equations, in the approximation of non-relativity we derive the Morse-type potential, whose energy spectrum is the GMO mass formula and its modified accurate mass formula. According to the symmetry of s-c quarks, the heavy flavor hadrons which made of u,d and c quarks may be classified by SU(3) octet and decuplet. Then some simple mass formulas are obtained, from this we predict some masses of unknown hadrons.

  19. DNA nanotechnology: understanding and optimisation through simulation

    E-Print Network [OSTI]

    Thomas E. Ouldridge

    2014-11-07

    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.

  20. Unraveling siRNA Unzipping Kinetics with Graphene

    E-Print Network [OSTI]

    Santosh Mogurampelly; Swati Panigrahi; Dhananjay Bhattacharyya; A. K. Sood; Prabal K. Maiti

    2012-07-19

    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.

  1. Conditions for positioning of nucleosomes on DNA

    E-Print Network [OSTI]

    Michael Sheinman; Ho-Ryun Chung

    2015-04-29

    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.}

  2. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

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

    1986-01-01

    A method for the simultaneous flow cytometric measurement of the total DNA content and the level of DNA synthesis in normal and malignant cells is disclosed. The sensitivity of the method allows a study of cell cycle traverse rates for large scale cell populations as well as single cell measurements. A DNA stain such as propidium iodide is used as the probe for the measurement of total DNA content and a monoclonal antibody reactive with a DNA precursor such as bromodeoxyuridine (BrdU) is used as a probe for the measurement of BrdU uptake by the cells as a measure of DNA synthesis.

  3. Effects of thermolysis and ferrocyanide quenching on quantum-confined CdS stabilized by polynucleotides

    SciTech Connect (OSTI)

    Bigham, S.R.; Coffer, J.L. [Texas Christian Univ., Fort Worth, TX (United States)

    1993-12-31

    Cadmium sulfide semiconductor clusters in the quantum confined size regime (Q-CdS) may be successfully stabilized by double-stranded deoxyribonucleic acid (DNA) from calf thymus and E. Coli as well as by single-stranded ribonucleic acids (RNA) in the forms of Poly[A], Poly[C], Poly[G] and Poly [U]. These Q-CdS/ploynucleotide clusters exhibit broad trap emission characteristic of both cadmium and sulfur related defect sites at the semiconductor surface. Here the paper discusses differences in the nature of the stabilizer-cluster interaction between single-stranded and double-stranded polynucleotides, as probed by monitoring changes in photoluminescence after thermolysis or ferrocyanide addition. Thermolysis of Q-CdS/polynucleotide samples affects the interfacial interaction between cluster and stabilizer as demonstrated by a shift in the emission maximum and a change in quantum yield. Stern-Volmer analysis of photoluminescence quenching with ferrocyanide anions exhibits nonlinear behavior. Ferrocyanide anions quench the photoluminescene of Q-CdS/DNA approximately 38% more efficiently (in terms of integrated intensity) than Q-CdS/RNA after 0.17 mN addition. Such behavior suggests that single-stranded polynucleotides are better than double-stranded polynucleotides in terms of protecting the semiconductor surface from the highly negatively charged ferrocyanide anion.

  4. Role of global warming on the statistics of record-breaking temperatures S. Redner1,

    E-Print Network [OSTI]

    Redner, Sidney

    Role of global warming on the statistics of record-breaking temperatures S. Redner1, * and Mark R in Philadelphia, as a function of the number of years of observation. We then consider the case of global warming question arises: is global warming the cause of such heat waves or are they merely statistical fluctuations

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

    E-Print Network [OSTI]

    Balmforth, Neil

    displacement wave can lead to catastrophic erosional incision of a moraine damming a glacial lake incision can also breach moraines damming glacial lakes. In a few of these examples, the incipient channel of extreme climate conditions or intense glacier melting). However, several other dam-break events appear

  6. Role of Symmetry Breaking on the Optical Transitions in Lead-Salt Quantum Dots

    E-Print Network [OSTI]

    Van Stryland, Eric

    Role of Symmetry Breaking on the Optical Transitions in Lead-Salt Quantum Dots Gero Nootz to explain optical transitions in lead-salt QDs. Thus, while the band anisotropy of the bulk semiconductor functions. These studies clarify the controversy of the origin of spectral features in lead-salt QDs

  7. Analytical relation between quark confinement and chiral symmetry breaking in odd-number lattice QCD

    E-Print Network [OSTI]

    Hideo Suganuma; Takahiro M. Doi; Takumu Iritani

    2013-12-21

    To clarify the relation between confinement and chiral symmetry breaking in QCD, we consider a temporally odd-number lattice, with the temporal lattice size $N_t$ being odd. We here use an ordinary square lattice with the normal (nontwisted) periodic boundary condition for link-variables in the temporal direction. By considering ${\\rm Tr} (\\hat{U}_4\\hat{\

  8. A CP Based Branching Tool for Breaking Symmetries in Crude-Oil Operations Scheduling

    E-Print Network [OSTI]

    Grossmann, Ignacio E.

    A CP Based Branching Tool for Breaking Symmetries in Crude-Oil Operations Scheduling Sylvain Mouret Goals Optimize the schedule of operations for the crude-oil unloading and blending problem using in the MINLP model Use CP inference techniques to improve performance 1 / 14 #12;Crude-oil operations

  9. A Symmetry-Breaking Tool for the Optimization of Crude-Oil Operations Scheduling

    E-Print Network [OSTI]

    Grossmann, Ignacio E.

    A Symmetry-Breaking Tool for the Optimization of Crude-Oil Operations Scheduling Sylvain Mouret the schedule of operations for the crude-oil unloading and blending problem using a continuous and Mann (2003) #12;Crude-oil operations scheduling problem Scheduling horizon [0, H] 4 types of resources

  10. UNIVERSITY OF CALIFORNIA, SAN DIEGO MOLD: A System for Breaking Down Large Visualization

    E-Print Network [OSTI]

    Baden, Scott B.

    UNIVERSITY OF CALIFORNIA, SAN DIEGO MOLD: A System for Breaking Down Large Visualization and Post thanks go out to Scott Baden and Peter Diamessis for their countless hours of help with MOLD. Thanks (NPACI) under NSF contract ACI9619020, by the UC MICRO program award number 99-007, and by Sun

  11. Low-energy signals of strongly-coupled electroweak symmetry-breaking scenarios

    E-Print Network [OSTI]

    Antonio Pich; Ignasi Rosell; Joaquin Santos; Juan Jose Sanz-Cillero

    2015-10-12

    Generic strongly-coupled scenarios of electroweak symmetry breaking usually contain towers of heavy states. We analyze the imprints that the lightest bosonic excitations leave on the couplings of the low-energy electroweak effective Lagrangian. The different quantum numbers of the heavy states imply different patterns of low-energy couplings, with characteristic correlations which could be identified in future data samples.

