National Library of Energy BETA

Sample records for dna double helix

  1. 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

  2. Extreme bendability of DNA double helix due to bending asymmetry

    E-Print Network [OSTI]

    Hossein Salari; B. Eslami-Mossallam; M. S. Naderi; M. R. Ejtehadi

    2015-05-23

    Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.

  3. Extreme bendability of DNA double helix due to bending asymmetry

    E-Print Network [OSTI]

    Salari, Hossein; Naderi, M S; Ejtehadi, M R

    2015-01-01

    Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model w...

  4. Single Helix to Double Gyroid in Chiral Block Copolymers

    SciTech Connect (OSTI)

    C Chen; H Hsueh; Y Chiang; R Ho; S Akasaka; H Hasegawa

    2011-12-31

    An order-order phase transition of chiral block copolymers (BCPs*) from single helix to double gyroid (H* {yields} G) through a nucleation and growth process was demonstrated. The H* and G phases can be obtained by solution casting from fast and slow solvent evaporation, respectively, suggesting that the H* phase is a metastable phase. Consequently, the coexistence of H* and G phases can be found in the solution-cast samples from intermediate solvent evaporation. To truly examine the transition mechanism of the H* {yields} G, electron tomography was carried out to directly visualize the morphological evolution in real space, in particular, the transition zone at interface. Unlike the mechanisms for the transitions of block copolymers (BCPs) by considering the interdomain spacing matching, a significant mismatch in the lattices for the H* {yields} G was found. Consequently, the transition may require an adjustment on the geometric dimensions to justify corresponding lattice mismatch. As a result, the morphological observations from electron tomography offer new insights into BCP phase transitions.

  5. Double helix boron-10 powder thermal neutron detector

    DOE Patents [OSTI]

    Wang, Zhehui; Morris, Christopher L.; Bacon, Jeffrey D.

    2015-06-02

    A double-helix Boron-10 powder detector having intrinsic thermal neutron detection efficiency comparable to 36'' long, 2-in diameter, 2-bar Helium-3 detectors, and which can be used to replace such detectors for use in portal monitoring, is described. An embodiment of the detector includes a metallic plate coated with Boron-10 powder for generating alpha and Lithium-7 particles responsive to neutrons impinging thereon supported by insulators affixed to at least two opposing edges; a grounded first wire wound in a helical manner around two opposing insulators; and a second wire having a smaller diameter than that of the first wire, wound in a helical manner around the same insulators and spaced apart from the first wire, the second wire being positively biased. A gas, disposed within a gas-tight container enclosing the plate, insulators and wires, and capable of stopping alpha and Lithium-7 particles and generating electrons produces a signal on the second wire which is detected and subsequently related to the number of neutrons impinging on the plate.

  6. Waltzing route towards double-helix formation in cholesteric shells

    E-Print Network [OSTI]

    Alexandre Darmon; Michael Benzaquen; Olivier Dauchot; Teresa Lopez-Leon

    2015-12-18

    We study cholesteric order in liquid crystal shells with planar degenerate anchoring. We observe that the bipolar and radial configurations intensively reported for bulk droplets have a higher degree of complexity when the liquid crystal is confined to a spherical shell. The bipolar configuration is replaced by a structure where the boojums are linked to a stack of disclination rings that spans the shell, while the radial configuration exhibits a double helix structure where two disclinations wind around each other. Our results confirm recent numerical simulations and highlight the complexity of the defect structures arising when cholesteric liquid crystals are confined to spherical geometries. We also show that the position of the boojums is only ruled by the shell geometry, independently of the cholesteric pitch. To understand quantitatively this behavior, we develop a simple yet insightful theoretical framework which captures the essence of the observed phenomenology. We also show that the transition between the two configurations is solely governed by the confinement ratio c = h/p, where h is the average shell thickness and p is the cholesteric pitch. Finally, we perform a dynamical study of this transition, and report a fascinating defect waltz due to a chemical Lehmann effect.

  7. DETAILED MOLECULAR OBSERVATIONS TOWARD THE DOUBLE HELIX NEBULA

    SciTech Connect (OSTI)

    Torii, K.; Enokiya, R.; Hasegawa, K.; Kudo, N.; Fukui, Y.; Morris, M. R.

    2014-07-01

    The Double Helix Nebula (DHN), located 100 pc above Sgr A* in the Galactic center (GC), is a unique structure whose morphology suggests it is a magnetic feature. Recent molecular observations toward the DHN revealed two candidate molecular counterparts of the DHN at radial velocities of –35 km s{sup –1} and 0 km s{sup –1} and discussed the model in which the DHN has its origin at the circumnuclear disk in the GC. In this paper, new CO observations toward the DHN using the Caltech Submillimeter Observatory and Mopra telescopes are presented. The higher-resolution observations of ?1 pc scale reveal the detailed distributions and kinematics of the two CO counterparts (the 0 km s{sup –1} and –35 km s{sup –1} features) and provide new information on their physical conditions. As a result, we find that the 0 km s{sup –1} feature with a mass of 3.3 × 10{sup 4} M {sub ?} coincides with the infrared emission of the DHN, indicating clear association with the DHN. The association of the –35 km s{sup –1} feature, with a mass of 0.8 × 10{sup 4} M {sub ?}, is less clear compared with the 0 km s{sup –1} feature, but the complementary distribution between the molecular gas and the DHN and velocity variation along the DHN support its association with the DHN. The two molecular features are highly excited, as shown by the relatively high CO J = 2-1/J = 1-0 intensity ratios of ?1.0, and have kinetic temperatures of ?30 K, consistent with the typical molecular clouds in the GC.

  8. 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

  9. 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.

  10. 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.

  11. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix

    SciTech Connect (OSTI)

    Horton, J. R.; Wang, H.; Mabuchi, M. Y.; Zhang, X.; Roberts, R. J.; Zheng, Y.; Wilson, G. G.; Cheng, X.

    2014-09-27

    MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.

  12. Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix

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

    Horton, J. R.; Wang, H.; Mabuchi, M. Y.; Zhang, X.; Roberts, R. J.; Zheng, Y.; Wilson, G. G.; Cheng, X.

    2014-09-27

    MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNAmore »molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.« less

  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. Mechanism of RNA Double Helix-Propagation at Atomic Resolution Srividya Mohan, Chiaolong Hsiao, Halena VanDeusen, Ryan Gallagher, Eric Krohn,

    E-Print Network [OSTI]

    Williams, Loren

    Mechanism of RNA Double Helix-Propagation at Atomic Resolution Srividya Mohan, Chiaolong Hsiao-strand propagation, we propose an atomic resolution reaction mechanism. This mechanism, called the stack. The stack-ratchet mechanism extends and adds detail to the classic zipper model proposed by Porschke

  15. Helix coupling

    DOE Patents [OSTI]

    Ginell, W.S.

    1982-03-17

    A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the U sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

  16. Helix coupling

    DOE Patents [OSTI]

    Ginell, William S. (Encino, CA)

    1989-04-25

    A coupling for connecting helix members in series, which consists of a pair of U-shaped elements, one of which is attached to each helix end with the "U" sections of the elements interlocked. The coupling is particularly beneficial for interconnecting helical Nitinol elements utilized in thermal actuators or engines. Each coupling half is attached to the associated helix at two points, thereby providing axial load while being easily removed from the helix, and reusable.

  17. 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.

  18. The Crystal Structure of a Junction Between Two Z-DNA Helices

    E-Print Network [OSTI]

    Rich, Alexander

    The double helix of DNA, when composed of dinucleotide purine-pyrimidine repeats, can adopt a left-handed helical structure called Z-DNA. For reasons not entirely understood, such dinucleotide repeats in genomic sequences ...

  19. SOLVING LARGE DOUBLE DIGESTION PROBLEMS FOR DNA RESTRICTION MAPPING BY USING

    E-Print Network [OSTI]

    SOLVING LARGE DOUBLE DIGESTION PROBLEMS FOR DNA RESTRICTION MAPPING BY USING BRANCH;Solving Large Double Digestion Problems for DNA Restriction Mapping by Using Branch-and-Bound Integer.S.A. Abstract. The double digestion problem for DNA restriction mapping has been proved to be NP

  20. 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

  1. Self-Assembly of DNA Double-Double Crossover Complexes into High-Density, Doubly Connected, Planar Structures

    E-Print Network [OSTI]

    Brun, Yuriy

    consisting of two DNA double helices connected by two reciprocal exchanges (crossovers). In 1998, Winfree et connected by a total of six reciprocal exchanges. We use DDX complexes to self-assemble high-density, doubly reciprocal exchanges connecting each pair of adjacent helices. Figure 1b shows how the complexes might tile

  2. 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.

  3. 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.

  4. 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

  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. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Analysis of Two Widespread Versions of a Bacterial Replicative DNA Polymerase

    E-Print Network [OSTI]

    Guenther, Joel Michael

    2010-01-01

    caveat for the dsDNA-binding HhH (helix-hairpin-helix) motifpolymerase contains two HhH motifs [5], but the regions

  11. 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.

  12. Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA

    E-Print Network [OSTI]

    Kim, Doyoun

    Base extrusion is a major structural feature at the junction between B- and Z-DNA (the B–Z junction) where a base pair is broken, and the two bases are extruded from the double helix. Despite the demonstration of base ...

  13. 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.

  14. 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.

  15. 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?

  16. 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.

  17. The Unseen Genome: Gems among the Junk Just when scientists thought they had DNA almost figured out, they are discovering in

    E-Print Network [OSTI]

    Jacob, Eshel Ben

    celebrated the 50th anniversary of the discovery of the double helix, and the Human Genome Project announced to humans. The genome is home to many more actors than just the protein-coding genes. The extentThe Unseen Genome: Gems among the Junk Just when scientists thought they had DNA almost figured out

  18. To understanding of the mechanisms of DNA deactivation in ion therapy of cancer cells

    E-Print Network [OSTI]

    Piatnytskyi, D V; Perepelytsya, S M; Volkov, S N

    2015-01-01

    The changes of medium in the living cell during ion beam therapy are considered as the probable reason of disruption of the cancer cells functioning. As the most probable molecular product appeared in the cell after the passage of high energy ions, the hydrogen peroxide molecule is picked out. The possibility of the formation of stable complexes of hydrogen peroxide molecules with the sites of DNA nonspecific recognition (phosphate groups of the double helix backbone) is studied. Due to the negative charge on the oxygen atoms of PO$_{4}^{-}$ the counterions that under natural conditions neutralize the DNA double helix have been also taken into consideration. The complexes consisting of oxygen atoms of DNA phosphate group, H$_2$O$_2$ and H$_2$O molecules, and Na$^{+}$ counterion have been considered. The complex energies have been determined with accounting of electrostatic and van der Waals interactions in the framework of atom-atom potential functions. The stability of various configurations of molecular com...

  19. C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices

    E-Print Network [OSTI]

    Bansal, Manju

    C-H..O Hydrogen Bonds in Minor Groove of A-tracts in DNA Double Helices Anirban Ghosh and Manju-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within leads to a narrow minor groove in these regions. # 1999 Academic Press Keywords: C-H..O hydrogen bonds

  20. 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.

  1. 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

  2. Comment on "Monomer Dynamics in Double- and Single-Stranded DNA Polymers"

    E-Print Network [OSTI]

    J. Tothova; B. Brutovsky; V. Lisy

    2005-09-15

    It is discussed that the kinetics observed by Shusterman et al. [Phys. Rev. Lett. 92, 048303] for long dsDNA is not the Rouse one and, in fact, the macromolecule behaves (approximately) as the Zimm polymer.

  3. 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

  4. 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.

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

    SciTech Connect (OSTI)

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

    2010-01-01

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

  6. 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,...

  7. 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

  8. 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) ...

  9. Energetics of [alpha]-helix formation in peptides and proteins

    E-Print Network [OSTI]

    Schubert, Christian Reinhold

    2009-01-01

    This thesis focuses on the energetics of !-helix formation in peptides and proteins. The [alpha]-helix is the most prevalent type of secondary structure found in proteins, and has arguably dominated our thinking about ...

  10. 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...

  11. 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.

  12. 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.

  13. 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.

  14. Motifs in Protein SequencesMotifs in Protein Sequences Examples: Helix-Turn-Helix, Zinc-finger,

    E-Print Network [OSTI]

    Narasimhan, Giri

    -finger, Homeobox domain, Hairpin-beta motif, Calcium-binding motif, Beta-alpha-beta motif, Coiled-coil motifs. Examples: Helix-Turn-Helix, Zinc-finger, Homeobox domain, Hairpin-beta motif, Calcium-binding motif, Beta-alpha-beta minimum energy configuration? Unfolded Molten Globule State Folded Native State Rapid (

  15. 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.

  16. Role of hydration and intramolecular interactions in the helix-coil transition and helix-helix assembly in a deca-alanine peptide

    E-Print Network [OSTI]

    Tomar, Dheeraj S; Pettitt, B M; Asthagiri, D

    2015-01-01

    For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of attractive protein-solvent interactions are separated into a short-range part arising from interactions with solvent in the first hydration shell and the remaining long-range part. In the helix-coil transition, short-range attractive protein-solvent interactions outweigh hydrophobic hydration and favor the unfolded coil states. Analysis of enthalpic effects shows that it is the favorable hydration of the peptide backbone that favors the unfolded state. Protein intramolecular interactions favor the helix state and are decisive in folding. In the pairing of two helices, the cavity contribution outweighs short-range attractive protein-water interactions. However, long-range, protein-solvent attractive interactions can either enhance or reverse this trend depending on the mutual or...

  17. Concentration-Temperature Superposition of Helix Folding Rates in Gelatin

    E-Print Network [OSTI]

    J. L. Gornall; E. M. Terentjev

    2006-03-05

    We study the kinetics of helix-coil transition in water solutions of gelatin (collagen protein) by optical rotation techniques combined with thermal characterization. By examining the rates of secondary helix folding, and covering a very wide range of solution concentrations, we are able to identify a universal exponential dependence of folding rate on concentration and quench temperature. We demonstrate a new concentration-temperature superposition of data at all temperatures and concentrations, and build the corresponding master curve. The results support the concept of a diffuse helix-coil transition. We find no concentration dependance of the normalized rate constant, suggesting first order (single) kinetics of secondary helix folding dominate in the early stages of renaturation.

  18. Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque

    E-Print Network [OSTI]

    Dekker, Nynke

    in this paper. HelixMC advances crystallography-derived base-pair level models (BPLMs) to simulate kilobase. These calculations recovered the experimental bending persistence length of dsRNA within the error of the simulations modulus relative to dsDNA. Further blind predictions of helix torsional properties, however, exposed

  19. 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.

  20. 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.

  1. 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...

  2. The synaptic acetylcholinesterase tetramer assembles around a polyproline II helix

    E-Print Network [OSTI]

    Sussman, Joel L.

    The synaptic acetylcholinesterase tetramer assembles around a polyproline II helix Hay Dvir1 of disulfide linkages between the AChE tetramer subunits and ColQ. The P59Q mutation in ColQ, which causes­PRAD interactions. A model is proposed for the synaptic AChET tetramer. The EMBO Journal (2004) 23, 4394­4405. doi

  3. Osmotic Pressure Induced Coupling between Cooperativity and Stability of a Helix-Coil Transition

    E-Print Network [OSTI]

    Podgornik, Rudolf

    Osmotic Pressure Induced Coupling between Cooperativity and Stability of a Helix-Coil Transition interactions that alter the entropic cost of helix formation by their osmotic action can affect both. Consistent inclusion of osmotic pressure effects in a description of helix-coil transition, for poly

  4. Slow closure of denaturation bubbles in DNA: twist matters

    E-Print Network [OSTI]

    Anil Kumar Dasanna; Nicolas Destainville; John Palmeri; Manoel Manghi

    2013-04-24

    The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a non-zero torsional modulus in the duplex state, $\\kappa_\\phi=$200 to 300 kT. For DNAs of lengths N=40 to 100 base-pairs (bps) with a large initial bubble in their middle, long closure times of 0.1 to 100 microseconds are found. The bubble starts winding from both ends until it reaches a 10 bp metastable state. The final closure is limited by three competing mechanisms depending on $\\kappa_\\phi$ and N: arms diffusion until their alignment, bubble diffusion along the DNA until one end is reached, or local Kramers process (crossing over a torsional energy barrier). For clamped ends or long DNAs, the closure occurs via this latter temperature activated mechanism, yielding for the first time a good quantitative agreement with experiments.

  5. Solving the Double Digestion Problem as a MixedInteger Linear Program \\Lambda

    E-Print Network [OSTI]

    Zhang, Yin

    Solving the Double Digestion Problem as a Mixed­Integer Linear Program \\Lambda Zhijun Wu y and Yin Zhang z August, 2001 Abstract. The double digestion problem for DNA restriction mapping is known­scale double digestion problems. Key Words. DNA sequencing, restriction mapping, double digestion, NP

  6. MHK Technologies/Hydro Helix | 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 APPENDIXsource HistoryScenarios Towards 2050Enermar < MHKHydro Helix < MHK Technologies

  7. Role of solvation in pressure-induced helix stabilization

    E-Print Network [OSTI]

    Best, Robert B; Mittal, Jeetain

    2015-01-01

    In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\\alpha}-helices. However all simulations to date have obtained a qualitatively opposite result within the experimen- tal pressure range. We show that using a protein force field (Amber03w) parametrized in conjunction with an accurate water model (TIP4P/2005) recovers the correct pressure- dependence and an overall stability diagram for helix formation similar to that from experi- ment; on the other hand, we confirm that using TIP3P water results in a very weak pressure destabilization of helices. By carefully analyzing the contributing factors, we show that this is not merely a consequence of different peptide conformations sampled using TIP3P. Rather, there is a critical role for the solvent itself in determining the dependence of total system volume (peptide and solvent) on helix content. Helical peptide structures exclude a smaller volume to water,...

  8. Role of solvation in pressure-induced helix stabilization

    E-Print Network [OSTI]

    Robert B. Best; Cayla Miller; Jeetain Mittal

    2015-03-12

    In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\\alpha}-helices. However all simulations to date have obtained a qualitatively opposite result within the experimen- tal pressure range. We show that using a protein force field (Amber03w) parametrized in conjunction with an accurate water model (TIP4P/2005) recovers the correct pressure- dependence and an overall stability diagram for helix formation similar to that from experi- ment; on the other hand, we confirm that using TIP3P water results in a very weak pressure destabilization of helices. By carefully analyzing the contributing factors, we show that this is not merely a consequence of different peptide conformations sampled using TIP3P. Rather, there is a critical role for the solvent itself in determining the dependence of total system volume (peptide and solvent) on helix content. Helical peptide structures exclude a smaller volume to water, relative to non-helical structures with both the water models, but the total system volume for helical conformations is higher than non-helical conformations with TIP3P water at low to intermediate pressures, in contrast to TIP4P/2005 water. Our results further emphasize the importance of using an accurate water model to study protein folding under conditions away from standard temperature and pressure.