  12. 2012 EAGE www.firstbreak.org 97 special topicfirst break volume 30, July 2012

    E-Print Network [OSTI]

    Ali, Mohammed

    . Such estimation could be useful for monitoring network design, seismic risk management, and also for adjustment© 2012 EAGE www.firstbreak.org 97 special topicfirst break volume 30, July 2012 Passive Seismic 1@seismik.cz Expected level of seismic activity caused by volumetric changes Miroslav Hallo,1 Leo Eisner2* and Mohammed

  13. Trends and breaks in per-capita carbon dioxide emissions, 1870-2028

    E-Print Network [OSTI]

    Lanne, Markku

    2003-01-01

    We consider per-capita carbon dioxide emission trends in 16 early developed countries over the period 1870-2028. Using a multiple-break time series method we find more evidence for very early downturns in per-capita trends ...

  14. NANODIAMOND DUST AND THE FAR-ULTRAVIOLET QUASAR BREAK Luc Binette,1

    E-Print Network [OSTI]

    Morisset, Christophe

    NANODIAMOND DUST AND THE FAR-ULTRAVIOLET QUASAR BREAK Luc Binette,1 Gladis Magris C.,2 Yair curve consisting of nanodiamonds, composed of terrestrial cubic diamonds or with surface impurities intrinsic dust model requires a mixture of both cubic diamonds and Allende nanodiamonds and provides

  15. The Direct Breaking of Internal Waves at Steep1 Topography2

    E-Print Network [OSTI]

    Klymak, Jody M.

    1 The Direct Breaking of Internal Waves at Steep1 Topography2 Jody M. Klymak, Sonya Legg, Matthew H steep "supercritical" topography (i.e. topography that is steeper than internal wave energy13, but in those cases their17 wavelengths are of similar scale to the topography, whereas here they are quite

  16. Variational Inference for Stick-Breaking Beta Process Priors John Paisley1

    E-Print Network [OSTI]

    Carin, Lawrence

    Variational Inference for Stick-Breaking Beta Process Priors John Paisley1 jpaisley-parameter IBP, and does not extend to the beta process presented in (Hjort, 1990). Recently, Paisley et al., 2007); we discuss this difference in Sec- tion 4. Paisley et al. (2010) presented an inference

  17. Stick-Breaking Beta Processes and the Poisson Process John Paisley1

    E-Print Network [OSTI]

    Jordan, Michael I.

    Stick-Breaking Beta Processes and the Poisson Process John Paisley1 David M. Blei3 Michael I to Paisley et al. (2010) can be obtained from the characterization of the beta process as a Poisson process beta pro- cess was derived by Paisley et al. (2010). The derivation re- lied on a limiting process

  18. 10/12/2004 Comp 120 Fall 2004 1 No class Thursday 14 October (Fall Break!)

    E-Print Network [OSTI]

    Bishop, Gary

    ·1 10/12/2004 Comp 120 Fall 2004 1 October 12 · No class Thursday 14 October (Fall Break!) · GB gone 17 through 20 October · Review for 2nd Exam on Tuesday 19 October · Ask Questions! 10/12/2004 Comp 120 Fall 2004 2 Chapter 1 · Computer Abstractions · Input/Output/Memory/Datapath/Control · Instruction

  19. Conformal symmetry breaking and degeneracy of high-lying unflavored mesons

    E-Print Network [OSTI]

    Kirchbach, Mariana; Compean, Cliffor; Raya, Alfredo

    2012-01-01

    We show that though conformal symmetry can be broken by the dilaton, such can happen without breaking the conformal degeneracy patterns in the spectra. We departure from S^1XS^3 slicing of AdS_5 noticing that the inverse radius, R, of S^3 relates to the temperature of the deconfinement phase transition and has to satisfy, \\hbar c/R >> \\Lambda_{QCD}. We then focus on the eigenvalue problem of the S^3 conformal Laplacian, given by 1/R^2 (K^2+1), with K^2 standing for the Casimir invariant of the so(4) algebra. Such a spectrum is characterized by a (K+1)^2 fold degeneracy of its levels, with K\\in [0,\\infty). We then break the conformal S^3 metric as, d\\tilde{s}^2=e^{-b\\chi} ((1+b^2) d\\chi^2 +\\sin^2\\chi (d\\theta ^2 +\\sin^2\\theta d\\varphi ^2)), and attribute the symmetry breaking scale, b\\hbar^2c^2/R^2, to the dilaton. We show that such a metric deformation is equivalent to a breaking of the conformal curvature of S^3 by a term proportional to b\\cot \\chi, and that the perturbed conformal Laplacian is equivalent to...

  20. A BreakEven Formulation for Evaluating Branch Predictor Energy Efficiency #

    E-Print Network [OSTI]

    Huang, Wei

    A Break­Even Formulation for Evaluating Branch Predictor Energy Efficiency # Michele Co, Dee A demonstrated that a better branch pre­ dictor can increase the energy­efficiency of the system, even if the new a simple, effective metric for eval­ uating the tradeoff between processor energy­efficiency and branch

  1. Short-pulse equation: well-posedness and wave breaking Dmitry Pelinovsky

    E-Print Network [OSTI]

    Pelinovsky, Dmitry

    Short-pulse equation: well-posedness and wave breaking Dmitry Pelinovsky Department of Mathematics-629 (2010) #12;Properties of the short-pulse equation The short-pulse equation is a model for propagation of ultra-short pulses with few cycles on the pulse scale [Schäfer, Wayne 2004]: uxt = u + 1 6 ` u3 ´ xx

  2. Short-pulse equation: well-posedness and wave breaking Dmitry Pelinovsky

    E-Print Network [OSTI]

    Pelinovsky, Dmitry

    Short-pulse equation: well-posedness and wave breaking Dmitry Pelinovsky Department of Mathematics, Communications in PDE 35, 613-629 (2010) #12;Properties of the short-pulse equation The short-pulse equation is a model for propagation of ultra-short pulses [Schäfer, Wayne 2004]: uxt = u + 1 6 ` u3´ xx , where all

  3. Generation, propagation, and breaking of an internal wave beam Heather A. Clark and Bruce R. Sutherlanda

    E-Print Network [OSTI]

    Sutherland, Bruce

    Generation, propagation, and breaking of an internal wave beam Heather A. Clark and Bruce R of internal gravity waves generated by the large-amplitude vertical oscillations of a circular cylinder predictions and experimental investigations of waves generated by small-amplitude cylinder oscillations

  4. Coherent States and Spontaneous Symmetry Breaking in Light Front Scalar Field Theory

    SciTech Connect (OSTI)

    Vary, J.P.; Chakrabarti, D.; Harindranath, A.; Lloyd, R.; Martinovic, L.; Spence, J.R.; /Iowa State U.

    2005-12-14

    Recently developed nuclear many-body techniques provide novel results when applied to constituent quark models and to light-front scalar field theory. We show how spontaneous symmetry breaking arises and is consistent with a coherent state ansatz in a variational treatment. The kink and the kink-antikink topological features are identified and the onset of symmetry restoration is demonstrated.

  5. Experimental and Theoretical Investigations of Energy Transfer and Hydrogen-Bond Breaking in the Water Dimer

    E-Print Network [OSTI]

    Reisler, Hanna

    Experimental and Theoretical Investigations of Energy Transfer and Hydrogen-Bond Breaking, Georgia 30322, United States *W Web-Enhanced Feature *S Supporting Information ABSTRACT: The hydrogen determination of the dissociation energy (D0) of (D2O)2. The value obtained, 1244 ± 10 cm-1 (14.88 ± 0.12 k

  6. Studying the Breaking Mechanism of Polymer-Based In-Situ Gelled Acids using Solid Breaker 

    E-Print Network [OSTI]

    Tian, Zhida

    2012-10-19

    of this study is to examine the working mechanisms of the solid breaker and the factors that affect the breaking time. The flowback of the spent acid and the core damage induced by it will also be assessed in detail. Viscosity and rheological experimental...

  7. IEEE Signal Processing Magazine, Special Issue: Big Data 1 Breaking the Curse of Dimensionality using

    E-Print Network [OSTI]

    IEEE Signal Processing Magazine, Special Issue: Big Data 1 Breaking the Curse of Dimensionality will discuss two promising tools to alleviate this curse when handling big data. First, instead of using full, Special Issue: Big Data 2 paper we show how to use this expertise to manage otherwise unmanageable big

  8. Information-Entropic for Travelling Solitons in Lorentz and CPT Breaking Systems

    E-Print Network [OSTI]

    R. A. C. Correa; Roldao da Rocha; A. de Souza Dutra

    2015-02-08

    In this work we group three research topics apparently disconnected, namely solitons, Lorentz symmetry breaking and entropy. Following a recent work [Phys. Lett. B 713 (2012) 304], we show that it is possible to construct in the context of travelling wave solutions a configurational entropy measure in functional space, from the field configurations. Thus, we investigate the existence and properties of travelling solitons in Lorentz and CPT breaking scenarios for a class of models with two interacting scalar fields. Here, we obtain a complete set of exact solutions for the model studied which display both double and single-kink configurations. In fact, such models are very important in applications that include Bloch branes, Skyrmions, Yang-Mills, Q-balls, oscillons and various superstring-motivated theories. We find that the so-called Configurational Entropy (CE) for travelling solitons, which we name as travelling Configurational Entropy (TCE), shows that the best value of parameter responsible to break the Lorentz symmetry is one where the energy density is distributed equally around the origin. In this way, the information-theoretical measure of travelling solitons in Lorentz symmetry violation scenarios opens a new window to probe situations where the parameters responsible for breaking the symmetries are random. In this case, the TCE selects the best value.

  9. Editing Functional Programs Without Breaking Them Edward Amsden Ryan Newton Jeremy Siek

    E-Print Network [OSTI]

    Tobin-Hochstadt, Sam

    Editing Functional Programs Without Breaking Them Edward Amsden Ryan Newton Jeremy Siek Indiana how general-purpose program- ming might proceed given this set of editing actions. Categories types to guide the editing opera- tions on terms. Rather than entering programs as text, programmers

  10. EFFECT OF MOISTURE ON BENDING AND BREAKING RESISTANCE (IF COMMERCIAL ORIENTED STRANDBOARDS1

    E-Print Network [OSTI]

    ) ABSTRACT This is ZI short addendum to an earlier paper (Wu and Suchsland 1997) on bending resistance (E.1EFFECT OF MOISTURE ON BENDING AND BREAKING RESISTANCE (IF COMMERCIAL ORIENTED STRANDBOARDS1 Qinglin the quality and performance of OSB. In an F ) ~ ~ ~ ~ ~ ~ ~ ~Wu and Suchsland However, the paper did

  11. 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

  12. Infrared Luminous Lyman Break Galaxies: A Population that Bridges LBGs and SCUBA Galaxies

    E-Print Network [OSTI]

    Huang, J.-S.; Rigopoulou, D.; Willner, S. P.; Papovich, C.; Shu, C.; Ashby, M. L. N.; Barmby, P.; Bundy, K.; Conselice, C. J.; Egami, E.; Pé rez-Gonzá lez, P. G.; Rosenberg, J. L.; Smith, H. A.; Wilson, Graham Wallace; Fazio, G. G.

    2005-11-20

    A deep mid- and far-infrared survey in the extended Groth strip (EGS) area gives 3.6 to 8 ?m flux densities or upper limits for 253 Lyman break galaxies (LBGs). The LBGs are a diverse population but with properties correlated ...

  13. AEGIS: Infrared Spectroscopy of an Infrared-luminous Lyman Break Galaxy at z = 3.01

    E-Print Network [OSTI]

    Huang, J.-S.; Rigopoulou, D.; Papovich, C.; Ashby, M. L. N.; Willner, S. P.; Ivison, R.; Laird, E. S.; Webb, T.; Wilson, Graham Wallace; Barmby, P.; Chapman, S.; Conselice, C. J.; McLeod, B.; Shu, C. G.; Smith, H. A.; Le Floc'h, E.; Egami, E.; Willmer, C. A. N.; Fazio, G. G.

    2007-05-01

    We report the detection of rest-frame 6.2 and 7.7 ?m emission features arising from polycyclic aromatic hydrocarbons (PAHs) in the Spitzer IRS spectrum of an infrared-luminous Lyman break galaxy at z = 3.01. This is currently ...

  14. Breaking NLM-MAC Generator Mohammad Ali Orumiehchiha1, Josef Pieprzyk1, and Ron Steinfeld2

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    of the cipher. Due to a high correlation between the input variables and the output sequences of the combiningBreaking NLM-MAC Generator Mohammad Ali Orumiehchiha1, Josef Pieprzyk1, and Ron Steinfeld2 1 Center generator, designed by HoonJae Lee, SangMin Sung, HyeongRag Kim, is the strengthened version of the LM

  15. Numerical Simulation of Breaking Waves Using Level-Set Navier-Stokes Method 

    E-Print Network [OSTI]

    Dong, Qian

    2010-07-14

    ) equations were employed for the prediction of nonlinear wave-interaction and wave-breaking phenomena over sloping beaches. In the level-set finite-analytic Navier-Stokes (FANS) method, the free surface is represented by the zero level-set function...

  16. Experimental Study on Kinematics and Dynamics of Breaking Waves in Deep Water 

    E-Print Network [OSTI]

    Lim, Ho Joon

    2011-10-21

    improved accuracy. This modified technique was used for measuring of a NaCl concentration in deionized water to validate a new normalization technique. In the second part of this thesis, a plunging breaking wave in deep water has been studied. Using...