  9. Solution Structure of a Designed Four-R-Helix Bundle Maquette Scaffold

    E-Print Network [OSTI]

    Gibney, Brian R.

    Solution Structure of a Designed Four-R-Helix Bundle Maquette Scaffold Jack J. Skalicky, Brian R Abstract: The solution structure of a de novo designed disulfide-bridged two-R-helix peptide that self-SS-R unit forms a noncovalent dimer, (R-SS-R)2, in solution. The structure confirms many expected design

  10. Dispersion relations for a plasma-filled helix-loaded-waveguide

    SciTech Connect (OSTI)

    Makowski, M.A.; Hooper, E.B.; Stallard, B.W.

    1994-01-01

    The propagation of waves on bounded, magnetized plasma columns arises in connection with a variety of applications. To this end dispersion relations axe developed for a variety of multi-region circularly symmetric configurations. These include, a sheath helix in free space, a plasma column in free space, a plasma filled conducting tube, a plasma filled sheath-helix in free space, a sheath helix within a conducting cylinder, a plasma filled sheath-helix within a conducting cylinder, and a plasma column within a sheath-helix contained within a conducting cylinder. The latter configuration is of the most interest for whistler wave excitation for plasma thruster applications, since it includes the effect of a vacuum region separating the plasma column from the helical excitation structure.

  11. Comparative study of metallic and dielectric helix photonic metamaterial

    E-Print Network [OSTI]

    Texas at Arlington, University of

    ," Opt. Lett. 26(9), 584­586 (2001). 4. J. K. Gansel, M. Thiel, M. S. Rill, M. Decker, K. Bade, V. Saile, different characteristics: optical performances of circular polarizers with single-, double-, and multi. Ozin, "New route to three-dimensional photonic bandgap materials: silicon double inversion of polymer

  12. Ionization Spectroscopy of a DNA Base: Vacuum-Ultraviolet Mass-Analyzed Threshold Ionization Spectroscopy of Jet-Cooled Thymine

    E-Print Network [OSTI]

    Kim, Sang Kyu

    to ionizing radiation.1-8 After the initial ionization of a nucleic acid base, the hole trapped in that base migrates along the DNA helix through hopping and/or tunneling mechanisms, resulting in various types-based molecular devices. According to the hopping mechanism, charge migration in DNA occurs through hole/electron

  13. 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

  14. 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, ...

  15. 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

  16. Proofreading RNA: Structure of RNA Polymerase II's Backtracked...

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

    State Print Wednesday, 25 November 2009 00:00 Proofreading Ensures Functional Proteins Genes encoded in DNA are made up of nucleotides wound into a double helix of...

  17. 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

  18. 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.

  19. Emergence of the Persistent Spin Helix in Semiconductor Quantum Wells

    SciTech Connect (OSTI)

    Koralek, Jake; Weber, Chris; Orenstein, Joe; Bernevig, Andrei; Zhang, Shoucheng; Mack, Shawn; Awschalom, David

    2011-08-24

    According to Noether's theorem, for every symmetry in nature there is a corresponding conservation law. For example, invariance with respect to spatial translation corresponds to conservation of momentum. In another well-known example, invariance with respect to rotation of the electron's spin, or SU(2) symmetry, leads to conservation of spin polarization. For electrons in a solid, this symmetry is ordinarily broken by spin-orbit (SO) coupling, allowing spin angular momentum to flow to orbital angular momentum. However, it has recently been predicted that SU(2) can be recovered in a two-dimensional electron gas (2DEG), despite the presence of SO coupling. The corresponding conserved quantities include the amplitude and phase of a helical spin density wave termed the 'persistent spin helix' (PSH). SU(2) is restored, in principle, when the strength of two dominant SO interactions, the Rashba ({alpha}) and linear Dresselhaus ({beta}{sub 1}), are equal. This symmetry is predicted to be robust against all forms of spin-independent scattering, including electron-electron interactions, but is broken by the cubic Dresselhaus term ({beta}{sub 3}) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as {alpha} {yields} {beta}{sub 1}. Here we observe experimentally the emergence of the PSH in GaAs quantum wells (QW's) by independently tuning {alpha} and {beta}{sub 1}. Using transient spin-grating spectroscopy (TSG), we find a spin-lifetime enhancement of two orders of magnitude near the symmetry point. Excellent quantitative agreement with theory across a wide range of sample parameters allows us to obtain an absolute measure of all relevant SO terms, identifying {beta}{sub 3} as the main SU(2) violating term in our samples. The tunable suppression of spin-relaxation demonstrated in this work is well-suited for application to spintronics.

  20. Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition

    E-Print Network [OSTI]

    Artem Badasyan; Shushanik Tonoyan; Achille Giacometti; Rudolf Podgornik; V. Adrian Parsegian; Yevgeni Mamasakhlisov; Vladimir Morozov

    2012-05-15

    Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to the helical state formation; and geometric, indicating how many repeating units are affected by the formation of one helical state. Depending on their effect on the helix-coil transition, solvents or co-solutes can be classified with respect to their action on these parameters. Solvent interactions that alter the entropic cost of helix formation by their osmotic action can affect both the stability (transition temperature) and the cooperativity (transition interval) of the helix-coil transition. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition for poly(L-glutamic acid) in solution with polyethylene glycol can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition.

  1. Structures of Minimal Catalytic Fragments of Topoisomerase V Reveals Conformational Changes Relevant for DNA Binding

    SciTech Connect (OSTI)

    Rajan, Rakhi; Taneja, Bhupesh; Mondragón, Alfonso

    2010-12-03

    Topoisomerase V is an archaeal type I topoisomerase that is unique among topoisomerases due to presence of both topoisomerase and DNA repair activities in the same protein. It is organized as an N-terminal topoisomerase domain followed by 24 tandem helix-hairpin-helix (HhH) motifs. Structural studies have shown that the active site is buried by the (HhH) motifs. Here we show that the N-terminal domain can relax DNA in the absence of any HhH motifs and that the HhH motifs are required for stable protein-DNA complex formation. Crystal structures of various topoisomerase V fragments show changes in the relative orientation of the domains mediated by a long bent linker helix, and these movements are essential for the DNA to enter the active site. Phosphate ions bound to the protein near the active site helped model DNA in the topoisomerase domain and show how topoisomerase V may interact with DNA.

  2. Repair of radiation-induced heat-labile sites is independent of DNA-PKcs, XRCC1 or PARP

    SciTech Connect (OSTI)

    Stenerlöw, Bo; Karlsson, Karin H.; Radulescu, Irina; Rydberg, Bjorn; Stenerlow, Bo

    2008-04-29

    Ionizing radiation induces a variety of different DNA lesions: in addition to the most critical DNA damage, the DSB, numerous base alterations, SSBs and other modifications of the DNA double-helix are formed. When several non-DSB lesions are clustered within a short distance along DNA, or close to a DSB, they may interfere with the repair of DSBs and affect the measurement of DSB induction and repair. We have previously shown that a substantial fraction of DSBs measured by pulsed-field gel electrophoresis (PFGE) are in fact due to heat-labile sites (HLS) within clustered lesions, thus reflecting an artifact of preparation of genomic DNA at elevated temperature. To further characterize the influence of HLS on DSB induction and repair, four human cell lines (GM5758, GM7166, M059K, U-1810) with apparently normal DSB rejoining were tested for bi-phasic rejoining after gamma irradiation. When heat-released DSBs were excluded from the measurements the fraction of fast rejoining decreased to less than 50% of the total. However, neither the half-times of the fast (t{sub 1/2} = 7-8 min) or slow (t{sub 1/2} = 2.5 h) DSB rejoining were changed significantly. At t=0 the heat-released DSBs accounted for almost 40% of the DSBs, corresponding to 10 extra DSB/cell/Gy in the initial DSB yield. These heat-released DSBs were repaired within 60-90 min in all tested cells, including M059K cells treated with wortmannin or DNA-PKcs defect M059J cells. Furthermore, cells lacking XRCC1 or Poly(ADP-ribose) polymerase-1 (PARP-1) rejoined both total DSBs and heat-released DSBs similar to normal cells. In summary, the presence of heat-labile sites have a substantial impact on DSB induction yields and DSB rejoining rates measured by pulsed-field gel electrophoresis, and HLS repair is independent of DNA-PKcs, XRCC1 and PARP.

  3. Sustainability Double Degree Double Degree Info

    E-Print Network [OSTI]

    Grünwald, Niklaus J.

    Sustainability Double Degree Double Degree Info: · 36 credits in B for graduation. Sustainability Core: Take each course below for a total of 17 -20 credits. Term/Grade Course _____ ____ *NR 350 (4) Sustainable

  4. ANOMALOUS RADIO EMISSION FROM DUST IN THE HELIX1 S. Casassus,2

    E-Print Network [OSTI]

    Readhead, Anthony

    ANOMALOUS RADIO EMISSION FROM DUST IN THE HELIX1 S. Casassus,2 A. C. S. Readhead,3 T. J. Pearson,3 detection of a new component of foreground Galactic emission. The anomalous foreground at $10­30 GHz, unexplained by tradi- tional emission mechanisms, correlates with 100 m dust emission. We use planetary

  5. Systematic control of protein interaction using a modular ERK -helix linker

    E-Print Network [OSTI]

    Spudich, James A.

    Systematic control of protein interaction using a modular ERK -helix linker Sivaraj, genetically encoded linker, namely, an ERK [genetically encoded polypeptide motif based on alternating between calmodulin and its binding pep- tides, combined with FRET to determine the effect of the ERK

  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. Architecture of a Serine Recombinase-DNA Regulatory Complex

    SciTech Connect (OSTI)

    Mouw, Kent W.; Rowland, Sally-J.; Gajjar, Mark M.; Boocock, Martin R.; Stark, W. Marshall; Rice, Phoebe A. (Glasgow); (UC)

    2008-04-29

    An essential feature of many site-specific recombination systems is their ability to regulate the direction and topology of recombination. Resolvases from the serine recombinase family assemble an interwound synaptic complex that harnesses negative supercoiling to drive the forward reaction and promote recombination between properly oriented sites. To better understand the interplay of catalytic and regulatory functions within these synaptic complexes, we have solved the structure of the regulatory site synapse in the Sin resolvase system. It reveals an unexpected synaptic interface between helix-turn-helix DNA-binding domains that is also highlighted in a screen for synapsis mutants. The tetramer defined by this interface provides the foundation for a robust model of the synaptic complex, assembled entirely from available crystal structures, that gives insight into how the catalytic activity of Sin and other serine recombinases may be regulated.

  8. The Triple Helix Model and the Meta-Stabilization of Urban Technologies in Smart Cities

    E-Print Network [OSTI]

    Leydesdorff, Loet

    2010-01-01

    The Triple Helix model of university-industry-government relations can be generalized from a neo-institutional model of networks to a neo-evolutionary model of how three selection environments operate upon one another. The neo-evolutionary model enables us to appreciate both organizational integration in university-industry-government relations and differentiation among functions like the generation of intellectual capital, creation of wealth, and their attending legislation. The specification of innovation systems in terms of nations, sectors, cities, and regions can then be formulated as empirical questions: is synergy generated among functions in networks of relations? This Triple Helix model enables us to study the knowledge base of an urban economy in terms of a trade-off between locally stabilized and (potentially locked-in) trajectories versus the techno-economic and cultural development regimes which work with one more degree of freedom at the global level. The meta-stabilizing potentials of urban tec...

  9. The earliest events in protein folding: Helix dynamics in proteins and model peptides

    SciTech Connect (OSTI)

    Dyer, R.B.; Williams, S.; Woodruff, W.H. [Los Alamos National Lab., NM (United States)] [and others

    1996-12-31

    The earliest events in protein folding are critically important in determining the folding pathway, but have proved difficult to study by conventional approaches. We have developed new rapid initiation methods and structure-specific probes to interrogate the earliest events of protein folding. Our focus is the pathways. Folding or unfolding reactions are initiated on a fast timescale (10 ns) using a laser induced temperature jump (15 C) and probed with time-resolved infrared spectroscopy. We obtained the kinetics of the helix-coil transition for a model 21-residue peptide. The observed rate constant k{sub obs} = k{sub f} + k{sub u} for reversible kinetics; from the observed rate (6 x 10{sup 6} s{sup -1}) and the equilibrium constant favoring folding of 7.5 at 27 C, we calculate a folding lifetime of 180 ns and an unfolding lifetime of 1.4 {mu}s. The {open_quotes}molten globule{close_quotes} form of apomyoglobin (horse, pH*3, 0.15M NaCl) shows similar kinetics for helix that is unconstrained by tertiary structure (helix with an unusually low Amide I frequency, near 1633 cm{sup -1}). In {open_quotes}native{close_quotes} apomyoglobin (horse, pH*5.3, 10 mM NaCl) two very different rates (45 ns and 70 {mu}s) are observed and we infer that a third occurs on a timescales inaccessible to our experiment (> 1 ms). We suggest that the slower processes are due to helix formation that is rate-limited by the formation of tertiary structure.

  10. 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.

  11. Double Muscling in Cattle. 

    E-Print Network [OSTI]

    Kieffer, Nat M.; Cartwright, T.C.

    1980-01-01

    ,;J Cover photo: This lO-month-old bull is the product of a two-breed cross. He shows classic symptoms of double muscling and illustrates that the double-muscled gene is the same in different breeds of cattlr Double Muscling ......... In Cattle... Nat M. Kieffer Professor T. C. Cartwright Professor The Texas Agricultural Experiment Station (Department of Animal Science) 2 Contents 2 Summary 3 Introduction 3 Historical Background 4 Physical Characteristics of Double-Muscled Cattle 4...

  12. Chromosome doubling method

    DOE Patents [OSTI]

    Kato, Akio

    2006-11-14

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

  13. 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...

  14. 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...

  15. Speckle noise suppression using a helix-free ferroelectric liquid crystal cell

    SciTech Connect (OSTI)

    Andreev, A L; Andreeva, T B; Kompanets, I N; Zalyapin, N V

    2014-12-31

    We have studied the method for suppressing speckle noise in patterns produced by a laser based on a fast-response electro-optical cell with a ferroelectric liquid crystal (FLC) in which helicoid is absent, i.e., compensated for. The character of smectic layer deformation in an electric field is considered along with the mechanism of spatially inhomogeneous phase modulation of a laser beam passing through the cell which is accompanied by the destruction of phase relations in the beam. Advantages of a helix-free FLC cell are pointed out as compared to helical crystal cells studied previously. (liquid crystal devices)

  16. Interpretation of the Helix Planetary Nebula using Hydro-Gravitational-Dynamics: Planets and Dark Energy

    E-Print Network [OSTI]

    Carl H. Gibson; Rudolph E. Schild

    2007-11-02

    Hubble Space Telescope images of the Helix Planetary Nebula are interpreted using the hydro-gravitational-dynamics theory (HGD) of Gibson 1996-2006. HGD claims that baryonic-dark-matter (BDM) dominates the halo masses of galaxies (Schild 1996) as Jovian (Primordial-fog-particle [PFP]) Planets (JPPs) in proto-globular-star-cluster (PGC) clumps for all galaxy halo diameters bounded by stars. From HGD, supernova Ia (SNe Ia) events always occur in planetary nebulae (PNe) within PGCs. The dying central star of a PNe slowly accretes JPP mass to grow the white-dwarf to instability. Plasma jets, winds and radiation driven by contraction and spin-up of the carbon star evaporate JPPs revealing its Oort accretional cavity. SNe Ia events may thus be obscured or not obscured by radiation-inflated JPP atmospheres producing systematic SNe Ia distance errors, so the otherwise mysterious ``dark energy'' concept is unnecessary. HST/ACS and WFPC2 Helix images show >7,000 cometary globules and SST/IRAC images show >20,000-40,000, here interpreted as gas-dust cocoons of JPPs evaporated by the spin powered radiation of the PNe central white-dwarf. Observed JPP masses fossilizes the primordial density existing when the plasma universe fragmented into proto-superclusters, proto-clusters, and proto-galaxies. Pulsar scintillation spectra support the postulated multi-planet atmospheres.

  17. Interpretation of the Helix Planetary Nebula using Hydro-Gravitational-Dynamics: Planets and Dark Energy

    E-Print Network [OSTI]

    Gibson, C H; Gibson, Carl H.; Schild, Rudolph E.

    2007-01-01

    Hubble Space Telescope (HST/ACS) images of the Helix Planetary Nebula (NGC 7293) are interpreted using the hydro-gravitational-dynamics theory (HGD) of Gibson 1996-2006. HGD predicts that baryonic-dark-matter (BDM) dominates the mass of galaxies (Schild 1996) as Jovian (promordial-fog-particle, PFP) Planets (JPPs) in proto-globular-star-cluster (PGC) clumps within galaxy halo diameters surrounding its stars. From HGD, supernova Ia (SNe Ia) events normally occur in planetary nebulae (PNe) within PGCs where binary clustering cascades of merging planets produce central binary star systems. As central stars of PNe, binaries exchange mass and accrete JPPs to grow white-dwarfs to $1.44 M_{\\sun}$ instability within ionized (Oort cloud) cavities bounded by evaporating JPPs. SNe Ia events are thus intermittently obscured by radiation-inflated JPP atmospheres producing systematic SNe Ia distance errors, so the otherwise mysterious ``dark energy'' concept is unnecessary. HST/ACS and WFPC2 Helix images show $>7000$ comet...

  18. 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.

  19. Direct Computation of Long Time Processes in Peptides and Proteins: Reaction Path Study of the Coil-to-Helix

    E-Print Network [OSTI]

    Straub, John E.

    , Boston, Massachusetts 2Institute for Advanced Studies, The Hebrew University of Jerusalem, Givat Ram 3 hydrogen bonds form in the early stages of the coil-to-helix transi- tion, (2) the peptide first of atomistic models of a peptide in solution for extended times.11,12 The simulations have been used

  20. The Fusion Core Complex of the Peste des Petits Ruminants Virus Is a Six-Helix Bundle Assembly

    E-Print Network [OSTI]

    Srinivasan, N.

    The Fusion Core Complex of the Peste des Petits Ruminants Virus Is a Six-Helix Bundle Assembly (PPRV) fusion protein (F) to obtain insights into the mechanism by which these repeats influence PPRV-mediated cell fusion. Both HR1 and HR2 inhibit PPRV-mediated syncytia formation in Vero cells in vitro. Of these

  1. Current-voltage characteristics of seven-helix proteins from a cubic array of amino acids

    E-Print Network [OSTI]

    Alfinito, Eleonora

    2015-01-01

    The electrical properties of a set of seven-helix transmembrane proteins, whose space arrangement (3D structure) is known, are investigated by using regular arrays of the amino acids. These structures, specifically cubes, have topological features similar to those shown by the chosen proteins. The theoretical results show a good agreement between the predicted current-voltage characteristics obtained from a cubic array and those obtained from a detailed 3D structure. The agreement is confirmed by available experiments on bacteriorhodopsin. Furthermore, all the analyzed proteins are found to share the same critical behaviour of the voltage-dependent conductance and of its variance. In particular, the cubic arrangement evidences a short plateau of the excess conductance and its variance at high voltages. The results of the present investigation show the possibility to predict the I-V characteristics of multiple-protein sample even in the absence of a detailed knowledge of their 3D structure.