  17. Remote sensing of breaking wave phase speeds with application to non-linear depth inversions

    E-Print Network [OSTI]

    Haller, Merrick

    Remote sensing of breaking wave phase speeds with application to non-linear depth inversions high-resolution remote sensing video and surface elevation records from fixed, in-situ wave gages. Wave phase speeds are extracted from the remote sensing data using a feature tracking technique, and local

  18. SUCTION BREAK TO CONTROL SLOPE-INDUCED MOISTURE VARIATION IN LAYERED COVERS

    E-Print Network [OSTI]

    Aubertin, Michel

    was not affected even after 78 days without water infiltration. Also, in situ tests with large precipitation lead capacity. This study showed that a suction break could be used to improve the performance of inclined CCBE jours sans infiltrations d'eau. Les essais d'infiltration avec des taux de précipitations élevés ont

  19. All Your Face Are Belong to Us: Breaking Facebook's Social Authentication

    E-Print Network [OSTI]

    Keromytis, Angelos D.

    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

  20. 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

  1. Low-energy signals of strongly-coupled electroweak symmetry-breaking scenarios

    E-Print Network [OSTI]

    Pich, Antonio; Santos, Joaquin; Sanz-Cillero, Juan Jose

    2015-01-01

    Generic strongly-coupled scenarios of electroweak symmetry breaking usually contain towers of heavy states. We analyze the imprints that the lightest bosonic excitations leave on the couplings of the low-energy electroweak effective Lagrangian. The different quantum numbers of the heavy states imply different patterns of low-energy couplings, with characteristic correlations which could be identified in future data samples.

  2. Numerical simulation of breaking waves by a multi-scale turbulence model

    E-Print Network [OSTI]

    Zhao, Qun

    and diffusion are of the same order at the trough level. Above the trough level, turbulent convection dominates-dimensional MAC type finite difference method. The third-order upwind scheme proposed by Kawamura and KawaharaNumerical simulation of breaking waves by a multi-scale turbulence model Qun Zhaoa,*, Steve

  3. WHERE DOES FLUID-LIKE TURBULENCE BREAK DOWN IN THE SOLAR WIND?

    SciTech Connect (OSTI)

    Perri, S.; Carbone, V.; Veltri, P.

    2010-12-10

    Power spectra of the magnetic field in solar wind display a Kolmogorov law f {sup -5/3} at intermediate range of frequencies f, say within the inertial range. Two spectral breaks are also observed: one separating the inertial range from an f {sup -1} spectrum at lower frequencies, and another one between the inertial range and an f {sup -7/3} spectrum at higher frequencies. The breaking of fluid-like turbulence at high frequencies has been attributed to either the occurrence of kinetic Alfven wave fluctuations above the ion-cyclotron frequency or to whistler turbulence above the frequency corresponding to the proton gyroradius. Using solar wind data, we show that the observed high-frequency spectral break seems to be independent of the distance from the Sun, and then of both the ion-cyclotron frequency and the proton gyroradius. We suppose that the observed high-frequency break could be either caused by a combination of different physical processes or associated with a remnant signature of coronal turbulence.

  4. SPH Study of the Evolution of Water-Water Interfaces in Dam Break Flows

    E-Print Network [OSTI]

    Jian, Wei; Liang, Dongfang; Shao, Songdong; Chen, Ridong; Liu, Xingnian

    2015-04-08

    but also tides and tsunamis. 465 466 467 20 5.1 Model setup and computational parameters 468 469 The numerical setup of this hypothetical dam-break problem consists of a 2000 m long 470 horizontal water tank. Water is initially...

  5. 2014-2015 Trip Information Fall Break: October 22-25, 2014

    E-Print Network [OSTI]

    Almor, Amit

    Click Here Poverty & Elderly; Christmas in Action; Spartanburg, SC Trip Leader: Tina Mauer Christmas disadvantaged homeowners. For more information Click Here Poverty & Homelessness; Habitat for Humanity; John Click Here Spring Break: March 7-14, 2015 Hunger & Poverty; C.R.O.S. Ministries; West Palm Beach, FL

  6. Propagation of continental break-up in the southwestern South China Sea

    E-Print Network [OSTI]

    Nicolas, Chamot-Rooke

    Lhomond, 75231 Paris Cedex 05, France 2present address: Gdosciences Azur, Pierre & Marie Curie University on the southwestern tip of the South China Sea oceanic basin, where propagation of continental break-up occurred of the South China Sea basin, one of the best examples of an ocea- nic basin with a propagating ridge geometry

  7. FRONTIERS ARTICLE Imaging bond breaking and vibrational energy transfer in small water

    E-Print Network [OSTI]

    Reisler, Hanna

    FRONTIERS ARTICLE Imaging bond breaking and vibrational energy transfer in small water containing it is possible to generate accurate potential energy surfaces (PESs) for small clusters, such as those of water (REMPI) are used to determine accurate bond dissociation energies (D0) of (H2O)2, (H2O)3, HCl­H2O and NH3

  8. DNA analysis conference in Santa Fe

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet Hanford Advisory Board6/23/2014DLFM libraryDNA OrigamiDNA

  9. Conformal symmetry breaking and degeneracy of high-lying unflavored mesons

    E-Print Network [OSTI]

    Mariana Kirchbach; Adrian Pallares-Rivera; Cliffor Compean; Alfredo Raya

    2012-07-13

    We show that though conformal symmetry can be broken by the dilaton, such can happen without breaking the conformal degeneracy patterns in the spectra. We departure from R^1XS^3 slicing of AdS_5 noticing that the inverse radius, R, of S^3 relates to the temperature of the deconfinement phase transition and has to satisfy, \\hbar c/R >> \\Lambda_{QCD}. We then focus on the eigenvalue problem of the S^3 conformal Laplacian, given by 1/R^2 (K^2+1), with K^2 standing for the Casimir invariant of the so(4) algebra. Such a spectrum is characterized by a (K+1)^2 fold degeneracy of its levels, with K\\in [0,\\infty). We then break the conformal S^3 metric as, d\\tilde{s}^2=e^{-b\\chi} ((1+b^2/4) d\\chi^2 +\\sin^2\\chi (d\\theta ^2 +\\sin^2\\theta d\\varphi ^2)), and attribute the symmetry breaking scale, b\\hbar^2c^2/R^2, to the dilaton. We show that such a metric deformation is equivalent to a breaking of the conformal curvature of S^3 by a term proportional to b\\cot \\chi, and that the perturbed conformal Laplacian is equivalent to (\\tilde{K}^2 +c_K), with c_K a representation constant, and \\tilde{K}^2 being again an so(4) Casimir invariant, but this time in a representation unitarily inequivalent to the 4D rotational. In effect, the spectra before and after the symmetry breaking are determined each by eigenvalues of a Casimir invariant of an so(4) algebra, a reason for which the degeneracies remain unaltered though the conformal group symmetry breaks at the level of the representation of its algebra. We fit the S^3 radius and the \\hbar^2c^2b/R^2 scale to the high-lying excitations in the spectra of the unflavored mesons, and observe the correct tendency of the \\hbar c /R=373 MeV value to notably exceed \\Lambda_{QCD}. The size of the symmetry breaking scale is calculated as \\hbar c \\sqrt{b}/R=673.7 MeV.