  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. Neutrinoless double beta decay

    E-Print Network [OSTI]

    K. Zuber

    2012-01-23

    The physics potential of neutrinoless double beta decay is discussed. Furthermore, experimental considerations are presented as well as the current status of experiments. Finally an outlook towards the future, work on nuclear matrix elements and alternative processes is given.

  4. Double Beta Decay

    E-Print Network [OSTI]

    Steven R. Elliott; Petr Vogel

    2002-02-27

    The motivation, present status, and future plans of the search for the neutrinoless double beta decay are reviewed. It is argued that, motivated by the recent observations of neutrino oscillations, there is a reasonable hope that neutrinoless double beta decay corresponding to the neutrino mass scale suggested by oscillations, of about 50 meV, actually exists. The challenges to achieve the sensitivity corresponding to this mass scale, and plans to overcome them, are described.

  5. 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...

  6. Enzyme Structure Provides Insights into Cancer and Aging

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

    Enzyme Structure Provides Insights into Cancer and Aging Print XPD helicase is an enzyme that unwinds the DNA double helix; it is one component of an essential repair mechanism...

  7. 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.

  8. Folding a protein with equal probability of being helix or hairpin

    E-Print Network [OSTI]

    Chun-Yu Lin; Nan-Yow Chen; Chung-Yu Mou

    2011-12-01

    We explore the possibility for the native state of a protein being inherently a multi-conformation state in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2D4X: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native states: one has a helix structure, while the other has a hairpin structure and their energy difference is less than 2% of that of local minimums. Two degenerate native states are stabilized by an energy barrier of the order 10kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that degenerate native states are stabilized by subtle balance between different interactions in proteins; furthermore, for small proteins, degeneracy only happens for proteins of sizes being around 18 amino acids or 40 amino acids. These results provide important clues to the study of native structures of proteins.

  9. 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

  10. 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...

  11. A matterless double slit

    E-Print Network [OSTI]

    B. King; A. Di Piazza; C. H. Keitel

    2013-01-29

    Double-slits provide incoming photons with a choice. Those that survive the passage have chosen from two possible paths which interfere to distribute them in a wave-like manner. Such wave-particle duality continues to be challenged and investigated in a broad range of disciplines with electrons, neutrons, helium atoms, C60 fullerenes, Bose-Einstein condensates and biological molecules. All variants have hitherto involved material constituents. We present a matterless double-slit scenario in which photons generated from virtual electron-positron pair annihilation in head-on collisions of a probe laser field with two ultra-intense laser beams form a double-slit interference pattern. Such electromagnetic fields are predicted to induce material-like behaviour in the vacuum, supporting elastic scattering between photons. Our double-slit scenario presents on the one hand a realisable method to observe photon-photon scattering, and demonstrates on the other, the possibility of both controlling light with light and non-locally investigating features of the quantum vacuum's structure.

  12. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, D.R.

    1982-09-23

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

  13. Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Heinrich Päs; Werner Rodejohann

    2015-07-01

    We review the potential to probe new physics with neutrinoless double beta decay $(A,Z) \\to (A,Z+2) + 2 e^-$. Both the standard long-range light neutrino mechanism as well as short-range mechanisms mediated by heavy particles are discussed. We also stress aspects of the connection to lepton number violation at colliders and the implications for baryogenesis.

  14. Neutrinoless double beta decay

    E-Print Network [OSTI]

    Petr Vogel

    2006-11-17

    The status of the search for neutrinoless double beta decay is reviewed. The effort to reach the sensitivity needed to cover the effective Majorana neutrino mass corresponding to the degenerate and inverted mass hierarchy is described. Various issues concerning the theory (and phenomenology) of the relation between the $0\

  15. Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Päs, Heinrich

    2015-01-01

    We review the potential to probe new physics with neutrinoless double beta decay $(A,Z) \\to (A,Z+2) + 2 e^-$. Both the standard long-range light neutrino mechanism as well as short-range mechanisms mediated by heavy particles are discussed. We also stress aspects of the connection to lepton number violation at colliders and the implications for baryogenesis.

  16. 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

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

    SciTech Connect (OSTI)

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

    2014-10-15

    Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex and an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.

  18. WHY SEARCH FOR DOUBLE BETA DECAY?

    E-Print Network [OSTI]

    Kayser, B.

    2010-01-01

    the search for neutrinoless double beta decay may prove verySearching for neutrinoless double beta decay is the onlysensitivity of neutrinoless double beta decay. The potential

  19. New and Notable Melting under Stress

    E-Print Network [OSTI]

    Langowski, Jörg

    strain forms a compact ``supercoil'', distribut- ing its elastic energy into writhe (wind- ing Research Center, D-69120 Heidelberg, Germany How does DNA fold into the compact structure of a chromosome of the helix axis around itself) and twist (the actual local under- or over- winding of the double helix). Now

  20. Double Beta Decay Experiments

    SciTech Connect (OSTI)

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

    2011-11-23

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

  1. for doubling solar panel

    E-Print Network [OSTI]

    An outline for doubling solar panel efficiency C o l o ra do S c ho o l of M i ne s Ma g a z i ne Take a look at a solar panel on a sunny Colorado day and, if you're like most people, you won't see physics professor and solar energy researcher, who admits to checking out his panels and their energy

  2. Structures of Mycobacterium tuberculosis DosR and DosR?DNA Complex Involved in Gene Activation during Adaptation to Hypoxic Latency

    SciTech Connect (OSTI)

    Wisedchaisri, Goragot; Wu, Meiting; Rice, Adrian E.; Roberts, David M.; Sherman, David R.; Hol, Wim G.J. (UWASH)

    2010-07-20

    On encountering low oxygen conditions, DosR activates the transcription of 47 genes, promoting long-term survival of Mycobacterium tuberculosis in a non-replicating state. Here, we report the crystal structures of the DosR C-terminal domain and its complex with a consensus DNA sequence of the hypoxia-induced gene promoter. The DosR C-terminal domain contains four {alpha}-helices and forms tetramers consisting of two dimers with non-intersecting dyads. In the DNA-bound structure, each DosR C-terminal domain in a dimer places its DNA-binding helix deep into the major groove, causing two bends in the DNA. DosR makes numerous protein-DNA base contacts using only three amino acid residues per subunit: Lys179, Lys182, and Asn183. The DosR tetramer is unique among response regulators with known structures.

  3. 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

  4. Parallel Molecular Computations of Pairwise Exclusive-Or (XOR) Using DNA "String Tile" Self-Assembly

    E-Print Network [OSTI]

    LaBean, Thomas H.

    Parallel Molecular Computations of Pairwise Exclusive-Or (XOR) Using DNA "String Tile" Self-Assembly, we describe the first parallel molecular computation using DNA tiling self-assembly in which a large strands that self-assemble through Watson-Crick base pairing to produce two double helices which

  5. Adhesion-Induced DNA Naturation A. E. Allahverdyan,1,2

    E-Print Network [OSTI]

    Adhesion-Induced DNA Naturation A. E. Allahverdyan,1,2 Zh. S. Gevorkian,1,3,4 Chin-Kun Hu,4 and Th of the genetic information. We shall study the adsorption and surface (adhesion) induced naturation of a double some features of DNA (see below), our model predicts two mechanisms of adhesion-induced naturation

  6. 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...

  7. 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

  8. 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.

  9. 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.

  10. 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.

  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. Neutrinoless Double Phys 135c Spring 2007

    E-Print Network [OSTI]

    Golwala, Sunil

    Neutrinoless Double Beta Decay Phys 135c Spring 2007 Michael Mendenhall #12;Theory Overview #12 beta decays #12;neutrinoless double beta decays n e- p beta decay e #12;neutrinoless double beta decays n e- p beta decay e n e- p n e- p double beta decay e e #12;neutrinoless double beta decays n e- p

  13. 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.

  14. 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.

  15. 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

  16. Double acting bit holder

    DOE Patents [OSTI]

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

    1994-01-01

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

  17. Double Chooz: Latest results

    E-Print Network [OSTI]

    J. I. Crespo-Anadón; for the Double Chooz collaboration

    2014-12-11

    The latest results from the Double Chooz experiment on the neutrino mixing angle $\\theta_{13}$ are presented. A detector located at an average distance of 1050 m from the two reactor cores of the Chooz nuclear power plant has accumulated a live time of 467.90 days, corresponding to an exposure of 66.5 GW-ton-year (reactor power $\\times$ detector mass $\\times$ live time). A revised analysis has boosted the signal efficiency and reduced the backgrounds and systematic uncertainties compared to previous publications, paving the way for the two detector phase. The measured $\\sin^2 2\\theta_{13} = 0.090^{+0.032}_{-0.029}$ is extracted from a fit to the energy spectrum. A deviation from the prediction above a visible energy of 4 MeV is found, being consistent with an unaccounted reactor flux effect, which does not affect the $\\theta_{13}$ result. A consistent value of $\\theta_{13}$ is measured in a rate-only fit to the number of observed candidates as a function of the reactor power, confirming the robustness of the result.

  18. Nitroxide Side-Chain Dynamics in a Spin-Labeled Helix-Forming Peptide Revealed by High-Frequency (139.5-GHz) EPR Spectroscopy

    E-Print Network [OSTI]

    Griffin, Robert G.

    Nitroxide Side-Chain Dynamics in a Spin-Labeled Helix-Forming Peptide Revealed by High-Frequency High-frequency electron paramagnetic resonance (EPR) spec- troscopy has been performed on a nitroxide sulfur. The spin sensitivity of high-frequency EPR is excel- lent with less than 20 pmol of sample

  19. A Speculation into the Origin of Neutral Globules In Planetary Nebulae: Could the Helix's Comets Really Be Comets?

    E-Print Network [OSTI]

    Grant Gussie

    1995-02-08

    A novel explanation for the origin of the cometary globules within NGC 7293 (the "Helix" planetary nebula) is examined; that these globules originate as massive cometary bodies at large astrocentric radii. The mass of such hypothetical cometary bodies would have to be several orders of magnitude larger than any such bodies observed in our solar system in order to supply the observed mass of neutral gas. It is however shown that comets at "outer Oort cloud" like distances are likely to survive past the red giant and asymptotic giant branch evolutionary phases of the central star, allowing them to survive until the formation of the planetary nebula. Some observational tests of this hypothesis are proposed.

  20. 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.

  1. 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.

  2. Species Doubling and Chiral Lagrangians

    E-Print Network [OSTI]

    Michael Creutz; Michel Tytgat

    1996-05-15

    Coupling gauge fields to the chiral currents from an effective Lagrangian for pseudoscalar mesons naturally gives rise to a species doubling phenomenon similar to that seen with fermionic fields in lattice gauge theory.

  3. 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

  4. 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.

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

    DOE Patents [OSTI]

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

    2002-01-01

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

  6. Predicting Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    M. Hirsch; Ernest Ma; J. W. F. Valle; A. Villanova del Moral

    2005-07-12

    We give predictions for the neutrinoless double beta decay rate in a simple variant of the A_4 family symmetry model. We show that there is a lower bound for the neutrinoless double beta decay amplitude even in the case of normal hierarchical neutrino masses, corresponding to an effective mass parameter |m_{ee}| >= 0.17 \\sqrt{\\Delta m^2_{ATM}}. This result holds both for the CP conserving and CP violating cases. In the latter case we show explicitly that the lower bound on |m_{ee}| is sensitive to the value of the Majorana phase. We conclude therefore that in our scheme, neutrinoless double beta decay may be accessible to the next generation of high sensitivity experiments.

  7. New Double Soft Emission Theorems

    E-Print Network [OSTI]

    Freddy Cachazo; Song He; Ellis Ye Yuan

    2015-03-16

    We study the behavior of the tree-level S-matrix of a variety of theories as two particles become soft. By analogy with the recently found subleading soft theorems for gravitons and gluons, we explore subleading terms in double soft emissions. We first consider double soft scalar emissions and find subleading terms that are controlled by the angular momentum operator acting on hard particles. The order of the subleading theorems depends on the presence or not of color structures. Next we obtain a compact formula for the leading term in a double soft photon emission. The theories studied are a special Galileon, DBI, Einstein-Maxwell-Scalar, NLSM and Yang-Mills-Scalar. We use the recently found CHY representation of these theories in order to give a simple proof of the leading order part of all these theorems

  8. Neutrinoless Double Beta Decay Constraints

    E-Print Network [OSTI]

    Hiroaki Sugiyama

    2003-07-25

    A brief overview is given of theoretical analyses with neutrinoless double beta decay experiments. Theoretical bounds on the ``observable'', _betabeta, are presented. By using experimental bounds on _betabeta, allowed regions are obtained on the m_l-cos{2theta_12} plane, where m_l stands for the lightest neutrino mass. It is shown that Majorana neutrinos can be excluded by combining possible results of future neutrinoless double beta decay and {}^3H beta decay experiments. A possibility to constrain one of two Majorana phases is discussed also.

  9. Neutrinoless double beta decay experiments

    E-Print Network [OSTI]

    K. Zuber

    2006-10-04

    The study of neutrinoless double beta decay is of outmost importance for neutrino physics. It is considered to be the gold plated channel to probe the fundamental character of neutrinos and to determine the neutrino mass. From the experimental point about nine different isotopes are explored for the search. After a general introduction follows a short discussion on nuclear matrix element calculations and supportive measurements. The current experimental status of double beta searches is presented followed by a short discussion of the ideas and proposals for large scale experiments.

  10. An autoinhibitory helix in the C-terminal region of phospholipase C-[beta] mediates G[alpaha subscript q] activation

    SciTech Connect (OSTI)

    Lyon, Angeline M.; Tesmer, Valerie M.; Dhamsania, Vishan D.; Thal, David M.; Gutierrez, Joanne; Chowdhury, Shoaib; Suddala, Krishna C.; Northup, John K.; Tesmer, John J.G. (Michigan); (NIH)

    2012-03-16

    The enzyme phospholipase C-{beta} (PLC{beta}) is a crucial regulator of intracellular calcium levels whose activity is controlled by heptahelical receptors that couple to members of the G{sub q} family of heterotrimeric G proteins. We have determined atomic structures of two invertebrate homologs of PLC{beta} (PLC21) from cephalopod retina and identified a helix from the C-terminal regulatory region that interacts with a conserved surface of the catalytic core of the enzyme. Mutations designed to disrupt the analogous interaction in human PLC{beta}3 considerably increase basal activity and diminish stimulation by G{alpha}{sub q}. G{alpha}{sub q} binding requires displacement of the autoinhibitory helix from the catalytic core, thus providing an allosteric mechanism for activation of PLC{beta}.

  11. Characteristic impedance and capacitance analysis of Blumlein type pulse forming line of accelerator based on tape helix

    SciTech Connect (OSTI)

    Zhang Yu; Liu Jinliang; Fan Xuliang; Zhang Hongbo; Wang Shiwen; Feng Jiahuai [College of Opto-electronic Science and Engineering, National University of Defense Technology, Changsha, 410073 (China)

    2011-10-15

    In this paper, the electromagnetic dispersion theory and the classic telegraph equations were combined to calculate the important parameters of the helical Blumlein pulse forming line (BPFL) of accelerator based on tape helix. In the work band of the BPFL at several hundred ns range, electromagnetic dispersion characteristics were almost determined by the zeroth harmonic. In order to testify the dispersion theory of BPFL in this paper, filling dielectrics, such as de-ionized water, transformer oil, and air were employed in the helical BPFL, respectively. Parameters such as capacitance, inductance, characteristic impedance, and pulse duration of the BPFL were calculated. Effects of dispersion on these parameters were analyzed. Circuit simulation and electromagnetic simulation were carried out to prove these parameters of BPFL filled with these three kinds of dielectrics, respectively. The accelerator system was set up, and experimental results also corresponded to the theoretical calculations. The average theoretical errors of impedances and pulse durations were 3.5% and 3.4%, respectively, which proved the electromagnetic dispersion analyses in this paper.

  12. 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

  13. Effect of secondary structure on the potential of mean force for poly-L-lysine in the alpha-Helix and beta-sheet conformations

    SciTech Connect (OSTI)

    Grigsby, J.J.; Blanch, H.W.; Prausnitz, J.M.

    2001-10-30

    Because poly-L-lysine (PLL) can exist in the {alpha}-helix or {beta}-sheet conformation depending on solution preparation and solution conditions, PLL is a suitable candidate to probe the dependence of protein interactions on secondary structure. The osmotic second virial coefficient and weight-average molecular weight are reported from low-angle laser-light scattering measurements for PLL as a function of NaCl concentration, pH, and {alpha}-helix or {beta}-sheet content. Interactions between PLL molecules become more attractive as salt concentration increases due to screening of PLL charge by salt ions and at low salt concentration become more attractive as pH increases due to decreased net charge on PLL. The experimental results show that interactions are stronger for the {beta}-sheet conformation than for the {alpha}-helix conformation. A spherically-symmetric model for the potential of mean force is used to account for specific interactions not described by DLVO theory and to show how differences in secondary structure affect PLL interactions.

  14. Constraining neutrinoless double beta decay

    E-Print Network [OSTI]

    L. Dorame; D. Meloni; S. Morisi; E. Peinado; J. W. F. Valle

    2011-11-23

    A class of discrete flavor-symmetry-based models predicts constrained neutrino mass matrix schemes that lead to specific neutrino mass sum-rules (MSR). We show how these theories may constrain the absolute scale of neutrino mass, leading in most of the cases to a lower bound on the neutrinoless double beta decay effective amplitude.

  15. 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.

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

    E-Print Network [OSTI]

    Bahcall, John N.

    2009-01-01

    Limits From Neutrinoless Double-Beta Decay (Rev. ),” ina next generation neutrinoless double beta decay search andPARTICLES? NO NEUTRINOLESS DOUBLE BETA DECAY AND INVERTED

  18. A Search for Neutrinoless Double Beta Decay of Te-130

    E-Print Network [OSTI]

    Bryant, Adam Douglas

    2010-01-01

    far unobserved, neutrinoless double beta decay is a possibleright for the neutrinoless double beta decay of 130 Te. Thisprocess, with neutrinoless double beta decay being the most

  19. Nuclear matrix elements for double beta decay

    E-Print Network [OSTI]

    Vadim Rodin

    2009-10-30

    The present status of calculations of the nuclear matrix elements for neutrinoless double beta decay is reviewed. A proposal which allows in principle to measure the neutrinoless double beta decay Fermi matrix element is briefly described.