  10. Why do continents break-up parallel to ancient orogenic belts? A. Vauchez*, G. Barruol and A. Tommasi?

    E-Print Network [OSTI]

    Barruol, Guilhem

    Why do continents break-up parallel to ancient orogenic belts? A. Vauchez*, G. Barruol and A belts Ocean-opening through rifting and continent break-up is frequently related to the occurrence Atlantic oceans provide spectacularexamples of parallelism be- tween rifts and older orogenic belts

  11. Hydrogen Bond Networks: Structure and Evolution after Hydrogen Bond Breaking John B. Asbury, Tobias Steinel, and M. D. Fayer*

    E-Print Network [OSTI]

    Fayer, Michael D.

    Hydrogen Bond Networks: Structure and Evolution after Hydrogen Bond Breaking John B. Asbury, TobiasVed: September 1, 2003; In Final Form: December 18, 2003 The nature of hydrogen bonding networks following hydrogen bond breaking is investigated using vibrational echo correlation spectroscopy of the hydroxyl

  12. Analysis of the structural changes caused by positive DNA supercoiling

    E-Print Network [OSTI]

    Barth, Marita Christine

    2007-01-01

    The procession of helix-tracking enzymes along a DNA molecule results in the formation of supercoils in the DNA, with positive supercoiling (overwinding) generated ahead of the enzyme, and negative supercoiling (underwinding) ...

  13. Engineering of DNA-mediated assemblies for biosensing applications /

    E-Print Network [OSTI]

    Xu, Phyllis F.

    2013-01-01

    OF THE DISSERTATION Engineering of DNA-mediated assembliesCALIFORNIA, SAN DIEGO Engineering of DNA-mediated assembliesMaterials Science and Engineering by Phyllis F. Xu Committee

  14. Manipulation of cellular DNA repair by early adenovirus proteins

    E-Print Network [OSTI]

    Orazio, Nicole Ise

    2010-01-01

    The function of BLM in the DDR and in processing of DNA endscellular DNA damage response (DDR) functions to inhibit thespecific components of the DDR, and provides insight into

  15. DNA hybridization : fundamental studies and applications in directed assembly

    E-Print Network [OSTI]

    Bajaj, Manish G. (Manish Gopal)

    2005-01-01

    Programmed self-assembly using non-covalent DNA-DNA interactions is a promising technique for the creation of next-generation functional devices for electronic, optical, and magnetic applications. This thesis develops the ...

  16. Genome scanning : an AFM-based DNA sequencing technique

    E-Print Network [OSTI]

    Elmouelhi, Ahmed (Ahmed M.), 1979-

    2003-01-01

    Genome Scanning is a powerful new technique for DNA sequencing. The method presented in this thesis uses an atomic force microscope with a functionalized cantilever tip to sequence single stranded DNA immobilized to a mica ...

  17. Defining functional DNA elements in the human genome

    E-Print Network [OSTI]

    Kellis, Manolis

    With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements ...

  18. THE NEW YORK BOTANICAL GARDEN DNA BANK ACQUISITIONS POLICY

    E-Print Network [OSTI]

    Law, Wayne

    THE NEW YORK BOTANICAL GARDEN DNA BANK ACQUISITIONS POLICY The DNA Bank of The New York Botanical herbarium. Please contact Lisa M. Campbell, Plant Research Laboratory, The New York Botanical Garden, Bronx

  19. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs...

    Office of Scientific and Technical Information (OSTI)

    constructs. Application of STM allows direct observation of very stable CNT-DNA hybrid structures with the well-defined DNA wrapping angle of 63.4and a coiling period of...

  20. Dna electrophoresis in photopolymerized polyacrylamide gels on a microfluidic device 

    E-Print Network [OSTI]

    Lo, Chih-Cheng

    2009-05-15

    -throughput DNA gel electrophoresis. However, further progress toward dramatic improvements of separation performance over ultra-short distances requires a much more detailed understanding of the physics of DNA migration in the sieving gel matrix than is currently...

  1. Enhancement of in vitro Translation by Gold Nanoparticle – DNA Conjugates

    E-Print Network [OSTI]

    Park, Sunho

    Gold nanoparticle (AuNP)?DNA conjugates can enhance in vitro translation of a protein. Enhancement occurs via a combination of nonspecific adsorption of translation-related molecules and the ribosome to the AuNP?DNA and ...

  2. Role of DNA repair protein ERCC1 in skin cancer 

    E-Print Network [OSTI]

    Song, Liang

    2009-01-01

    Nucleotide excision repair (NER) is one of the major repair systems for removal of DNA lesions. The NER pathway has evolved mainly to repair UV-induced DNA damage and is also active against a broad range of endogenously ...

  3. A model for sample stacking in microcapillary DNA electrophoresis

    E-Print Network [OSTI]

    Srivastava, Alok Kumar, 1967-

    2002-01-01

    Sanger's method of chain termination is the method of choice in DNA sequencing, where electrophoresis is used to separate the different sized DNA. In the past decade, microfabricated capillary devices have been developed ...

  4. Flow cytometric measurement of total DNA and incorporated halodeoxyuridine

    DOE Patents [OSTI]

    Dolbeare, F.A.; Gray, J.W.

    1983-10-18

    A method for the simultaneous flow cylometric measurement of total cellular DNA content and of the uptake of DNA precursors as a measure of DNA synthesis during various phases of the cell cycle in normal and malignant cells in vitro and in vivo is described. The method comprises reacting cells with labelled halodeoxyuridine (HdU), partially denaturing cellular DNA, adding to the reaction medium monoclonal antibodies (mabs) reactive with HdU, reacting the bound mabs with a second labelled antibody, incubating the mixture with a DNA stain, and measuring simultaneously the intensity of the DNA stain as a measure of the total cellular DNA and the HdU incorporated as a measure of DNA synthesis. (ACR)

  5. Photoelectrochemical array platform for genomic scale DNA synthesis

    E-Print Network [OSTI]

    Emig, Christopher Joseph

    2006-01-01

    Molecular and synthetic biologists have increasing demand for large, high-fidelity constructs of synthetic DNA. Recent developments in harvesting oligonucleotides from DNA microarrays has proven that these can be assembled ...

  6. Single cell trapping and DNA damage analysis using microwell arrays

    E-Print Network [OSTI]

    Wood, David

    With a direct link to cancer, aging, and heritable diseases as well as a critical role in cancer treatment, the importance of DNA damage is well-established. The intense interest in DNA damage in applications ranging from ...

  7. Alternative Methods for Human Identification: Mitochondrial DNA Base Composition Profiling

    E-Print Network [OSTI]

    Applied Genetics Alternative Methods for Human Identification: Mitochondrial DNA Base Composition · Evaluation Experiments · Future directions #12;Applied Genetics Mitochondrial DNA · Mitochondria are organelles within cells ­ Produce energy via the Krebs Cycle · Separate genome from the nucleus ­ 16,569 bp

  8. The Genetic Structure of the Kuwaiti Population: Mitochondrial DNA Markers

    E-Print Network [OSTI]

    Theyab, Jasem

    2010-06-14

    the expansion of early Homo sapiens out of Africa. Kuwait is located in the Northeast portion of the Arabian Peninsula. This thesis investigated the mitochondrial DNA (mtDNA) genetic variation in 117 unrelated individuals to determine the genetic structure...

  9. Lectin cDNA and transgenic plants derived therefrom

    DOE Patents [OSTI]

    Raikhel, Natasha V. (Okemos, MI)

    2000-10-03

    Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.

  10. International Standards in Forensic DNA and

    E-Print Network [OSTI]

    documentary (technical) standards physical (measurement) standards Certified reference material to aidInternational Standards in Forensic DNA and Recent Forensic Science Activities in the United States John M. Butler, Ph.D. National Institute of Standards and Technology NIST Fellow & Special Assistant

  11. Isolation of Yeast DNA Prepare in advance

    E-Print Network [OSTI]

    Aris, John P.

    Isolation of Yeast DNA Prepare in advance: · 2.0 ml microfuge tubes containing 0.25 g of 0.5 mm600 ~1, or 1 ml saturated YPD culture at OD600 ~10). Centrifuge for 5 minutes at 2000 rpm. Discard will thaw during centrifugation. Transfer supernatant (200-225 µl) to a fresh 1.5 ml tube. Avoid

  12. Rewritable Memory by Controllable Nanopatterning of DNA

    E-Print Network [OSTI]

    Pierce, Niles A.

    ABSTRACT Fabricating a nanostructure capable of reversibly patterning molecules is a fundamental goal within nanotechnology, underlying diverse processes such as information storage, scaffold functioning of the device as rewritable memory. The bit state of each address is controlled by specific DNA

  13. Research Article DNA sequencing by microchip

    E-Print Network [OSTI]

    Barron, Annelise E.

    .1002/elps.200800389 1 Introduction The completion of the Human Genome Project [1, 2] has led to tremendous of the reasons for the early completion of the Human Genome Project was the technological advance- ment in DNA of personalized medicine based on the human genome cannot be fully realized until the cost of full human genome

  14. Advanced Review Mediators and dynamics of DNA

    E-Print Network [OSTI]

    Wang, Wei

    -wide classifies cell types uniquely and in several cases discriminates between healthy and cancerous cell types zinc fin- ger proteins, recognize the presence of methylated cytosines.4­13 DNMT1 maintains methylation mechanism that prevents the activation of these sequences.31­34 DNA methyla- tion is also present in genes

  15. Identification of animal images based on DNA

    E-Print Network [OSTI]

    Wolf, Lior

    ongus ? Given mtDNA, the algorithm identifies the correct unseen image #12;Data sets Fishes of Australia Regularized CCA #12;Results · 93 fish species, 82 for training, 11 for testing · Significantly better than chance or NN #12;Results Fish: 90% correct Birds: 72% correct Dorsal: 59% correct Head: 56% correct

  16. A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

    E-Print Network [OSTI]

    Bernstein, Bradley E.

    The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to

  17. Structural basis for the inhibition of human alkyladenine DNA by 3,N4-ethenocytosine containing DNA

    E-Print Network [OSTI]

    Lingaraju, Gondichatnahalli M.

    Reactive oxygen and nitrogen species, generated by neutrophils and macrophages in chronically inflamed tissues, readily damage DNA, producing a variety of potentially genotoxic etheno base lesions; such inflammation-related ...

  18. Validation of DNA probes for molecular cytogenetics by mapping onto immobilized circular DNA

    E-Print Network [OSTI]

    Greulich-Bode, Karin

    2009-01-01

    two linked P1 clones (‘3012’, ‘3015’) that contain one orcircular DNA molecule (‘3012’) as well as the RGB image (J)overlap between clones ‘3012’ and ‘3015’ and the location of

  19. RhoJ Regulates Melanoma Chemoresistance by Suppressing Pathways that Sense DNA Damage

    E-Print Network [OSTI]

    Ho, Hsiang; Aruri, Jayavani; Kapadia, Rubina; Mehr, Hootan; White, Michael A.; Ganesan, Anand K.

    2012-01-01

    Pathways that Sense DNA Damage $watermark-text Hsiang Ho 1 ,16. Roos WP, Kaina B. DNA damage-induced apoptosis: FromDNA lesions to the DNA damage response and apoptosis. Cancer

  20. An Investigation on Gel Electrophoresis with Quantum Dots End-labeled DNA 

    E-Print Network [OSTI]

    Chen, Xiaojia

    2009-05-15

    explored manipulating DNA fragments by end labeling DNA molecules with quantum dot nanocrystals. The quantum dot-DNA conjugates can be further modified through binding interactions with biotinylated single-stranded DNA primers. Single molecule visualization...

  1. Protein search for multiple targets on DNA

    E-Print Network [OSTI]

    Martin Lange; Maria Kochugaeva; Anatoly B. Kolomeisky

    2015-08-03

    Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations.

  2. Generation of Full-Length cDNA Library

    E-Print Network [OSTI]

    Chuong, Cheng-Ming

    Generation of Full- Length cDNA Library from Single Human Prostate Cancer Cells BioTechniques 27 are performed on fixed and per- meabilized cells. Subsequent RT-PCR generates full-length cDNA libraries. Flowchart of current method for generating a full-length cDNA library from single cells. Cell fixation

  3. Recent advances in yeast molecular biology: recombinant DNA. [Lead abstract

    SciTech Connect (OSTI)

    Not Available

    1982-09-01

    Separate abstracts were prepared for the 25 papers presented at a workshop focusing on chromosomal structure, gene regulation, recombination, DNA repair, and cell type control, that have been obtained by experimental approaches incorporating the new technologies of yeast DNA transformation, molecular cloning, and DNA sequence analysis. (KRM)

  4. Footprinting proteinDNA complexes using the hydroxyl radical

    E-Print Network [OSTI]

    Tullius, Thomas D.