  20. Investigations of ?-helix??-sheet transition pathways in a miniprotein using the finite-temperature string method

    SciTech Connect (OSTI)

    Ovchinnikov, Victor; Karplus, Martin; Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg

    2014-05-07

    A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex ?-helix??-sheet transition in a ?-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.

  1. Minimal Doubling and Point Splitting

    SciTech Connect (OSTI)

    Creutz, M.

    2010-06-14

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

  2. Neutrinoless Double Beta Decay Experiments

    E-Print Network [OSTI]

    Alberto Garfagnini

    2014-08-11

    Neutrinoless double beta decay is the only process known so far able to test the neutrino intrinsic nature: its experimental observation would imply that the lepton number is violated by two units and prove that neutrinos have a Majorana mass components, being their own anti-particle. While several experiments searching for such a rare decay have been performed in the past, a new generation of experiments using different isotopes and techniques have recently released their results or are taking data and will provide new limits, should no signal be observed, in the next few years to come. The present contribution reviews the latest public results on double beta decay searches and gives an overview on the expected sensitivities of the experiments in construction which will be able to set stronger limits in the near future.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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, ...

  10. 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

  11. Neutrinoless Double Beta Decay: Present and Future

    E-Print Network [OSTI]

    Oliviero Cremonesi

    2002-10-04

    Present status, and future plans for Double Beta Decay searches are reviewed. Given the recent observations of neutrino oscillations, a possibility to observe $\\beta\\beta(0\

  12. Review of double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2014-03-12

    The brief review of current experiments on search and studying of double beta decay processes is done. Best present limits on $\\langle m_{\

  13. Double perovskite catalysts for oxidative coupling

    DOE Patents [OSTI]

    Campbell, Kenneth D. (Charleston, WV)

    1991-01-01

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

  14. Modified helix-like instability structure on imploding z-pinch liners that are pre-imposed with a uniform axial magnetic field

    SciTech Connect (OSTI)

    Awe, T. J., E-mail: tjawe@sandia.gov; Jennings, C. A.; McBride, R. D.; Cuneo, M. E.; Lamppa, D. C.; Martin, M. R.; Rovang, D. C.; Sinars, D. B.; Slutz, S. A.; Owen, A. C.; Gomez, M. R.; Hansen, S. B.; Herrmann, M. C.; Jones, M. C.; McKenney, J. L.; Robertson, G. K.; Rochau, G. A.; Savage, M. E.; Stygar, W. A. [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185 (United States)] [Sandia National Laboratories, P.O. Box 5800, Albuquerque, New Mexico 87185 (United States); Tomlinson, K. [General Atomics, San Diego, California 92121 (United States)] [General Atomics, San Diego, California 92121 (United States); and others

    2014-05-15

    Recent experiments at the Sandia National Laboratories Z Facility have, for the first time, studied the implosion dynamics of magnetized liner inertial fusion (MagLIF) style liners that were pre-imposed with a uniform axial magnetic field. As reported [T. J. Awe et al., Phys. Rev. Lett. 111, 235005 (2013)] when premagnetized with a 7 or 10?T axial field, these liners developed 3D-helix-like hydrodynamic instabilities; such instabilities starkly contrast with the azimuthally correlated magneto-Rayleigh-Taylor (MRT) instabilities that have been consistently observed in many earlier non-premagnetized experiments. The helical structure persisted throughout the implosion, even though the azimuthal drive field greatly exceeded the expected axial field at the liner's outer wall for all but the earliest stages of the experiment. Whether this modified instability structure has practical importance for magneto-inertial fusion concepts depends primarily on whether the modified instability structure is more stable than standard azimuthally correlated MRT instabilities. In this manuscript, we discuss the evolution of the helix-like instability observed on premagnetized liners. While a first principles explanation of this observation remains elusive, recent 3D simulations suggest that if a small amplitude helical perturbation can be seeded on the liner's outer surface, no further influence from the axial field is required for the instability to grow.

  15. Structure of the unique SEFIR domain from human interleukin 17 receptor A reveals a composite ligand-binding site containing a conserved ?-helix for Act1 binding and IL-17 signaling

    SciTech Connect (OSTI)

    Zhang, Bing [Oklahoma State University, Stillwater, OK 74078 (United States); Liu, Caini; Qian, Wen [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Han, Yue [Oklahoma State University, Stillwater, OK 74078 (United States); Li, Xiaoxia, E-mail: lix@ccf.org [Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195 (United States); Deng, Junpeng, E-mail: lix@ccf.org [Oklahoma State University, Stillwater, OK 74078 (United States)

    2014-05-01

    Crystal structure of the SEFIR domain from human IL-17 receptor A provides new insights into IL-17 signaling. Interleukin 17 (IL-17) cytokines play a crucial role in mediating inflammatory and autoimmune diseases. A unique intracellular signaling domain termed SEFIR is found within all IL-17 receptors (IL-17Rs) as well as the key adaptor protein Act1. SEFIR-mediated protein–protein interaction is a crucial step in IL-17 cytokine signaling. Here, the 2.3 Å resolution crystal structure of the SEFIR domain of IL-17RA, the most commonly shared receptor for IL-17 cytokine signaling, is reported. The structure includes the complete SEFIR domain and an additional ?-helical C-terminal extension, which pack tightly together to form a compact unit. Structural comparison between the SEFIR domains of IL-17RA and IL-17RB reveals substantial differences in protein topology and folding. The uniquely long insertion between strand ?C and helix ?C in IL-17RA SEFIR is mostly well ordered, displaying a helix (?CC?{sub ins}) and a flexible loop (CC?). The DD? loop in the IL-17RA SEFIR structure is much shorter; it rotates nearly 90° with respect to the counterpart in the IL-17RB SEFIR structure and shifts about 12 Å to accommodate the ?CC?{sub ins} helix without forming any knots. Helix ?C was identified as critical for its interaction with Act1 and IL-17-stimulated gene expression. The data suggest that the heterotypic SEFIR–SEFIR association via helix ?C is a conserved and signature mechanism specific for IL-17 signaling. The structure also suggests that the downstream motif of IL-17RA SEFIR together with helix ?C could provide a composite ligand-binding surface for recruiting Act1 during IL-17 signaling.

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

    SciTech Connect (OSTI)

    Snodin, Benedict E. K. Mosayebi, Majid; Schreck, John S.; Romano, Flavio; Doye, Jonathan P. K.; Randisi, Ferdinando; 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.

  17. 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.

  18. 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.

  19. 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.

  20. Predicting neutrinoless double beta decay

    SciTech Connect (OSTI)

    Hirsch, M.; Villanova del Moral, A.; Valle, J.W.F. [AHEP Group, Instituto de Fisica Corpuscular - C.S.I.C./Universitat de Valencia, Edificio Institutos de Paterna, Apt 22085, E-46071 Valencia (Spain); Ma, Ernest [Physics Department, University of California, Riverside, California 92521 (United States); Institute for Particle Physics Phenomenology, University of Durham, Durham, DH1 3LE (United Kingdom)

    2005-11-01

    We give predictions for the neutrinoless double beta decay rate in a simple variant of the A{sub 4} family symmetry model. We show that there is a lower bound for the {beta}{beta}{sub 0{nu}} amplitude even in the case of normal hierarchical neutrino masses, corresponding to an effective mass parameter vertical bar m{sub ee} vertical bar {>=}0.17{radical}({delta}m{sub ATM}{sup 2}). This result holds both for the CP conserving and CP violating cases. In the latter case we show explicitly that the lower bound on vertical bar m{sub ee} vertical bar is sensitive to the value of the Majorana phase. We conclude therefore that in our scheme, {beta}{beta}{sub 0{nu}} may be accessible to the next generation of high sensitivity experiments.

  1. Double-Disk Dark Matter

    E-Print Network [OSTI]

    Fan, JiJi; Randall, Lisa; Reece, Matthew

    2013-01-01

    Based on observational tests and constraints on halo structure, dark matter is generally taken to be cold and essentially collisionless. On the other hand, given the large number of particles and forces in the visible world, a more complex dark sector could be a reasonable or even likely possibility. This hypothesis leads to testable consequences, perhaps portending the discovery of a rich hidden world neighboring our own. We consider a scenario that readily satisfies current bounds that we call Partially Interacting Dark Matter (PIDM). This scenario contains self-interacting dark matter, but it is not the dominant component. Even if PIDM contains only a fraction of the net dark matter density, comparable to the baryonic fraction, the subdominant component's interactions can lead to interesting and potentially observable consequences. Our primary focus will be the special case of Double-Disk Dark Matter (DDDM), in which self-interactions allow the dark matter to lose enough energy to lead to dynamics similar ...

  2. The tropical double description method

    E-Print Network [OSTI]

    Allamigeon, Xavier; Goubault, Eric

    2010-01-01

    We develop a tropical analogue of the classical double description method allowing one to compute an internal representation (in terms of vertices) of a polyhedron defined externally (by inequalities). The heart of the tropical algorithm is a characterization of the extreme points of a polyhedron in terms of a system of constraints which define it. We show that checking the extremality of a point reduces to checking whether there is only one minimal strongly connected component in an hypergraph. The latter problem can be solved in almost linear time, which allows us to eliminate quickly redundant generators. We report extensive tests (including benchmarks from an application to static analysis) showing that the method outperforms experimentally the previous ones by orders of magnitude. The present tools also lead to worst case bounds which improve the ones provided by previous methods.

  3. Double Integrals: GENERAL REGION The main difficulty in evaluating a double integral

    E-Print Network [OSTI]

    Knopf, Dan

    Double Integrals: GENERAL REGION The main difficulty in evaluating a double integral was being able to compute the single variable integrals that arose because the double integral could written as repeated single variable integrals and either choice of order of integration used. So we could always choose

  4. 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.

  5. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1988-10-11

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

  6. Double beta decay: experiments and theory review

    E-Print Network [OSTI]

    A. Nucciotti

    2007-07-28

    Neutrinoless double beta decay is one of the most powerful tools to set the neutrino mass absolute scale and establish whether the neutrino is a Majorana particle. After a summary of the neutrinoless double beta decay phenomenology, the present status of the experimental search for this rare decay is reported and the prospects for next generation experiments are reviewed.

  7. Neutrinoless double beta decay and neutrino physics

    E-Print Network [OSTI]

    Werner Rodejohann

    2012-08-20

    The connection of neutrino physics with neutrinoless double beta decay is reviewed. After presenting the current status of the PMNS matrix and the theoretical background of neutrino mass and lepton mixing, we will summarize the various implications of neutrino physics for double beta decay. The influence of light sterile neutrinos and other exotic modifications of the three neutrino picture is also discussed.

  8. Reliability Estimation for Double Containment Piping

    SciTech Connect (OSTI)

    L. Cadwallader; T. Pinna

    2012-08-01

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

  9. 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

  10. Neutrinoless Double Beta Decay in Light of SNO Salt Data

    E-Print Network [OSTI]

    Murayama, Hitoshi

    2009-01-01

    Limits From Neutrinoless Double-Beta Decay (Rev. ),” incan also cause neutrinoless double-beta decay (see e.g. , [LBNL-53996 Neutrinoless Double Beta Decay in Light of SNO

  11. Resonance and Double Negative Behavior in Metamaterials

    E-Print Network [OSTI]

    Yue Chen; Robert P. Lipton

    2013-05-03

    A generic class of metamaterials is introduced and is shown to exhibit frequency dependent double negative effective properties. We develop a rigorous method for calculating the frequency intervals where either double negative or double positive effective properties appear and show how these intervals imply the existence of propagating Bloch waves inside sub-wavelength structures. The branches of the dispersion relation associated with Bloch modes are shown to be explicitly determined by the Dirichlet spectrum of the high dielectric phase and the generalized electrostatic spectra of the complement.

  12. Neutrinoless Double Beta Decay and Neutrino Masses

    E-Print Network [OSTI]

    Michael Duerr

    2012-06-04

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

  13. Development of double-decker pulse radiolysis

    SciTech Connect (OSTI)

    Kan, K.; Kondoh, T.; Yang, J.; Ogata, A.; Norizawa, K.; Yoshida, Y. [Institute of Scientific and Industrial Research, Osaka University, Osaka (Japan)

    2012-07-15

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

  14. Double-reed exhaust valve engine

    DOE Patents [OSTI]

    Bennett, Charles L.

    2015-06-30

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

  15. Search for: "neutrinoless double beta decay" | DOE PAGES

    Office of Scientific and Technical Information (OSTI)

    neutrinoless double beta decay" Find + Advanced Search Advanced Search All Fields: "neutrinoless double beta decay" Title: Full Text: Bibliographic Data: Creator Author: Name...

  16. SciTech Connect: "neutrinoless double beta decay"

    Office of Scientific and Technical Information (OSTI)

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

  17. Double-Disk Dark Matter

    E-Print Network [OSTI]

    JiJi Fan; Andrey Katz; Lisa Randall; Matthew Reece

    2013-07-31

    Based on observational constraints on large scale structure and halo structure, dark matter is generally taken to be cold and essentially collisionless. On the other hand, given the large number of particles and forces in the visible world, a more complex dark sector could be a reasonable or even likely possibility. This hypothesis leads to testable consequences, perhaps portending the discovery of a rich hidden world neighboring our own. We consider a scenario that readily satisfies current bounds that we call Partially Interacting Dark Matter (PIDM). This scenario contains self-interacting dark matter, but it is not the dominant component. Even if PIDM contains only a fraction of the net dark matter density, comparable to the baryonic fraction, the subdominant component's interactions can lead to interesting and potentially observable consequences. Our primary focus will be the special case of Double-Disk Dark Matter (DDDM), in which self-interactions allow the dark matter to lose enough energy to lead to dynamics similar to those in the baryonic sector. We explore a simple model in which DDDM can cool efficiently and form a disk within galaxies, and we evaluate some of the possible observational signatures. The most prominent signal of such a scenario could be an enhanced indirect detection signature with a distinctive spatial distribution. Even though subdominant, the enhanced density at the center of the galaxy and possibly throughout the plane of the galaxy can lead to large boost factors, and could even explain a signature as large as the 130 GeV Fermi line. Such scenarios also predict additional dark radiation degrees of freedom that could soon be detectable and would influence the interpretation of future data, such as that from Planck and from the Gaia satellite. We consider this to be the first step toward exploring a rich array of new possibilities for dark matter dynamics.

  18. Double layer capacitors : automotive applications and modeling

    E-Print Network [OSTI]

    New, David Allen, 1976-

    2004-01-01

    This thesis documents the work on the modeling of double layer capacitors (DLCs) and the validation of the modeling procedure. Several experiments were conducted to subject the device under test to a variety of ...

  19. Double logarithmic asymptotic behavior in quantum chromodynamics

    SciTech Connect (OSTI)

    Kirschner, R.

    1981-08-01

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

  20. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1987-02-06

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

  1. CP Violation in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    T. Fukuyama; K. Matsuda; H. Nishiura

    1997-08-19

    We argue three-flavour neutrino mixing. We consider the neutrinos as Majorana particles and see how the neutrinoless double beta decay constrains the neutrino mixing angles. Our formulation is widely valid and is applied to the neutrino oscillation experiment.

  2. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    Gómez-Cadenas, J J

    2015-01-01

    This paper reviews the current status and future outlook of neutrinoless double beta decay searches, which try to provide an answer to the fundamental question of whether neutrinos are Dirac or Majorana particles.

  3. Probing neutrinoless double beta decay with SNO+

    E-Print Network [OSTI]

    Evelina Arushanova; Ashley R. Back

    2015-05-01

    Probing neutrinoless double beta decay is one of the primary goals for SNO+, SNOLAB's multi-purpose neutrino detector. In order to achieve this goal the SNO detector has been adapted so that it can be filled with Te-loaded liquid scintillator. During the initial double beta phase the target loading is 0.3% natural Te, which equates to $\\sim790$ kg of double beta isotope. Estimating the sensitivity to neutrinoless double beta decay requires a well understood background model. For SNO+ this is provided by a comprehensive study considering all possible background contributions, whether they originate from within the liquid scintillator cocktail, the surrounding parts of the detector or other irreducible backgrounds. Given these considerations, for five years running in the initial phase, the expected sensitivity is $T_{1/2}^{0\

  4. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    J. J. Gómez-Cadenas; Justo Martín-Albo

    2015-02-25

    This paper reviews the current status and future outlook of neutrinoless double beta decay searches, which try to provide an answer to the fundamental question of whether neutrinos are Dirac or Majorana particles.

  5. Probing neutrinoless double beta decay with SNO+

    E-Print Network [OSTI]

    Arushanova, Evelina

    2015-01-01

    Probing neutrinoless double beta decay is one of the primary goals for SNO+, SNOLAB's multi-purpose neutrino detector. In order to achieve this goal the SNO detector has been adapted so that it can be filled with Te-loaded liquid scintillator. During the initial double beta phase the target loading is 0.3% natural Te, which equates to $\\sim790$ kg of double beta isotope. Estimating the sensitivity to neutrinoless double beta decay requires a well understood background model. For SNO+ this is provided by a comprehensive study considering all possible background contributions, whether they originate from within the liquid scintillator cocktail, the surrounding parts of the detector or other irreducible backgrounds. Given these considerations, for five years running in the initial phase, the expected sensitivity is $T_{1/2}^{0\

  6. Double shell tank waste analysis plan

    SciTech Connect (OSTI)

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

    1994-12-15

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

  7. Neutrinoless double beta decay with scalar bilinears

    E-Print Network [OSTI]

    H. V. Klapdor-Kleingrothaus; U. Sarkar

    2002-11-18

    One possible probe to physics beyond the standard model is to look for scalar bilinears, which couple to two fermions of the standard model. We point out that the scalar bilinears allow new diagrams contributing to the neutrinoless double beta decay. The upper bound on the neutrinoless double beta decay lifetime would then give new constraints on the ratio of the masses of these scalars to their couplings to the fermions.

  8. Neutrinoless Double Beta Decay and CP Violation

    E-Print Network [OSTI]

    Patrick J. O'Donnell; Utpal Sarkar

    1993-05-27

    We study the relation between the Majorana neutrino mass matrices and the neutrinoless double beta decay when CP is not conserved. We give an explicit form of the decay rate in terms of a rephasing invariant quantity and demonstrate that in the presence of CP violation it is impossible to have vanishing neutrinoless double beta decay in the case of two neutrino generations (or when the third generation leptons do not mix with other leptons and hence decouple).

  9. Searches for neutrinoless double beta decay

    E-Print Network [OSTI]

    B. Schwingenheuer

    2012-01-24

    Neutrinoless double beta decay is a lepton number violating process whose observation would also establish that neutrinos are their own anti-particles. There are many experimental efforts with a variety of techniques. Some (EXO, Kamland-Zen, GERDA phase I and CANDLES) started take data in 2011 and EXO has reported the first measurement of the half life for the double beta decay with two neutrinos of $^{136}$Xe. The sensitivities of the different proposals are reviewed.

  10. Wavelength-doubling optical parametric oscillator

    DOE Patents [OSTI]

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

    2007-07-24

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

  11. Vol 440|16 March 2006 NEWS & VIEWS

    E-Print Network [OSTI]

    Cai, Long

    or now-standard molecular cloning approaches. The molecular engineer is thus armed with two of the basic, in the 50 years since the discovery of the DNA double helix2 , a detailed understanding of the energetics design is the `tile model' developed in Ned Seeman's laboratory5 . This uses as its basic building- block

  12. 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.

  13. Ortho-positronium observation in the Double Chooz Experiment

    E-Print Network [OSTI]

    Y. Abe; J. C. dos Anjos; J. C. Barriere; E. Baussan; I. Bekman; M. Bergevin; T. J. C. Bezerra; L. Bezrukov; E. Blucher; C. Buck; J. Busenitz; A. Cabrera; E. Caden; L. Camilleri; R. Carr; M. Cerrada; P. -J. Chang; E. Chauveau; P. Chimenti; A. P. Collin; E. Conover; J. M. Conrad; J. I. Crespo-Anadon; K. Crum; A. S. Cucoanes; E. Damon; J. V. Dawson; J. Dhooghe; D. Dietrich; Z. Djurcic; M. Dracos; M. Elnimr; A. Etenko; M. Fallot; F. von Feilitzsch; J. Felde; S. M. Fernandes; V. Fischer; D. Franco; M. Franke; H. Furuta; I. Gil-Botella; L. Giot; M. Goger-Neff; L. F. G. Gonzalez; L. Goodenough; M. C. Goodman; C. Grant; N. Haag; T. Hara; J. Haser; M. Hofmann; G. A. Horton-Smith; A. Hourlier; M. Ishitsuka; J. Jochum; C. Jollet; F. Kaether; L. N. Kalousis; Y. Kamyshkov; D. M. Kaplan; T. Kawasaki; E. Kemp; H. de Kerret; D. Kryn; M. Kuze; T. Lachenmaier; C. E. Lane; T. Lasserre; A. Letourneau; D. Lhuillier; H. P. Lima Jr; M. Lindner; J. M. Lopez-Castano; J. M. LoSecco; B. Lubsandorzhiev; S. Lucht; J. Maeda; C. Mariani; J. Maricic; J. Martino; T. Matsubara; G. Mention; A. Meregaglia; T. Miletic; R. Milincic; A. Minotti; Y. Nagasaka; Y. Nikitenko; P. Novella; L. Oberauer; M. Obolensky; A. Onillon; A. Osborn; C. Palomares; I. M. Pepe; S. Perasso; P. Pfahler; A. Porta; G. Pronost; J. Reichenbacher; B. Reinhold; M. Rohling; R. Roncin; S. Roth; B. Rybolt; Y. Sakamoto; R. Santorelli; A. C. Schilithz; S. Schonert; S. Schoppmann; M. H. Shaevitz; R. Sharankova; S. Shimojima; D. Shrestha; V. Sibille; V. Sinev; M. Skorokhvatov; E. Smith; J. Spitz; A. Stahl; I. Stancu; L. F. F. Stokes; M. Strait; A. Stuken; F. Suekane; S. Sukhotin; T. Sumiyoshi; Y. Sun; R. Svoboda; K. Terao; A. Tonazzo; H. H. Trinh Thi; G. Valdiviesso; N. Vassilopoulos; C. Veyssiere; M. Vivier; S. Wagner; N. Walsh; H. Watanabe; C. Wiebusch; L. Winslow; M. Wurm; G. Yang; F. Yermia; V. Zimmer

    2014-10-07

    The Double Chooz experiment measures the neutrino mixing angle $\\theta_{13}$ by detecting reactor $\\bar{\

  14. 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.

  15. 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.

  16. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, S.K.

    1998-03-24

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

  17. 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....

  18. Responsive Double Network Hydrogels of Interpenetrating DNA and CB[8] Host–Guest Supramolecular Systems

    E-Print Network [OSTI]

    Li, Chuang; Rowland, Matthew J.; Shao, Yu; Cao, Tianyang; Chen, Chun; Jia, Haoyang; Zhou, Xu; Yang, Zhongqiang; Scherman, Oren A.; Liu, Dongsheng

    2015-04-20

    was dissolved in a minimal amount of diethyl ether and 2 M hydrogen chloride in diethyl ether (15 mL) was added. The reaction was stirred for 4 hours and concentrated in vacuo to yield a yellow solid. The crude product was then triturated in diethyl ether... Hz and 1%, respectively, and the changes in the shear storage modulus (G’) and shear-loss modulus (G”) were measured from 20 to 70 ºC at a rate of 2 ºC min-1; iv) Flow sweep was performed at 25 Fracture with shear rate varying from 0.001 to 100 s-1...

  19. 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

  20. 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

  1. The search for neutrinoless double beta decay

    E-Print Network [OSTI]

    J. J. Gomez-Cadenas; J. Martin-Albo; M. Mezzetto; F. Monrabal; M. Sorel

    2012-01-16

    In the last two decades the search for neutrinoless double beta decay has evolved into one of the highest priorities for understanding neutrinos and the origin of mass. The main reason for this paradigm shift has been the discovery of neutrino oscillations, which clearly established the existence of massive neutrinos. An additional motivation for conducting such searches comes from the existence of an unconfirmed, but not refuted, claim of evidence for neutrinoless double decay in $^{76}\\text{Ge}$. As a consequence, a new generation of experiments, employing different detection techniques and $\\beta\\beta$ isotopes, is being actively promoted by experimental groups across the world. In addition, nuclear theorists are making remarkable progress in the calculation of the neutrinoless double beta decay nuclear matrix elements, thus eliminating a substantial part of the theoretical uncertainties affecting the particle physics interpretation of this process. In this report, we review the main aspects of the double beta decay process and some of the most relevant experiments. The picture that emerges is one where searching for neutrinoless double beta decay is recognized to have both far-reaching theoretical implications and promising prospects for experimental observation in the near future.

  2. 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

  3. Recent Results in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Lisa J. Kaufman

    2013-05-14

    The search for neutrinoless double beta decay is a rich source for new physics. The observation of this decay will lead to understanding of the absolute mass scale of neutrinos, the Majorana nature of the neutrino (whether the neutrino is its own anti-particle), and lepton number violation. Double beta decay is being investigated around the world by several experiments using different candidate isotopes. There has been much progress made in experimental techniques recently such that achieving sensitivity to neutrino masses at 50 meV and below will be possible in the near future. A summary of recent results in neutrinoless double beta decay is discussed with a look toward the experimental goals for the future.

  4. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    M. Hirsch

    2006-09-15

    Neutrinoless double beta decay violates lepton number by two units, a positive observation therefore necessarily implies physics beyond the standard model. Here, three possible contributions to neutrinoless double beta decay are briefly reviewed: (a) The mass mechanism and its connection to neutrino oscillations; (b) Left-right symmetric models and the lower limit on the right-handed W boson mass; and (c) R-parity violating supersymmetry. In addition, the recently published ``extended black box'' theorem is briefly discussed. Combined with data from oscillation experiments this theorem provides proof that the neutrinoless double beta decay amplitude must receive a non-zero contribution from the mass mechanism, if neutrinos are indeed Majorana particles.

  5. Precision Muon Reconstruction in Double Chooz

    E-Print Network [OSTI]

    Double Chooz collaboration; Y. Abe; J. C. dos Anjos; J. C. Barriere; E. Baussan; I. Bekman; M. Bergevin; T. J. C. Bezerra; L. Bezrukov; E. Blucher; C. Buck; J. Busenitz; A. Cabrera; E. Caden; L. Camilleri; R. Carr; M. Cerrada; P. -J. Chang; E. Chauveau; P. Chimenti; A. P. Collin; E. Conover; J. M. Conrad; J. I. Crespo-Anadón; K. Crum; A. Cucoanes; E. Damon; J. V. Dawson; D. Dietrich; Z. Djurcic; M. Dracos; M. Elnimr; A. Etenko; M. Fallot; F. von Feilitzsch; J. Felde; S. M. Fernandes; V. Fischer; D. Franco; M. Franke; H. Furuta; I. Gil-Botella; L. Giot; M. Göger-Neff; L. F. G. Gonzalez; L. Goodenough; M. C. Goodman; C. Grant; N. Haag; T. Hara; J. Haser; M. Hofmann; G. A. Horton-Smith; A. Hourlier; M. Ishitsuka; J. Jochum; C. Jollet; F. Kaether; L. N. Kalousis; Y. Kamyshkov; D. M. Kaplan; T. Kawasaki; E. Kemp; H. de Kerret; D. Kryn; M. Kuze; T. Lachenmaier; C. E. Lane; T. Lasserre; A. Letourneau; D. Lhuillier; H. P. Lima Jr; M. Lindner; J. M. López-Casta no; J. M. LoSecco; B. Lubsandorzhiev; S. Lucht; J. Maeda; C. Mariani; J. Maricic; J. Martino; T. Matsubara; G. Mention; A. Meregaglia; T. Miletic; R. Milincic; A. Minotti; Y. Nagasaka; Y. Nikitenko; P. Novella; M. Obolensky; L. Oberauer; A. Onillon; A. Osborn; C. Palomares; I. M. Pepe; S. Perasso; P. Pfahler; A. Porta; G. Pronost; J. Reichenbacher; B. Reinhold; M. Röhling; R. Roncin; S. Roth; B. Rybolt; Y. Sakamoto; R. Santorelli; A. C. Schilithz; S. Schönert; S. Schoppmann; M. H. Shaevitz; R. Sharankova; S. Shimojima; V. Sibille; V. Sinev; M. Skorokhvatov; E. Smith; J. Spitz; A. Stahl; I. Stancu; L. F. F. Stokes; M. Strait; A. Stüken; F. Suekane; S. Sukhotin; T. Sumiyoshi; Y. Sun; R. Svoboda; K. Terao; A. Tonazzo; H. H. Trinh Thi; G. Valdiviesso; N. Vassilopoulos; C. Veyssiere; M. Vivier; S. Wagner; H. Watanabe; C. Wiebusch; L. Winslow; M. Wurm; G. Yang; F. Yermia; V. Zimmer

    2014-08-15

    We describe a muon track reconstruction algorithm for the reactor anti-neutrino experiment Double Chooz. The Double Chooz detector consists of two optically isolated volumes of liquid scintillator viewed by PMTs, and an Outer Veto above these made of crossed scintillator strips. Muons are reconstructed by their Outer Veto hit positions along with timing information from the other two detector volumes. All muons are fit under the hypothesis that they are through-going and ultrarelativistic. If the energy depositions suggest that the muon may have stopped, the reconstruction fits also for this hypothesis and chooses between the two via the relative goodness-of-fit. In the ideal case of a through-going muon intersecting the center of the detector, the resolution is ~40 mm in each transverse dimension. High quality muon reconstruction is an important tool for reducing the impact of the cosmogenic isotope background in Double Chooz.

  6. The double-beta decay: Theoretical challenges

    SciTech Connect (OSTI)

    Horoi, Mihai

    2012-11-20

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

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

    SciTech Connect (OSTI)

    Suhonen, Jouni

    2013-12-30

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

  8. 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 ...

  9. 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 ...

  10. 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

  11. The COBRA Double Beta Decay Experiment

    SciTech Connect (OSTI)

    Dawson, J. V. [Department of Physics and Astronomy, University of Sussex, Brighton. BN1 9QH (United Kingdom)

    2007-03-28

    The progress of the COBRA neutrinoless double beta decay experiment is discussed. Potential backgrounds are described. Estimates on the contamination levels of 214Bi in the detectors have been made using previously acquired low background data. New crystals with a different passivation material show an improved background count rate of approximately one order of magnitude.

  12. Double tracks test site characterization report

    SciTech Connect (OSTI)

    NONE

    1996-05-01

    This report presents the results of site characterization activities performed at the Double Tracks Test Site, located on Range 71 North, of the Nellis Air Force Range (NAFR) in southern Nevada. Site characterization activities included reviewing historical data from the Double Tracks experiment, previous site investigation efforts, and recent site characterization data. The most recent site characterization activities were conducted in support of an interim corrective action to remediate the Double Tracks Test Site to an acceptable risk to human health and the environment. Site characterization was performed using a phased approach. First, previously collected data and historical records sere compiled and reviewed. Generalized scopes of work were then prepared to fill known data gaps. Field activities were conducted and the collected data were then reviewed to determine whether data gaps were filled and whether other areas needed to be investigated. Additional field efforts were then conducted, as required, to adequately characterize the site. Characterization of the Double Tracks Test Site was conducted in accordance with the US Department of Energy`s (DOE) Streamlined Approach for Environmental Restoration (SAFER).

  13. Cretan Hieroglyphic Wool Units (LANA, double mina)

    E-Print Network [OSTI]

    Younger, John G.

    2005-01-01

    Minoan Hieroglyphic document CHIC *089, on analogy with Linear A and B wool documents, records the wool of a certain type of cloth as the equivalent in weight of 3 double minas, that is 1 wool unit (or the wool from 4 sheep).

  14. Scale evolution of double parton correlations

    E-Print Network [OSTI]

    Tomas Kasemets

    2014-11-17

    We review the effect of scale evolution on a number of different correlations in double parton scattering (DPS). The strength of the correlations generally decreases with the scale but at a rate which greatly varies between different types. Through studies of the evolution, an understanding of which correlations can be of experimental relevance in different processes and kinematical regions is obtained.

  15. Neutrinoless double beta decay in seesaw models

    E-Print Network [OSTI]

    Mattias Blennow; Enrique Fernandez-Martinez; Jacobo Lopez-Pavon; Javier Menendez

    2014-05-12

    We study the general phenomenology of neutrinoless double beta decay in seesaw models. In particular, we focus on the dependence of the neutrinoless double beta decay rate on the mass of the extra states introduced to account for the Majorana masses of light neutrinos. For this purpose, we compute the nuclear matrix elements as functions of the mass of the mediating fermions and estimate the associated uncertainties. We then discuss what can be inferred on the seesaw model parameters in the different mass regimes and clarify how the contribution of the light neutrinos should always be taken into account when deriving bounds on the extra parameters. Conversely, the extra states can also have a significant impact, cancelling the Standard Model neutrino contribution for masses lighter than the nuclear scale and leading to vanishing neutrinoless double beta decay amplitudes even if neutrinos are Majorana particles. We also discuss how seesaw models could reconcile large rates of neutrinoless double beta decay with more stringent cosmological bounds on neutrino masses.

  16. Double Tracks revegetation and monitoring plan

    SciTech Connect (OSTI)

    NONE

    1997-07-01

    This document is a reclamation plan for short-term and long-term stabilization of land disturbed by activities associated with interim clean-up of radionuclide-contaminated surface soil at the Double Tracks site. This document has been prepared to provide general reclamation practices and procedures that will be followed during restoration of the cleanup site. Reclamation demonstration plots were established near the site in the fall of 1994 to evaluate the performance of several native species and to evaluate different irrigation strategies. Results of the study at Double Tracks, as well as the results from numerous studies conducted at other sites (Area 11 and Area 19 of the Nevada Test Site), have been summarized and incorporated into this final reclamation plan for the interim cleanup of the Double Tracks site, located northwest of the Nevada Test Site on the Nellis Air Force Range. Surface soils at Double Tracks were contaminated as a result of the detonation of a device containing plutonium and depleted uranium using chemical explosives. The total amount of Pu deposited on the site was between 980 and 1,600 grams and was scattered downwind south of the detonation site. Short-term stabilization consists of the application of a chemical soil stabilizer that is applied immediately following excavation of the contaminated soils to minimize Pu resuspension. Long-term stabilization is accomplished by the establishment of a permanent vegetation.

  17. Double layer capacitor prospects look good

    SciTech Connect (OSTI)

    1995-07-01

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

  18. 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...

  19. 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-

  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. Diapycnal advection by double diffusion and turbulence in the ocean

    E-Print Network [OSTI]

    St. Laurent, Louis C

    1999-01-01

    Observations of diapycnal mixing rates are examined and related to diapycnal advection for both double-diffusive and turbulent regimes. The role of double-diffusive mixing at the site of the North Atlantic Tracer Release ...

  2. The effects of double-diffusion on a baroclinic vortex

    E-Print Network [OSTI]

    Smith, Wendy Marie

    1987-01-01

    Laboratory experiments were performed to study the combined effects of double-diffusion and rotation on an oceanic intrusion. Intrusions are driven across density-compensated fronts by the divergence of the double-diffusive ...

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

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

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

  4. Computer code for double beta decay QRPA based calculations

    E-Print Network [OSTI]

    Bertulani, Carlos A. - Department of Physics and Astronomy, Texas A&M University

    the experimental bound [11] on neutrinoless double beta decay (## 0# ). The only way out would be to have two

  5. Neutrinoless Double Beta Decay and Physics Beyond the Standard Model

    E-Print Network [OSTI]

    Frank F. Deppisch; Martin Hirsch; Heinrich Päs

    2012-08-03

    Neutrinoless double beta decay is the most powerful tool to probe not only for Majorana neutrino masses but for lepton number violating physics in general. We discuss relations between lepton number violation, double beta decay and neutrino mass, review a general Lorentz invariant parametrization of the double beta decay rate, highlight a number of different new physics models showing how different mechanisms can trigger double beta decay, and finally discuss possibilities to discriminate and test these models and mechanisms in complementary experiments.

  6. Sensitivity of CUORE to Neutrinoless Double-Beta Decay

    E-Print Network [OSTI]

    Alessandria, F.

    2013-01-01

    of CUORE to Neutrinoless Double-Beta Decay b c,:L d e f F .s t results on neutrinoless double beta decay of T e w i t hthe study of neutrinoless double beta decay, J . C r y s t .

  7. The Majorana Neutrinoless Double-Beta Decay Experiment

    E-Print Network [OSTI]

    Washington at Seattle, University of - Department of Physics, Electroweak Interaction Research Group

    The Majorana Neutrinoless Double-Beta Decay Experiment Pre-conceptual Design Proposal November 22 Motivation for Neutrinoless Double-Beta Decay Experiments . . . . . . . . . 4 2.1.1 Community Guidance Neutrinoless Double-Beta Decay Results . . . . . . . . . . . . . . . . . . . . 12 2.5 Next

  8. Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion

    SciTech Connect (OSTI)

    Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A.

    2014-10-02

    Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.

  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. 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 ...

  11. 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...