    Footprinting protein­DNA complexes using the hydroxyl radical Swapan S Jain & Thomas D Tullius.2008.72 Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA­protein complexes. The high reactivity and lack of base specificity of the hydroxyl radical makes it an excellent

  5. Single-DNA Molecule Nanomotor Regulated by Photons

    E-Print Network [OSTI]

    Tan, Weihong

    Single-DNA Molecule Nanomotor Regulated by Photons Huaizhi Kang, Haipeng Liu, Joseph A. Phillips the design of a single-molecule nanomotor driven by photons. The nanomotor is a DNA hairpin photonic wires,8 enzyme assemblies,9 and functional DNA probes.10,11 Similar to RNA or protein

  6. Advances in DNA Testing for Genealogy and Anthropology

    E-Print Network [OSTI]

    Aazhang, Behnaam

    Advances in DNA Testing for Genealogy and Anthropology Join the MIT Enterprise Forum of Texas that are affecting Genealogy, Anthropology, Medicine, and more. In the second half of the program, Russ Capper company in the world for Genealogy (Family Tree DNA). Family Tree DNA has collaborated with other

  7. Can we model DNA at the mesoscale ? Comment on: Fluctuations in the DNA double helix: A critical review

    E-Print Network [OSTI]

    Peyrard, Michel

    2015-01-01

    Comment on "Fluctuations in the DNA double helix: A critical review" by Frank-Kamenetskii and Prakash

  8. DNA digestion protocol & hints Overview: Although it is pretty standard to digest DNA with restriction enzymes, here

    E-Print Network [OSTI]

    Doering, Tamara

    Liu 4/2004 DNA digestion protocol & hints Overview: Although it is pretty standard to digest DNA in molecular biology (3.1.1-3.1.2) Materials: · DNA sample in water or TE buffer · 10x digestion buffer.1 to 4 µg 10x Digestion buffer 2 µl 5 µl Enzyme ? ? Water Rest of volume Rest of volume 2. Add the enzyme

  9. Carrier DNA For Yeast Transformation Preparation of high molecular weight single stranded carrier DNA for yeast transformations.

    E-Print Network [OSTI]

    Aris, John P.

    minute pulses. Chill on ice for 1 minute in between. The DNA solution should not heat above room into ice bucket to cool quickly. Keep on ice. This denaturation step also sterilizes the DNA. 10. Freeze to collect solution at bottom of tube. Place on ice. 3. Sonicate DNA solution in tube with tip sonifier

  10. Oncogenic Radiation Abscopal Effects In Vivo: Interrogating Mouse Skin

    SciTech Connect (OSTI)

    Mancuso, Mariateresa, E-mail: mariateresa.mancuso@enea.it [Laboratory of Radiation Biology and Biomedicine, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome (Italy); Leonardi, Simona [Laboratory of Radiation Biology and Biomedicine, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome (Italy); Giardullo, Paola; Pasquali, Emanuela [Department of Radiation Physics, Guglielmo Marconi University, Rome (Italy); Tanori, Mirella [Laboratory of Radiation Biology and Biomedicine, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome (Italy); De Stefano, Ilaria [Department of Radiation Physics, Guglielmo Marconi University, Rome (Italy); Casciati, Arianna [Laboratory of Radiation Biology and Biomedicine, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome (Italy); Naus, Christian C. [Department of Cellular and Physiological Sciences, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia (Canada); Pazzaglia, Simonetta; Saran, Anna [Laboratory of Radiation Biology and Biomedicine, Agenzia Nazionale per le Nuove Tecnologie, l'Energia e lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome (Italy)

    2013-08-01

    Purpose: To investigate the tissue dependence in transmission of abscopal radiation signals and their oncogenic consequences in a radiosensitive mouse model and to explore the involvement of gap junction intercellular communication (GJIC) in mediating radiation tumorigenesis in off-target mouse skin. Methods and Materials: Patched1 heterozygous (Ptch1{sup +/?}) mice were irradiated at postnatal day 2 (P2) with 10 Gy of x-rays. Individual lead cylinders were used to protect the anterior two-thirds of the body, whereas the hindmost part was directly exposed to radiation. To test the role of GJICs and their major constituent connexin43 (Cx43), crosses between Ptch1{sup +/?} and Cx43{sup +/?} mice were similarly irradiated. These mouse groups were monitored for their lifetime, and skin basal cell carcinomas (BCCs) were counted and recorded. Early responses to DNA damage - Double Strand Breaks (DSBs) and apoptosis - were also evaluated in shielded and directly irradiated skin areas. Results: We report abscopal tumor induction in the shielded skin of Ptch1{sup +/?} mice after partial-body irradiation. Endpoints were induction of early nodular BCC-like tumors and macroscopic infiltrative BCCs. Abscopal tumorigenesis was significantly modulated by Cx43 status, namely, Cx43 reduction was associated with decreased levels of DNA damage and oncogenesis in out-of-field skin, suggesting a key role of GJIC in transmission of oncogenic radiation signals to unhit skin. Conclusions: Our results further characterize the nature of abscopal responses and the implications they have on pathologic processes in different tissues, including their possible underlying mechanistic bases.

  11. T4 DNA condensation in water-alcohol media

    E-Print Network [OSTI]

    M. O. Gallyamov; O. A. Pyshkina; V. G. Sergeyev; I. V. Yaminsky

    2011-07-21

    The process of compaction of high molecular weight DNA T4 is investigated directly in a AFM liquid cell. The AFM-images of globules formed by DNA molecules in the result of compaction in water-alcohol environments at high izopropanol concentration (80%) are received; it is found that at intermediate concentration of izopropanol (40-50%) the DNA molecules form partially compacted formations in which the separate coils of macromolecules twist in toroidal structures. It is shown using the technique of deconvolution of the AFM-images that the globule include only one closely packed DNA molecule. The model of DNA packing is proposed on the basis of AFM experiment.

  12. Preparation of DNA-containing extract for PCR amplification

    DOE Patents [OSTI]

    Dunbar, John M.; Kuske, Cheryl R.

    2006-07-11

    Environmental samples typically include impurities that interfere with PCR amplification and DNA quantitation. Samples of soil, river water, and aerosol were taken from the environment and added to an aqueous buffer (with or without detergent). Cells from the sample are lysed, releasing their DNA into the buffer. After removing insoluble cell components, the remaining soluble DNA-containing extract is treated with N-phenacylthiazolium bromide, which causes rapid precipitation of impurities. Centrifugation provides a supernatant that can be used or diluted for PCR amplification of DNA, or further purified. The method may provide a DNA-containing extract sufficiently pure for PCR amplification within 5–10 minutes.

  13. Effective Field Theory of Emergent Symmetry Breaking in Deformed Atomic Nuclei

    E-Print Network [OSTI]

    T. Papenbrock; H. A. Weidenmüller

    2015-05-07

    Spontaneous symmetry breaking in non-relativistic quantum systems has previously been addressed in the framework of effective field theory. Low-lying excitations are constructed from Nambu-Goldstone modes using symmetry arguments only. We extend that approach to finite systems. The approach is very general. To be specific, however, we consider atomic nuclei with intrinsically deformed ground states. The emergent symmetry breaking in such systems requires the introduction of additional degrees of freedom on top of the Nambu-Goldstone modes. Symmetry arguments suffice to construct the low-lying states of the system. In deformed nuclei these are vibrational modes each of which serves as band head of a rotational band.