  12. Double pulse Thomson scattering system at RTP

    SciTech Connect (OSTI)

    Beurskens, M.N.; Barth, C.J.; Chu, C.C.; Donne, A.J.; Herranz, J.A.; Lopes Cardozo, N.J.; van der Meiden, H.J.; Pijper, F.J. [FOM-Instituut voor Plasmafysica `Rijnhuizen`, Associatie Euratom-FOM, 3430 BE Nieuwegein (The Netherlands)] [FOM-Instituut voor Plasmafysica `Rijnhuizen`, Associatie Euratom-FOM, 3430 BE Nieuwegein (The Netherlands)

    1997-01-01

    In this article a double pulse multiposition Thomson scattering diagnostic, under construction at RTP, is discussed. Light from a double pulsed ruby laser (pulse separation: 10{endash}800 {mu}s, max. 2{times}12.5 J) is scattered by the free electrons of the tokamak plasma and relayed to a Littrow polychromator for spectral analysis. The spectrally resolved light is recorded by two ICCD detectors. Simulations show that the system sensitivity will be such that electron temperatures in the range of 100 eV{endash}7 keV can be determined with an accuracy as good as 2{percent}{endash}3{percent} for electron densities of 10{sup 20} m{sup {minus}3}, with a spatial resolution down to 2.6 mm. With this diagnostic the dynamics of small scale structures in the electron temperature profile will be studied. {copyright} {ital 1997 American Institute of Physics.}

  13. JUNO and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Shao-Feng Ge; Werner Rodejohann

    2015-07-20

    We study the impact of the precision determination of oscillation parameters in the JUNO experiment on half-life predictions for neutrinoless double beta decay. We show that the solar neutrino mixing angle can be measured by JUNO with below 1% uncertainty. This implies in particular that the minimal value of the effective mass in the inverted mass ordering will be known essentially without uncertainty. We demonstrate that this reduces the range of half-life predictions in order to test this value by a factor of two. The remaining uncertainty is caused by nuclear matrix elements. This has important consequences for future double beta decay experiments that aim at ruling out the inverted mass ordering or the Majorana nature of neutrinos.

  14. Fermion Doubling in Loop Quantum Gravity

    E-Print Network [OSTI]

    Jacob Barnett; Lee Smolin

    2015-07-05

    In this paper, we show that the Hamiltonian approach to loop quantum gravity has a fermion doubling problem. To obtain this result, we couple loop quantum gravity to a free massless scalar and a chiral fermion field, gauge fixing the many fingered time gauge invariance by interpreting the scalar field as a physical clock. We expand around a quantum gravity state based on a regular lattice and consider the limit where the bare cosmological constant is large but the fermonic excitations have energies low in Planck units. We then make the case for identifying the energy spectrum in this approximation with that of a model of lattice fermion theory which is known to double.

  15. Importance of neutrinoless double beta decay

    E-Print Network [OSTI]

    Utpal Sarkar

    2007-12-17

    A natural explanation for the smallness of the neutrino mass requires them to be Majorana particles violating lepton number by two units. Since lepton number violation can have several interesting consequences in particle physics and cosmology, it is of utmost importance to find out if there is lepton number violation in nature and what is its magnitude. The neutrinoless double beta decay experiment can answer these questions: if there is lepton number violation and if neutrinos are Majorana particles. In addition, the magnitude of neutrinoless double beta decay will constrain any other lepton number violating processes. This lepton number violation may also be relatd to the matter-antimatter asymmetry of the universe, dark matter and cosmological constant.

  16. JUNO and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Ge, Shao-Feng

    2015-01-01

    We study the impact of the precision determination of oscillation parameters in the JUNO experiment on half-life predictions for neutrinoless double beta decay. We show that the solar neutrino mixing angle can be measured by JUNO with below 1% uncertainty. This implies in particular that the minimal value of the effective mass in the inverted mass ordering will be known essentially without uncertainty. We demonstrate that this reduces the range of half-life predictions in order to test this value by a factor of two. The remaining uncertainty is caused by nuclear matrix elements. This has important consequences for future double beta decay experiments that aim at ruling out the inverted mass ordering or the Majorana nature of neutrinos.

  17. Recombination energy in double white dwarf formation

    E-Print Network [OSTI]

    Nandez, Jose L A; Lombardi, James C

    2015-01-01

    In this Letter we investigate the role of recombination energy during a common envelope event. We confirm that taking this energy into account helps to avoid the formation of the circumbinary envelope commonly found in previous studies. For the first time, we can model a complete common envelope event, with a clean compact double white dwarf binary system formed at the end. The resulting binary orbit is almost perfectly circular. In addition to considering recombination energy, we also show that between 1/4 and 1/2 of the released orbital energy is taken away by the ejected material. We apply this new method to the case of the double-white dwarf system WD 1101+364, and we find that the progenitor system at the start of the common envelope event consisted of a $\\sim1.5M_\\odot$ red giant star in a $\\sim 30$ day orbit with a white dwarf companion.

  18. Simulation of Double-Pulse Laser Ablation

    SciTech Connect (OSTI)

    Povarnitsyn, Mikhail E.; Khishchenko, Konstantin V.; Levashov, Pavel R. [Joint Institute for High Temperatures of RAS, Izhorskaya 13 Bldg 2, Moscow, 125412 (Russian Federation); Itina, Tatian E. [Laboratoire Hubert Curien, UMR CNRS 5516, 18 rue Benoit Lauras, Bat. F, 42000, St-Etienne (France)

    2010-10-08

    We investigate the physical reasons of a strange decrease in the ablation depth observed in femtosecond double-pulse experiments with increasing delay between the pulses. Two ultrashort pulses of the same energy produce the crater which is less than that created by a single pulse. Hydrodynamic simulation shows that the ablation mechanism is suppressed when the delay between the pulses exceeds the electron-ion relaxation time. In this case, the interaction of the second laser pulse with the expanding target material leads to the formation of the second shock wave suppressing the rarefaction wave created by the first pulse. The modeling of the double-pulse ablation for different delays between pulses confirms this explanation.

  19. 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).

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. Double Talk: Asturias's America in Cuculcán

    E-Print Network [OSTI]

    Unruh, Vicky

    1992-09-01

    Vicky Unruh, University of Kansas Double Talk: Asturias's America in Cuculcan^ M iguel Angel Asturias's Cuculcan, a dra- matic collage of color, sound, motion, and words, is his most overtly ethnographic play, and, as a product of his... vanguardist years, it is also the most radically experimental. Cuculcan did not appear in print until 1948,2 but Asturias de- scribed the work in progress in a 1932 journalis- tic essay, "Las posibilidades de un teatro americano."3 Although both Cuculcan...

  6. Double-clad nuclear fuel safety rod

    DOE Patents [OSTI]

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

    1984-01-01

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

  7. Neutrinoless Double Beta Decay and its "Inverse"

    E-Print Network [OSTI]

    Clemens A. Heusch; Peter Minkowski

    1996-11-18

    Recent considerations by these authors pointed out the attractive features which a search for the exchange of heavy Majorana neutrinos could have for solving the mass and the lepton number puzzles for all neutrinos, in TeV-level electron-electron scattering. In the present note, we show that, contrary to subsequently published arguments, non-observation of neutrinoless double beta decay has, to date, no bearing on the promise of this important task for future linear electron colliders.

  8. Tetraquark Production in Double Parton Scattering

    E-Print Network [OSTI]

    F. Carvalho; E. R. Cazaroto; V. P. Gonçalves; F. S. Navarra

    2015-11-23

    We develop a model to study tetraquark production in hadronic collisions. We focus on double parton scattering and formulate a version of the color evaporation model for the production of the $X(3872)$ and of the $T_{4c}$ tetraquark, a state composed by the $c \\bar{c} c \\bar{c}$ quarks. We find that the production cross section grows rapidly with the collision energy $\\sqrt{s}$ and make predictions for the forthcoming higher energy data of the LHC.

  9. Neutrinoless Double Beta Decay in Particle Physics

    E-Print Network [OSTI]

    Werner Rodejohann

    2010-11-22

    Neutrinoless double beta decay is a process of fundamental importance for particle physics. It can be mediated by light massive Majorana neutrinos (standard interpretation) or by something else (non-standard interpretations). We review its dependence on the neutrino parameters, its complementarity to other observables sensitive to neutrino mass, and emphasize its ability to distinguish different neutrino mass models. Then we discuss mechanisms different from light Majorana neutrino exchange, and show what can be learned from those and how they could be tested.

  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. Vibration of Generalized Double Well Oscillators

    E-Print Network [OSTI]

    Grzegorz Litak; Marek Borowiec; Arkadiusz Syta

    2006-10-20

    We have applied the Melnikov criterion to examine a global homoclinic bifurcation and transition to chaos in a case of a double well dynamical system with a nonlinear fractional damping term and external excitation. The usual double well Duffing potential having a negative square term and positive quartic term has been generalized to a double well potential with a negative square term and a positive one with an arbitrary real exponent $q > 2$. We have also used a fractional damping term with an arbitrary power $p$ applied to velocity which enables one to cover a wide range of realistic damping factors: from dry friction $p \\to 0$ to turbulent resistance phenomena $p=2$. Using perturbation methods we have found a critical forcing amplitude $\\mu_c$ above which the system may behave chaotically. Our results show that the vibrating system is less stable in transition to chaos for smaller $p$ satisfying an exponential scaling low. The critical amplitude $\\mu_c$ as an exponential function of $p$. The analytical results have been illustrated by numerical simulations using standard nonlinear tools such as Poincare maps and the maximal Lyapunov exponent. As usual for chosen system parameters we have identified a chaotic motion above the critical Melnikov amplitude $\\mu_c$.

  12. A background free double beta decay experiment

    E-Print Network [OSTI]

    Ioannis Giomataris

    2010-12-20

    We present a new detection scheme for rejecting backgrounds in neutrino less double beta decay experiments. It relies on the detection of Cherenkov light emitted by electrons in the MeV region. The momentum threshold is tuned to reach a good discrimination between background and good events. We consider many detector concepts and a range of target materials. The most promising is a high-pressure 136Xe emitter for which the required energy threshold is easily adjusted. Combination of this concept and a high pressure Time Projection Chamber could provide an optimal solution. A simple and low cost effective solution is to use the Spherical Proportional Counter that provides two delayed signals from ionization and Cherenkov light. In solid-state double beta decay emitters, because of their higher density, the considered process is out of energy range. An alternative solution could be the development of double decay emitters with lower density by using for instance the aerogel technique. It is surprising that a technology used for particle identification in high-energy physics becomes a powerful tool for rejecting backgrounds in such low-energy experiments.

  13. Double beta decays of {sup 106}Cd

    SciTech Connect (OSTI)

    Suhonen, Jouni [Department of Physics, P.O. Box 35 (YFL), FI-40014 University of Jyvaeskylae (Finland)

    2011-12-16

    The two-neutrino (2{nu}2{beta}) and neutrinoless (0{nu}2{beta}) double beta decays of {sup 106}Cd are studied for the transitions to the ground state 0{sub gs}{sup +} and 0{sup +} and 2{sup +} excited states in {sup 106}Pd by using realistic many-body wave functions calculated in the framework of the quasiparticle random-phase approximation. Effective, G-matrix-derived nuclear forces are used in realistic single-particle model spaces. All the possible channels, {beta}{sup +}{beta}{sup +}, {beta}{sup +}EC, and ECEC, are discussed for both the 2{nu}2{beta} and 0{nu}2{beta} decays. The associated half-lives are computed and particular attention is devoted to the study of the detectability of the resonant neutrinoless double electron capture (R0{nu}ECEC) process in {sup 106}Cd. The calculations of the present article constitute the thus far most complete and up-to-date investigation of the double-beta-decay properties of {sup 106}Cd.

  14. Double-Difference Tomography for Sequestration MVA

    SciTech Connect (OSTI)

    Westman, Erik

    2008-12-31

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

  15. 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

  16. 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

  17. 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.

  18. 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

  19. Exploring the Neutrinoless Double Beta Decay in the Inverted Neutrino Hierarchy with Bolometric Detectors

    E-Print Network [OSTI]

    Artusa, D. R.

    2014-01-01

    Exploring the Neutrinoless Double Beta Decay in the InvertedC. Giunti, Neutrinoless double-beta decay. A brief review,el- ements for neutrinoless double-beta decay and double-

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

    SciTech Connect (OSTI)

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

    2011-06-01

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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Optical double-slit particle measuring system

    DOE Patents [OSTI]

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

    1982-03-25

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

  6. Optical double-slit particle measuring system

    DOE Patents [OSTI]

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

    1984-01-01

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

  7. Neutrinoless double beta decay and QCD corrections

    E-Print Network [OSTI]

    Namit Mahajan

    2014-01-30

    We consider one loop QCD corrections and renormalization group running of the neutrinoless double beta decay amplitude focusing on the short-range part of the amplitude (without the light neutrino exchange) and find that these corrections can be sizeable. Depending on the operator under consideration, there can be moderate to large cancellations or significant enhancements. We discuss several specific examples in this context. Such large corrections will lead to significant shifts in the half-life estimates which currently are known to be plagued with the uncertainties due to nuclear physics inputs to the physical matrix elements.

  8. Neutrinoless double beta decay and neutrino masses

    SciTech Connect (OSTI)

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

    2012-07-27

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

  9. NGC 4340: Double Bar + Fossil Nuclear Ring

    E-Print Network [OSTI]

    P. Erwin; J. C. Vega Beltran; J. E. Beckman

    2000-10-03

    NGC 4340 is a double-barred SB0 galaxy in the Virgo cluster (Wozniak et al. 1995). Here, we present evidence that this galaxy also posseses a luminous stellar nuclear ring of relatively old stars with little or no gas. The ring lies just outside the inner bar, at the probable inner inner Lindblad resonance (IILR) of the outer bar. Careful inspection of the isophotes and unsharp masks shows that the two bars are slightly misaligned, which suggests they may be independently rotating.

  10. Double acting stirling engine phase control

    SciTech Connect (OSTI)

    Berchowitz, David M.

    1983-01-01

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

  11. The double contact nature of TT Herculis

    SciTech Connect (OSTI)

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

    2014-03-01

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

  12. A Microscopic Double-Slit Experiment

    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 HomeA Better Anode Design to Improve Lithium-Ion Batteries Print Lithium-ionAA Microscopic Double-Slit

  13. A Microscopic Double-Slit Experiment

    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 HomeA Better Anode Design to Improve Lithium-Ion Batteries Print Lithium-ionAA Microscopic Double-SlitA

  14. A Microscopic Double-Slit Experiment

    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 HomeA Better Anode Design to Improve Lithium-Ion Batteries Print Lithium-ionAA Microscopic Double-SlitAA

  15. A Microscopic Double-Slit Experiment

    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 HomeA Better Anode Design to Improve Lithium-Ion Batteries Print Lithium-ionAA Microscopic Double-SlitAAA

  16. Double Coil Condenser Apparatus - Energy Innovation Portal

    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 theCovalentLaboratory |Sector Full reportTown2008DonaldEnergyDouble

  17. 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.

  18. Double Field Theory on Group Manifolds (Thesis)

    E-Print Network [OSTI]

    Hassler, Falk

    2015-01-01

    This thesis deals with Double Field Theory (DFT), an effective field theory capturing the low energy dynamics of closed strings on a torus. It renders T-duality on a torus manifest by adding $D$ winding coordinates in addition to the $D$ space time coordinates. An essential consistency constraint of the theory, the strong constraint, only allows for field configurations which depend on half of the coordinates of the arising doubled space. I derive DFT${}_\\mathrm{WZW}$, a generalization of the current formalism. It captures the low energy dynamics of a closed bosonic string propagating on a compact group manifold. Its classical action and the corresponding gauge transformations arise from Closed String Field Theory up to cubic order in the massless fields. These results are rewritten in terms of a generalized metric and extended to all orders in the fields. There is an explicit distinction between background and fluctuations. For the gauge algebra to close, the latter have to fulfill a modified strong constrai...

  19. Double parton scattering at high energies

    E-Print Network [OSTI]

    Antoni Szczurek

    2015-04-24

    We discuss a few examples of rich newly developing field of double parton scattering. We start our presentation from production of two pairs of charm quark-antiquark and argue that it is the golden reaction to study the double parton scattering effects. In addition to the DPS we consider briefly also mechanism of single parton scattering and show that it gives much smaller contribution to the $c \\bar c c \\bar c$ final state. Next we discuss a perturbative parton-splitting mechanism which should be included in addition to the conventional DPS mechanism. We show that the presence of this mechanism unavoidably leads to collision energy and other kinematical variables dependence of so-called $\\sigma_{eff}$ parameter being extracted from different experiments. Next we briefly discuss production of four jets. We concentrate on estimation of the contribution of DPS for jets remote in rapidity. Understanding of this contribution is very important in the context of searches for BFKL effects known under the the name Mueller-Navelet jets. We discuss the situation in a more general context. Finally we briefly mention about DPS effects in production of $W^+ W^-$. Outlook closes the presentation.

  20. Renormalization of a Lorentz invariant doubled worldsheet theory

    E-Print Network [OSTI]

    Nibbelink, Stefan Groot; Patalong, Peter

    2013-01-01

    Manifestly T-duality covariant worldsheet string models can be constructed by doubling the coordinate fields. We describe the underlying gauge symmetry of a recently proposed Lorentz invariant doubled worldsheet theory that makes half of the worldsheet degrees of freedom redundant. By shifting the Lagrange multiplier, that enforces the gauge fixing condition, the worldsheet action can be cast into various guises. We investigate the renormalization of this theory using a non-linear background/quantum split by employing a normal coordinate expansion adapted to the gauge-fixed theory. The propagator of the doubled coordinates contains a projection operator encoding that half of them do not propagate. We determine the doubled target space equations of motion by requiring one-loop Weyl invariance. Some of them are generalizations of the conventional sigma model beta-functions, while others seem to be novel to the doubled theory: In particular, a dilaton equation seems related to the strong constraint of double fie...

  1. 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 ...

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

    E-Print Network [OSTI]

    Irina Nasteva; for the NEMO 3 Collaboration

    2008-10-03

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

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

    SciTech Connect (OSTI)

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

    2008-11-23

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

  4. Search for neutrinoless double beta decay with NEMO 3 experiment

    E-Print Network [OSTI]

    Zornitza Daraktchieva

    2009-01-18

    NEMO 3 experiment is designed to search for neutrinoless double beta decay. It is located in the Modane Underground Laboratory (LSM) and has been taking data since February 2003. The half- lives of two neutrino beta decay have been measured for seven isotopes. No evidence of neutrinoless double beta decay has been found. The limits on both the half-lives of the neutrinoless double beta decay and the corresponding Majorana effective masses are derived

  5. Neutrinoless Double Beta Decay in Supersymmetric Seesaw model

    E-Print Network [OSTI]

    Tai-Fu Feng; Xue-Qian Li; Yan-An Luo

    2002-09-26

    Inspired by the recent HEIDELBERG-MOSCOW double beta decay experiment, we discuss the neutrinoless double beta decay in the supersymmetric seesaw model. Our numerical analysis indicates that we can naturally explain the data of the observed neutrinoless double beta decay, as well as that of the solar and atmospheric neutrino experiments with at least one Majorana-like sneutrino of middle energy scale in the model.

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

    Office of Scientific and Technical Information (OSTI)

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

  7. Majorana Neutrino Masses from Neutrinoless Double Beta Decay and Cosmology

    E-Print Network [OSTI]

    V. Barger; K. Whisnant

    1999-04-08

    When three Majorana neutrinos describe the solar and atmospheric neutrino data via oscillations, a nonzero measurement of neutrinoless double beta ($0\

  8. Neutrinoless double beta decay can constrain neutrino dark matter

    E-Print Network [OSTI]

    V. Barger; S. L. Glashow; D. Marfatia; K. Whisnant

    2002-02-26

    We examine how constraints can be placed on the neutrino component of dark matter by an accurate measurement of neutrinoless double beta ($0\

  9. T-686: IBM Tivoli Integrated Portal Java Double Literal Denial...

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

    password) PLATFORM: Tivoli versions prior to 1.1.1.15. ABSTRACT: IBM Tivoli Integrated Portal Java Double Literal Denial of Service Vulnerability. reference LINKS: IBM ID: 1508061...

  10. 75 years of double beta decay: yesterday, today and tomorrow

    E-Print Network [OSTI]

    A. S. Barabash

    2011-01-24

    In this report I will briefly review the motivation and history of double beta decay search since the first consideration of two neutrino process (2$\\beta(2\

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

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

    year 2013 goal by converting 13,679 metric tons of depleted uranium hexafluoride (DUF6), more than doubling production a year earlier. EM's Portsmouth Paducah Project Office...

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

    Office of Scientific and Technical Information (OSTI)

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

  13. The MAJORANA DEMONSTRATOR: A Search for Neutrinoless Double-beta...

    Office of Scientific and Technical Information (OSTI)

    Conference: The MAJORANA DEMONSTRATOR: A Search for Neutrinoless Double-beta Decay of Germanium-76 Citation Details In-Document Search Title: The MAJORANA DEMONSTRATOR: A Search...

  14. Full Quantum Theory of ${C_{60}}$ Double-slit Diffraction

    E-Print Network [OSTI]

    Xiang-Yao Wu; Ji Ma; Bo-Jun Zhang; Hong Li; Xiao-Jing Liu; Nuo Ba; Si-Qi Zhang; Jing Wang; He Dong; Xin-Guo Yin

    2013-05-10

    In this paper, we apply the full new method of quantum theory to study the double-slit diffraction of ${C_{60}}$ molecules. We calculate the double-slit wave functions of ${C_{60}}$ molecules by Schr\\"{o}dinger equation, and calculate the diffraction wave function behind the slits with the Feynman path integral quantum theory, and then give the relation between the diffraction intensity of double-slit and diffraction pattern position. We compare the calculation results with two different double-slit diffraction experiments. When the decoherence effects are considered, the calculation results are in good agreement with the two experimental data.

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

    Office of Scientific and Technical Information (OSTI)

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

  16. Half-lives of Double $?^+$-decay with Two Neutrinos

    E-Print Network [OSTI]

    Yuejiao Ren; Zhongzhou Ren

    2015-01-07

    Nuclear double $\\beta ^-$-decays with two neutrinos were observed for many years and a systematic law describing the relation between their half-lives and decay energies was also proposed recently [Phys. Rev. C89, 064603 (2014)]. However, double $\\beta ^+$-decay ($\\beta ^+\\beta^+)$ with emission of both two positrons and two neutrinos has not been observed up to date. In this article, we perform a systematic analysis on the candidates of double $\\beta ^+$-decay, based on the 2012 nuclear mass table. Eight nuclei are found to be the good candidates for double $\\beta ^+$-decay and their half-lives are predicted according to the generalization of the systematic law to double $\\beta ^+$-decay. As far as we know, there is no theoretical result on double $\\beta ^+$-decay of nucleus $^{154}Dy$ and our result is the first prediction on this nucleus. This is also the first complete research on eight double $\\beta ^+$-decay candidates based on the available data of nuclear masses. It is expected that the calculated half-lives of double $\\beta ^+$-decay in this article will be useful for future experimental search of double $\\beta ^+$-decay.

  17. 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.

  18. 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.

  19. 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

  20. 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,...

  1. 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...

  2. 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

  3. 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,

  4. 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.

  5. 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.

  6. 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

  7. 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 ...

  8. Double-Slit Experiments with Microwave Billiards

    E-Print Network [OSTI]

    S. Bittner; B. Dietz; M. Miski-Oglu; P. Oria Iriarte; A. Richter; F. Schäfer

    2011-07-27

    Single and double-slit experiments are performed with two microwave billiards with the shapes of a rectangle, respectively, a quarter stadium. The classical dynamics of the former is regular, that of the latter is chaotic. Microwaves can leave the billiards via slits in the boundary, forming interference patterns on a screen. The aim is to determine the effect of the billiard dynamics on their structure. For this the development of a method for the construction of a directed wave packet by means of an array of multiple antennas was crucial. The interference patterns show a sensitive dependence not only on the billiard dynamics but also on the initial position and direction of the wave packet.

  9. Correlations and the neutrinoless double beta decay

    SciTech Connect (OSTI)

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

    2009-11-09

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

  10. Neutrinoless Double Beta Decay with SNO+

    E-Print Network [OSTI]

    J. Hartnell; for the SNO+ collaboration

    2012-01-30

    SNO+ will search for neutrinoless double beta decay by loading 780 tonnes of linear alkylbenzene liquid scintillator with O(tonne) of neodymium. Using natural Nd at 0.1% loading will provide 43.7 kg of 150Nd given its 5.6% abundance and allow the experiment to reach a sensitivity to the effective neutrino mass of 100-200 meV at 90% C.L in a 3 year run. The SNO+ detector has ultra low backgrounds with 7000 tonnes of water shielding and self-shielding of the scintillator. Distillation and several other purification techniques will be used with the aim of achieving Borexino levels of backgrounds. The experiment is fully funded and data taking with light-water will commence in 2012 with scintillator data following in 2013.

  11. Double beta decay and neutrino mass models

    E-Print Network [OSTI]

    Helo, J C; Ota, T; Santos, F A Pereira dos

    2015-01-01

    Neutrinoless double beta decay allows to constrain lepton number violating extensions of the standard model. If neutrinos are Majorana particles, the mass mechanism will always contribute to the decay rate, however, it is not a priori guaranteed to be the dominant contribution in all models. Here, we discuss whether the mass mechanism dominates or not from the theory point of view. We classify all possible (scalar-mediated) short-range contributions to the decay rate according to the loop level, at which the corresponding models will generate Majorana neutrino masses, and discuss the expected relative size of the different contributions to the decay rate in each class. We also work out the phenomenology of one concrete 2-loop model in which both, mass mechanism and short-range diagram, might lead to competitive contributions, in some detail.

  12. Double Shell Tank (DST) Utilities Specification

    SciTech Connect (OSTI)

    SUSIENE, W.T.

    2000-04-27

    This specification establishes the performance requirements and provides the references to the requisite codes and standards to he applied during the design of the Double-Shell Tank (DST) Utilities Subsystems that support the first phase of waste feed delivery (WFD). The DST Utilities Subsystems provide electrical power, raw/potable water, and service/instrument air to the equipment and structures used to transfer low-activity waste (LAW) and high-level waste (HLW) to designated DST staging tanks. The DST Utilities Subsystems also support the equipment and structures used to deliver blended LAW and HLW feed from these staging tanks to the River Protection Project (RPP) Privatization Contractor facility where the waste will be immobilized. This specification is intended to be the basis for new projects/installations. This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program.

  13. Double-rotor rotary engine and turbine

    SciTech Connect (OSTI)

    Lin, A.S.

    1990-04-03

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

  14. Heterotic $?$'-corrections in Double Field Theory

    E-Print Network [OSTI]

    Oscar A. Bedoya; Diego Marques; Carmen Nunez

    2014-12-15

    We extend the generalized flux formulation of Double Field Theory to include all the first order bosonic contributions to the $\\alpha '$ expansion of the heterotic string low energy effective theory. The generalized tangent space and duality group are enhanced by $\\alpha'$ corrections, and the gauge symmetries are generated by the usual (gauged) generalized Lie derivative in the extended space. The generalized frame receives derivative corrections through the spin connection with torsion, which is incorporated as a new degree of freedom in the extended bein. We compute the generalized fluxes and find the Riemann curvature tensor with torsion as one of their components. All the four-derivative terms of the action, Bianchi identities and equations of motion are reproduced. Using this formalism, we obtain the first order $\\alpha'$ corrections to the heterotic Buscher rules. The relation of our results to alternative formulations in the literature is discussed and future research directions are outlined.

  15. Neutrinoless Double Beta Decay in Gauge Theories

    E-Print Network [OSTI]

    J. D. Vergados

    1999-07-12

    Neutrinoless double beta decay is a very important process both from the particle and nuclear physics point of view. Its observation will severely constrain the existing models and signal that the neutrinos are massive Majorana particles. From the elementary particle point of view it pops up in almost every model. In addition to the traditional mechanisms, like the neutrino mass, the admixture of right handed currents etc, it may occur due to the R-parity violating supersymmetric (SUSY) interactions. From the nuclear physics point of view it is challenging, because: 1) The relevant nuclei have complicated nuclear structure. 2) The energetically allowed transitions are exhaust a small part of all the strength. 3) One must cope with the short distance behavior of the transition operators, especially when the intermediate particles are heavy (eg in SUSY models). Thus novel effects, like the double beta decay of pions in flight between nucleons, have to be considered. 4) The intermediate momenta involved are about 100 MeV. Thus one has to take into account possible momentum dependent terms in the nucleon current. We find that, for the mass mechanism, such modifications of the nucleon current for light neutrinos reduce the nuclear matrix elements by about 25 per cent, almost regardless of the nuclear model. In the case of heavy neutrinos the effect is much larger and model dependent. Taking the above effects into account, the available nuclear matrix elements for the experimentally interesting nuclei A = 76, 82, 96, 100, 116, 128, 130, 136 and 150 and the experimental limits on the life times we have extracted new stringent limits on the average neutrino mass and on the R-parity violating coupling for various SUSY models.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Double-nonlinear metamaterials Rongcao Yang1,2,a

    E-Print Network [OSTI]

    Double-nonlinear metamaterials Rongcao Yang1,2,a and Ilya V. Shadrivov1 1 Nonlinear Physics Centre 10 December 2010 We study a double-nonlinear metamaterial composed of a mixture of both nonlinear electric and nonlinear magnetic resonators. We predict multistable behavior in such metamaterial

  1. Countering Trusting Trust through Diverse Double-Compiling

    E-Print Network [OSTI]

    Sandhu, Ravi

    1 Countering Trusting Trust through Diverse Double-Compiling David A. Wheeler February 28, 2006 · Inadequate solutions & related work · Solution: Diverse double-compiling (DDC) ­ What it is ­ Why it works & broader implications 3 Trusting trust attack Compiler executable (malicious) Critical program (malicious

  2. Significant neutrinoless double beta decay with quasi-Dirac neutrinos

    E-Print Network [OSTI]

    Pei-Hong Gu

    2012-09-13

    A significant signal of neutrinoless double beta decay can be consistent with the existence of light quasi-Dirac neutrinos. To demonstrate this possibility, we consider a realistic model where the neutrino masses and the neutrinoless double beta decay can be simultaneously generated after a Peccei-Quinn symmetry breaking.

  3. Designing Truthful Spectrum Double Auctions with Local Markets

    E-Print Network [OSTI]

    Li, Baochun

    Designing Truthful Spectrum Double Auctions with Local Markets Wei Wang, Student Member, IEEE, Ben pieces in the market. We design a spectrum double auction that incorporates such locality in spectrum markets, while keeping the auction economically robust and computationally efficient. Our designs

  4. Maximal Matching for Double Auction Dengji Zhao1,2

    E-Print Network [OSTI]

    Zhang, Dongmo

    the problem of mechanism design for a double auc- tion market where multiple buyers and sellers buy and sell Design) platform, we show with experiments that the new matching method not only increases market price). Similar to the design of other market mechanisms, the main concerns of double auction design

  5. DoubleSpeed Safe Prime Generation David Naccache

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    prime generation is thus divided by two at the cost of generating primes of size k or k + 1 with equalDouble­Speed Safe Prime Generation David Naccache Gemplus Card International Applied Research method for doubling the speed of safe prime generation. The method is particularly suited to settings

  6. Double-Speed Safe Prime Generation David Naccache

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    at the cost of generating primes of size k or k + 1 with equal probability. The generation of RSA moduliDouble-Speed Safe Prime Generation David Naccache Gemplus Card International Applied Research method for doubling the speed of safe prime generation. The method is particularly suited to settings

  7. technology offer HPC/UHPC double wall elements

    E-Print Network [OSTI]

    Arnold, Anton

    buildings and towers like wind turbines, power plants or cooling towers. Fig. 1: UHPC double wall element to 20-45 mm in an easy and cost efficient way. Background Double wall elements are precast reinforced · Savings in material and weight · Savings in transport and crane costs · Dense structure of the precast

  8. Matched slow pulses using double electromagnetically induced transparency

    E-Print Network [OSTI]

    Lvovsky, Alexander

    Matched slow pulses using double electromagnetically induced transparency Andrew MacRae,* Geoff, 2008 We implement double electromagnetically induced transparency (DEIT) in rubidium vapor using Optical Society of America OCIS codes: 270.1670, 270.5585, 190.5530. Electromagnetically induced

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  1. Topoisomerase II Structure Suggests Novel DNA Cleavage Mechanism

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

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

  2. First results on neutrinoless double beta decay of Te-130 with the calorimetric cuoricino experiment

    E-Print Network [OSTI]

    2003-01-01

    Results on Neutrinoless Double Beta Decay of 130 Te with theEvidence for Neutrinoless Double Beta Decay” arXiv:hep-on “Evidence for neutrinoless double beta decay”- arXiv:hep-

  3. An Investigation and Characterization of Metal Foam Filled Double-Pipe Heat Exchangers

    E-Print Network [OSTI]

    Chen, Xi

    2014-01-01

    a metal foam filled double-pipe heat exchanger: a) Pressurein a metal foam filled double-pipe heat exchanger witha plain double-pipe heat exchanger: a) Total heat transfer

  4. Coronal electron confinement by double layers

    SciTech Connect (OSTI)

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

    2013-12-01

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

  5. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M. (Oak Ridge, TN)

    1995-01-01

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

  6. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M. (Oak Ridge, TN)

    1997-01-01

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

  7. Double Wick rotating Green-Schwarz strings

    E-Print Network [OSTI]

    Gleb Arutyunov; Stijn J. van Tongeren

    2015-05-05

    Via an appropriate field redefinition of the fermions, we find a set of conditions under which light cone gauge fixed world sheet theories of strings on two different backgrounds are related by a double Wick rotation. These conditions take the form of a set of transformation laws for the background fields, complementing a set of transformation laws for the metric and B field we found previously with a set for the dilaton and RR fields, and are compatible with the supergravity equations of motion. Our results prove that at least to second order in fermions, the AdS_5 x S^5 mirror model which plays an important role in the field of integrability in AdS/CFT, represents a string on `mirror AdS_5 x S^5', the background that follows from our transformations. We discuss analogous solutions for AdS_3 x S^3 x T^4 and AdS_2 x S^2 x T^6. The main ingredient in our derivation is the light cone gauge fixed action for a string on an (almost) completely generic background, which we explicitly derive to second order in fermions.

  8. Pionic contribution to neutrinoless double beta decay

    SciTech Connect (OSTI)

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

    2010-02-01

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

  9. 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

  10. Experimental research of double beta decay of atomic nuclei

    E-Print Network [OSTI]

    F. A. Danevich

    2011-12-26

    Results of several double beta decay experiments, performed with the help of low background crystal scintillators, are presented. In particular, the half-life value of the two-neutrino double beta decay of 116-Cd has been measured as 2.9 10^{19} yr, and the new half-life limit on the neutrinoless double beta decay of 116-Cd has been established as >1.7 10^{23} yr at 90%, which corresponds to a restriction on the neutrino mass <1.7 eV. New half-life bounds on the level of 10^{17}-10^{21} yr were set for double beta processes in 64-Zn, 70-Zn, 106-Cd, 108-Cd, 114-Cd, 136-Ce, 138-Ce, 142-Ce, 160-Gd, 180-W, and 186-W by using low-background CdWO4, GSO, and ZnWO4 crystal scintillators. The claim of discovery of the neutrinoless double beta decay of 76-Ge [Mod. Phys. Lett. A 16 (2001) 2409] was analyzed. The demands of the future high sensitivity double beta decay experiments, aiming to observe the neutrinoless double beta decay or to advance restrictions on the neutrino mass to < 0.01 eV, were considered. Requirements for their sensitivity and discovery potential were formulated. Two projects of double beta experiments with a sensitivity on the level of 10^{26}-10^{27} yr (CAMEO and CARVEL projects) were discussed. Scintillation properties and radioactive contamination of CaWO4, ZnWO4, CdWO4, PbWO4, GSO(Ce), CeF3, yttrium-aluminum garnet doped with neodymium (YAG:Nd) crystal scintillators were studied. Applicability of these scintillators to search for double beta decay was discussed.

  11. 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

  12. The classical double copy for Taub-NUT spacetime

    E-Print Network [OSTI]

    Luna, A; O'Connell, D; White, C D

    2015-01-01

    The double copy is a much-studied relationship between gauge theory and gravity amplitudes. Recently, this was generalised to an infinite family of classical solutions to Einstein's equations, namely stationary Kerr-Schild geometries. In this paper, we extend this to the Taub-NUT solution in gravity, which has a double Kerr-Schild form. The single copy of this solution is a dyon, whose electric and magnetic charges are related to the mass and NUT charge in the gravity theory. Finally, we find hints that the classical double copy extends to curved background geometries.

  13. Fabrication and Measurements of 500 MHz Double Spoke Cavity

    SciTech Connect (OSTI)

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

    2014-12-01

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

  14. Matched Slow Pulses Using Double Electromagnetically Induced Transparency

    E-Print Network [OSTI]

    Andrew MacRae; Geoff Campbell; A. I. Lvovsky

    2008-09-29

    We implement double electromagnetically-induced transparency (double EIT) in rubidium vapor, using a tripod-shaped energy level scheme consisting of hyperfine and magnetic sublevels of the 5S1/2 to 5P1/2 transition. We show experimentally that through the use of double EIT one can control the contrast of transparency windows as well as group velocities of the two signal fields. In particular, the group velocities can be equalized, which holds promise to greatly enhance nonlinear optical interaction between these fields.

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

    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 theCovalentLaboratory |Sector FullDOE Office of Science (SC) Double,

  16. 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.