  14. The response of plasma density to breaking inertial gravity wave in the lower regions of ionosphere

    SciTech Connect (OSTI)

    Tang, Wenbo Mahalov, Alex

    2014-04-15

    We present a three-dimensional numerical study for the E and lower F region ionosphere coupled with the neutral atmosphere dynamics. This model is developed based on a previous ionospheric model that examines the transport patterns of plasma density given a prescribed neutral atmospheric flow. Inclusion of neutral dynamics in the model allows us to examine the charge-neutral interactions over the full evolution cycle of an inertial gravity wave when the background flow spins up from rest, saturates and eventually breaks. Using Lagrangian analyses, we show the mixing patterns of the ionospheric responses and the formation of ionospheric layers. The corresponding plasma density in this flow develops complex wave structures and small-scale patches during the gravity wave breaking event.

  15. Modulational instability, wave breaking and formation of large scale dipoles in the atmosphere

    E-Print Network [OSTI]

    A. Iafrati; A. Babanin; M. Onorato

    2012-08-27

    In the present Letter we use the Direct Numerical Simulation (DNS) of the Navier-Stokes equation for a two-phase flow (water and air) to study the dynamics of the modulational instability of free surface waves and its contribution to the interaction between ocean and atmosphere. If the steepness of the initial wave is large enough, we observe a wave breaking and the formation of large scale dipole structures in the air. Because of the multiple steepening and breaking of the waves under unstable wave packets, a train of dipoles is released and propagate in the atmosphere at a height comparable with the wave length. The amount of energy dissipated by the breaker in water and air is considered and, contrary to expectations, we observe that the energy dissipation in air is larger than the one in the water. Possible consequences on the wave modelling and on the exchange of aerosols and gases between air and water are discussed.

  16. Twisted spectral triple for the Standard Model and spontaneous breaking of the Grand Symmetry

    E-Print Network [OSTI]

    Agostino Devastato; Pierre Martinetti

    2015-01-29

    Grand symmetry models in noncommutative geometry have been introduced to explain how to generate minimally (i.e. without adding new fermions) an extra scalar field beyond the standard model, which both stabilizes the electroweak vacuum and makes the computation of the mass of the Higgs compatible with its experimental value. In this paper, we use Connes-Moscovici twisted spectral triples to cure a technical problem of the grand symmetry, that is the appearance together with the extra scalar field of unbounded vectorial terms. The twist makes these terms bounded and - thanks to a twisted version of the first-order condition that we introduce here - also permits to understand the breaking to the standard model as a dynamical process induced by the spectral action. This is a spontaneous breaking from a pre-geometric Pati-Salam model to the almost-commutative geometry of the standard model, with two Higgs-like fields: scalar and vector.

  17. Quantitative similarity analysis of small-break loss-of-coolant accident scenarios

    SciTech Connect (OSTI)

    Prosek, A.; Kljenak, I.; Mavko, B. [Univ. of Ljubljana (Slovenia). Jozef Stefan Inst.

    1996-07-01

    Classifications of small-break loss-of-coolant accidents based on objective quantitative similarity analysis are proposed. Accident scenarios were simulated in a two-loop pressurized water reactor plant with the RELAP5/MOD3.1 computer code for break sizes ranging from 1.27 cm (0.5 in.) to 15.2 cm (6 in.), with different availability of auxiliary feedwater system or reactor coolant pump trip delay. Similarities between different accident simulations were evaluated by comparing relevant time-dependent parameters with fast Fourier transform and correlation methods. Quantification of similarity between accident simulations could eventually lead to further development of the Code Scaling, Applicability and Uncertainty methodology.

  18. RADIAL DEPENDENCE OF THE FREQUENCY BREAK BETWEEN FLUID AND KINETIC SCALES IN THE SOLAR WIND FLUCTUATIONS

    SciTech Connect (OSTI)

    Bruno, R.; Trenchi, L.

    2014-06-01

    We investigate the radial dependence of the spectral break separating the inertial from the dissipation range in power density spectra of interplanetary magnetic field fluctuations, between 0.42 and 5.3 AU, during radial alignments between MESSENGER and WIND for the inner heliosphere and between WIND and ULYSSES for the outer heliosphere. We found that the spectral break moves to higher and higher frequencies as the heliocentric distance decreases. The radial dependence of the corresponding wavenumber is of the kind ? {sub b} ? R {sup –1.08}, in good agreement with that of the wavenumber derived from the linear resonance condition for proton cyclotron damping. These results support conclusions from previous studies which suggest that a cyclotron-resonant dissipation mechanism must participate in the spectral cascade together with other possible kinetic noncyclotron-resonant mechanisms.

  19. Vacuum Bellows, Vacuum Piping, Cryogenic Break, and Copper Joint Failure Rate Estimates for ITER Design Use

    SciTech Connect (OSTI)

    L. C. Cadwallader

    2010-06-01

    The ITER international project design teams are working to produce an engineering design in preparation for construction of the International Thermonuclear Experimental Reactor (ITER) tokamak. During the course of this work, questions have arisen in regard to safety barriers and equipment reliability as important facets of system design. The vacuum system designers have asked several questions about the reliability of vacuum bellows and vacuum piping. The vessel design team has asked about the reliability of electrical breaks and copper-copper joints used in cryogenic piping. Research into operating experiences of similar equipment has been performed to determine representative failure rates for these components. The following chapters give the research results and the findings for vacuum system bellows, power plant stainless steel piping (amended to represent vacuum system piping), cryogenic system electrical insulating breaks, and copper joints.

  20. Translational Symmetry Breaking in Higgs & Gauge Theory, and the Cosmological Constant

    E-Print Network [OSTI]

    Evans, Nick; Scott, Marc

    2015-01-01

    We argue, at a very basic effective field theory level, that higher dimension operators in scalar theories that break symmetries at scales close to their ultraviolet completion cutoff, include terms that favour the breaking of translation (Lorentz) invariance, potentially resulting in striped, chequered board or general crystal-like phases. Such descriptions can be thought of as the effective low energy description of QCD-like gauge theories near their strong coupling scale where terms involving higher dimension operators are generated. Our low energy theory consists of scalar fields describing operators such as $\\bar{q} q$ and $\\bar{q} F^{(2n)} q$. Such scalars can have kinetic mixing terms that generate effective momentum dependent contributions to the mass matrix. We show that these can destabilize the translationally invariant vacuum. It is possible that in some real gauge theory such operators could become sufficiently dominant to realize such phases and it would be interesting to look for them in lattic...