  17. 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...

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

    Broader source: Energy.gov [DOE]

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

  19. Electrochemical Double-Layer Capacitors Using Carbon Nanotube Electrode Structures

    E-Print Network [OSTI]

    Schindall, Joel E.

    The structure and behavior of the electrical double-layer capacitor (EDLC) are described. The use of activated carbon electrodes is discussed and the limitations on voltage and accessible surface area are presented. Metrics ...

  20. Double beta decay experiments: beginning of a new era

    E-Print Network [OSTI]

    A. S. Barabash

    2012-09-19

    The review of current experiments on search and studying of double beta decay processes is done. Results of the most sensitive experiments are discussed and values of modern limits on effective Majorana neutrino mass ($) are given. New results on two neutrino double beta decay are presented. The special attention is given to new current experiments with mass of studied isotopes more than 100 kg, EXO--200 and KamLAND--Zen. These experiments open a new era in research of double beta decay. In the second part of the review prospects of search for neutrinoless double beta decay in new experiments with sensitivity to $$ at the level of $\\sim 0.01-0.1$ eV are discussed. Parameters and characteristics of the most perspective projects (CUORE, GERDA, MAJORANA, SuperNEMO, EXO, KamLAND--Zen, SNO+) are given.

  1. Evaluation of short-day onion doubled haploid lines 

    E-Print Network [OSTI]

    Walker, Ryan Lee

    2009-05-15

    Molecular marker analysis of seven putative onion (Allium cepa) doubled haploid (DH) lines developed at Texas A&M University was conducted to verify genetic homozygosity. Analysis was also conducted on five equivalent ...

  2. Comment on "Evidence for Neutrinoless Double Beta Decay"

    E-Print Network [OSTI]

    C. E. Aalseth; F. T. Avignone III; A. Barabash; F. Boehm; R. L. Brodzinski; J. I. Collar; P. J. Doe; H. Ejiri; S. R. Elliott; E. Fiorini; R. J. Gaitskell; G. Gratta; R. Hazama; K. Kazkaz; G. S. King III; R. T. Kouzes; H. S. Miley; M. K. Moe; A. Morales; J. Morales; A. Piepke; R. G. H. Robertson; W. Tornow; P. Vogel; R. A. Warner; J. F. Wilkerson

    2002-05-22

    We comment on the recent claim for the experimental observation of neutrinoless double-beta decay. We discuss several limitations in the analysis provided in that paper and conclude that there is no basis for the presented claim.

  3. Predicting an ultraviolet-tetraherz double resonance spectrum of formaldehyde

    E-Print Network [OSTI]

    Fenn, Emily E. (Emily Elizabeth)

    2006-01-01

    In preparation for performing a triple resonance experiment to study the Rydberg states of calcium monofluoride (CaF), a double resonance spectrum of formaldehyde will be recorded. A dye laser will populate a level in ...

  4. Nebraska: Company More than Doubles Annual Sales and Employees...

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

    than doubled their employees from 119 to 269 since 2010. Leveraging its EERE-supported hydrogen storage tank development, Hexagon is now an active player in the natural gas...

  5. The gauge algebra of double field theory and Courant brackets

    E-Print Network [OSTI]

    Hull, Chris

    We investigate the symmetry algebra of the recently proposed field theory on a doubled torus that describes closed string modes on a torus with both momentum and winding. The gauge parameters are constrained fields on the ...

  6. Performance of a double pass solar air collector

    SciTech Connect (OSTI)

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

    2010-11-15

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

  7. Band Tunneling through Double Barrier in Bilayer Graphene

    E-Print Network [OSTI]

    Hasan A. Alshehab; Hocine Bahlouli; Abderrahim El Mouhafid; Ahmed Jellal

    2014-01-20

    By taking into account the full four band energy spectrum, we calculate the transmission probability and conductance of electrons across symmetric and asymmetric double potential barrier with a confined interlayer potential difference in bilayer graphene. For energies less than the interlayer coupling \\gamma_{1}, E \\gamma_{1}, we obtain four possible ways for transmission resulting from the two propagating modes. We compute the associated transmission probabilities as well as their contribution to the conductance, study the effect of the double barrier geometry.

  8. Energy levels of double triangular graphene quantum dots

    SciTech Connect (OSTI)

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

    2014-09-28

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

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

    SciTech Connect (OSTI)

    Rosen, S.P.

    1983-01-01

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

  10. NEMO 3 double beta decay experiment: latest results

    E-Print Network [OSTI]

    A. S. Barabash

    2008-07-17

    The double beta decay experiment NEMO~3 has been taking data since February 2003. The aim of this experiment is to search for neutrinoless decay and investigate two neutrino double beta decay in seven different enriched isotopes ($^{100}$Mo,$^{82}$Se, $^{48}$Ca, $^{96}$Zr, $^{116}$Cd, $^{130}$Te and $^{150}$Nd). After analysis of the data corresponding to 693 days, no evidence for $0\

  11. Effect of nuclear deformation on double beta decay

    SciTech Connect (OSTI)

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

    2009-11-09

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

  12. Overconstrained estimates of neutrinoless double beta decay within the QRPA

    E-Print Network [OSTI]

    Amand Faessler; Gianluigi Fogli; Eligio Lisi; Vadim Rodin; Anna Maria Rotunno; Fedor Simkovic

    2008-05-29

    Estimates of nuclear matrix elements for neutrinoless double beta decay (0nu2beta) based on the quasiparticle random phase approximations (QRPA) are affected by theoretical uncertainties, which can be substantially reduced by fixing the unknown strength parameter g_pp of the residual particle-particle interaction through one experimental constraint - most notably through the two-neutrino double beta decay (2nu2beta) lifetime. However, it has been noted that the g_pp adjustment via 2\

  13. Deformed quantum double realization of the toric code and beyond

    E-Print Network [OSTI]

    Pramod Padmanabhan; Juan Pablo Ibieta Jimenez; Miguel Jorge Bernabé Ferreira; Paulo Teotonio-Sobrinho

    2015-12-10

    Quantum double models, such as the toric code, can be constructed from transfer matrices of lattice gauge theories with discrete gauge groups and parametrized by the center of the gauge group algebra and its dual. For general choices of these parameters the transfer matrix contains operators acting on links which can also be thought of as perturbations to the quantum double model driving it out of its topological phase and destroying the exact solvability of the quantum double model. We modify these transfer matrices with perturbations and extract exactly solvable models which remain in a quantum phase, thus nullifying the effect of the perturbation. The algebra of the modified vertex and plaquette operators now obey a deformed version of the quantum double algebra. The Abelian cases are shown to be in the quantum double phase whereas the non-Abelian phases are shown to be in a modified phase of the corresponding quantum double phase. These are illustrated with the groups $\\mathbb{Z}_n$ and $S_3$. The quantum phases are determined by studying the excitations of these systems namely their fusion rules and the statistics. We then go further to construct a transfer matrix which contains the other $\\mathbb{Z}_2$ phase namely the double semion phase. More generally for other discrete groups these transfer matrices contain the twisted quantum double models. These transfer matrices can be thought of as being obtained by introducing extra parameters into the transfer matrix of lattice gauge theories. These parameters are central elements belonging to the tensor products of the algebra and its dual and are associated to vertices and volumes of the three dimensional lattice. As in the case of the lattice gauge theories we construct the operators creating the excitations in this case and study their braiding and fusion properties.

  14. Neutrinoless Double Beta Decay with Negligible Neutrino Mass

    E-Print Network [OSTI]

    Biswajoy Brahmachari; Ernest Ma

    2002-02-27

    If the electron neutrino has an effective nonzero Majorana mass, then neutrinoless double beta decay will occur. However, the latter is possible also with a negligible neutrino mass. We show how this may happen in a simple model of scalar diquarks and dileptons. This possibility allows neutrino masses to be small and hierarchical, without conflicting with the possible experimental evidence of neutrinoless double beta decay.

  15. Possible background reductions in double beta decay experiments

    E-Print Network [OSTI]

    R. Arnold; C. Augier; J. Baker; A. Barabash; O. Bing; V. Brudanin; A. J. Caffrey; E. Caurier; K. Errahmane; A. -I. Etienvre; J. L. Guyonnet; F. Hubert; Ph. Hubert; C. Jollet; S. Jullian; O. Kochetov; V. Kovalenko; D. Lalanne; F. Leccia; C. Longuemare; Ch. Marquet; F. Mauger; H. W. Nicholson; H. Ohsumi; F. Piquemal; J-L. Reyss; X. Sarazin; Yu. Shitov; L. Simard; I. Stekl; J. Suhonen; C. S. Sutton; G. Szklarz; V. Timkin; V. Tretyak; V. Umatov; L. Vala; I. Vanyushin; V. Vasilyev; V. Vorobel; Ts. Vylov

    2003-02-19

    The background induced by radioactive impurities of $^{208}\\rm Tl$ and $^{214}\\rm Bi$ in the source of the double beta experiment NEMO-3 has been investigated. New methods of data analysis which decrease the background from the above mentioned contamination are identified. The techniques can also be applied to other double beta decay experiments capable of measuring independently the energies of the two electrons.

  16. 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

  17. 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 ...

  18. 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 ...

  19. 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...

  20. 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

  1. 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...

  2. 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 ...

  3. 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.

  4. 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

  5. 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

  6. What can we learn from neutrinoless double beta decay experiments?

    E-Print Network [OSTI]

    John N. Bahcall; Hitoshi Murayama; Carlos Pena-Garay

    2004-04-08

    We assess how well next generation neutrinoless double beta decay and normal neutrino beta decay experiments can answer four fundamental questions. 1) If neutrinoless double beta decay searches do not detect a signal, and if the spectrum is known to be inverted hierarchy, can we conclude that neutrinos are Dirac particles? 2) If neutrinoless double beta decay searches are negative and a next generation ordinary beta decay experiment detects the neutrino mass scale, can we conclude that neutrinos are Dirac particles? 3) If neutrinoless double beta decay is observed with a large neutrino mass element, what is the total mass in neutrinos? 4) If neutrinoless double beta decay is observed but next generation beta decay searches for a neutrino mass only set a mass upper limit, can we establish whether the mass hierarchy is normal or inverted? We base our answers on the expected performance of next generation neutrinoless double beta decay experiments and on simulations of the accuracy of calculations of nuclear matrix elements.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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...

  13. 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.

  14. TOWARDS A PRECISION MEASUREMENT OF THE HALF LIFE OF NEUTRINOLESS DOUBLE BETA DECAY OF 136

    E-Print Network [OSTI]

    Gratta, Giorgio

    ). Even if debatable, a first hint came from the claimed observation of neutrinoless double beta decay

  15. 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.

  16. 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.

  17. Bachelor programme European Studies Double Diploma 2014-2015 The third year (60 EC) of the Double Diploma Programme European Studies (old style)

    E-Print Network [OSTI]

    Twente, Universiteit

    1 Bachelor programme European Studies Double Diploma 2014-2015 The third year (60 EC) of the Double students who did their first two years at the University of Muenster and do their third year in 2014 arrangements For students of the old style double diploma programme who started their third year in Twente

  18. Gene Mutations Gene a finite segment of DNA specified

    E-Print Network [OSTI]

    Massey, Thomas N.

    mutation rates. · At low dose rate the genetic burden is carried by the male. · Genetic consequences Mass #12;Doubling Dose · Doubling dose is defined as the amount of radiation needed to produce twice the rate of genetic mutations than that would have been observed without radiation. · The doubling dose

  19. Mechanical seal having a double-tier mating ring

    DOE Patents [OSTI]

    Khonsari, Michael M.; Somanchi, Anoop K.

    2005-09-13

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

  20. The Spacetime of Double Field Theory: Review, Remarks, and Outlook

    E-Print Network [OSTI]

    Olaf Hohm; Dieter Lust; Barton Zwiebach

    2014-10-30

    We review double field theory (DFT) with emphasis on the doubled spacetime and its generalized coordinate transformations, which unify diffeomorphisms and b-field gauge transformations. We illustrate how the composition of generalized coordinate transformations fails to associate. Moreover, in dimensional reduction, the O(d,d) T-duality transformations of fields can be obtained as generalized diffeomorphisms. Restricted to a half-dimensional subspace, DFT includes `generalized geometry', but is more general in that local patches of the doubled space may be glued together with generalized coordinate transformations. Indeed, we show that for certain T-fold backgrounds with non-geometric fluxes, there are generalized coordinate transformations that induce, as gauge symmetries of DFT, the requisite O(d,d;Z) monodromy transformations. Finally we review recent results on the \\alpha' extension of DFT which, reduced to the half-dimensional subspace, yields intriguing modifications of the basic structures of generalized geometry.

  1. Exchange bias in Fe/Cr double superlattices.

    SciTech Connect (OSTI)

    Jiang, J. S.; Felcher, G. P.; Inomata, A.; Goyette, R.; Nelson, C.; Bader, S. D.

    1999-11-30

    Utilizing the oscillatory interlayer exchange coupling in Fe/Cr superlattices, we have constructed ''double superlattice'' structures where a ferromagnetic (F) and an antiferromagnetic (AF) Fe/Cr superlattice are coupled through a Cr spacer. The minor hysteresis loops in the magnetization are shifted from zero field, i.e., the F superlattice is exchange biased by the AF one. The double superlattices are sputter-deposited with (211) epitaxy and possess uniaxial in-plane magnetic anisotropy. The magnitude of the bias field is satisfactorily described by the classic formula for collinear spin structures. The coherent structure and insensitivity to atomic-scale roughness makes it possible to determine the spin distribution by polarized neutron reflectivity, which confirms that the spin structure is collinear. The magnetic reversal behavior of the double superlattices suggests that a realistic model of exchange bias needs to address the process of nucleating local reverse domains.

  2. Spin projection with double hybrid density functional theory

    SciTech Connect (OSTI)

    Thompson, Lee M.; Hratchian, Hrant P.

    2014-07-21

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

  3. Searching for Double Beta Decay with the Enriched Xenon Observatory

    SciTech Connect (OSTI)

    Hall, C.; /SLAC

    2007-03-16

    The Enriched Xenon Observatory (EXO) Collaboration is building a series of experiments to search for the neutrinoless double beta decay of {sup 136}Xe. The first experiment, known as EXO-200, will utilize 200 kg of xenon enriched to 80% in the isotope of interest, making it the largest double beta decay experiment to date by one order of magnitude. This experiment is rapidly being constructed, and will begin data taking in 2007. The EXO collaboration is also developing a technique to identify on an event-by-event basis the daughter barium ion of the double beta decay. If successful, this method would eliminate all conventional radioactive backgrounds to the decay, resulting in an ideal experiment. We summarize here the current status of EXO-200 construction and the barium tag R&D program.

  4. Q value of the 100Mo Double-Beta Decay

    E-Print Network [OSTI]

    S. Rahaman; V. -V. Elomaa; T. Eronen; J. Hakala; A. Jokinen; J. Julin; A. Kankainen; A. Saastamoinen; J. Suhonen; C. Weber; J. Äystö

    2007-12-20

    Penning trap measurements using mixed beams of 100Mo - 100Ru and 76Ge - 76Se have been utilized to determine the double-beta decay Q-values of 100Mo and 76Ge with uncertainties less than 200 eV. The value for 76Ge, 2039.04(16) keV is in agreement with the published SMILETRAP value. The new value for 100Mo, 3034.40(17) keV is 30 times more precise than the previous literature value, sufficient for the ongoing neutrinoless double-beta decay searches in 100Mo. Moreover, the precise Q-value is used to calculate the phase-space integrals and the experimental nuclear matrix element of double-beta decay.

  5. Heavy Sterile Neutrinos and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Manimala Mitra; Goran Senjanovic; Francesco Vissani

    2012-05-17

    Sterile neutrinos of mass up to a few tens of TeV can saturate the present experimental bound of neutrinoless double beta decay process. Due to the updated nuclear matrix elements, the bound on mass and mixing angle is now improved by one order of magnitude. We have performed a detailed analysis of neutrinoless double beta decay for the minimal Type I seesaw scenario. We have shown that in spite of the naive expectation that the light neutrinos give the dominant contribution, sterile neutrinos can saturate the present experimental bound of neutrinoless double beta decay process. However, in order to be consistent with radiative stability of light neutrino masses, the mass scale of sterile neutrinos should be less than 10 GeV.

  6. Short-range correlations and neutrinoless double beta decay

    E-Print Network [OSTI]

    M. Kortelainen; O. Civitarese; J. Suhonen; J. Toivanen

    2007-01-18

    In this work we report on the effects of short-range correlations upon the matrix elements of neutrinoless double beta decay. We focus on the calculation of the matrix elements of the neutrino-mass mode of neutrinoless double beta decays of 48Ca and 76Ge. The nuclear-structure components of the calculation, that is the participant nuclear wave functions, have been calculated in the shell-model scheme for 48Ca and in the proton-neutron quasiparticle random-phase approximation (pnQRPA) scheme for 76Ge. We compare the traditional approach of using the Jastrow correlation function with the more complete scheme of the unitary correlation operator method (UCOM). Our results indicate that the Jastrow method vastly exaggerates the effects of short-range correlations on the neutrinoless double beta decay nuclear matrix elements.

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

    SciTech Connect (OSTI)

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

    2014-07-28

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

  8. Double-Kasner Spacetime: Peculiar Velocities and Cosmic Jets

    E-Print Network [OSTI]

    C. Chicone; B. Mashhoon; K. Rosquist

    2011-06-20

    In dynamic spacetimes in which asymmetric gravitational collapse/expansion is taking place, the timelike geodesic equation appears to exhibit an interesting property: Relative to the collapsing configuration, free test particles undergo gravitational "acceleration" and form a double-jet configuration parallel to the axis of collapse. We illustrate this aspect of peculiar motion in simple spatially homogeneous cosmological models such as the Kasner spacetime. To estimate the effect of spatial inhomogeneities on cosmic jets, timelike geodesics in the Ricci-flat double-Kasner spacetime are studied in detail. While spatial inhomogeneities can significantly modify the structure of cosmic jets, we find that under favorable conditions the double-jet pattern can initially persist over a finite period of time for sufficiently small inhomogeneities.

  9. 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.}

  10. 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.

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

    SciTech Connect (OSTI)

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

    2009-01-15

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

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

    SciTech Connect (OSTI)

    MACKEY, T.C.

    2006-03-17

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

  13. Commutation Relations for Double Tensors of Two Equivalent D Electrons

    E-Print Network [OSTI]

    Chin-Sheng Wu

    2007-07-07

    We apply the Clebsch-Gordan and Racah coefficients to calculate the double tensors for two equivalent d electrons. We also obtain the commutation relations for these double tensors and choose certain quantum numbers, which produce a subgroup. From the root vectors of the commutation relations, we identify them with Lie algebra B2. Once we have the correct Lie algebra, it is feasible to use the Wigner-Eckart theorem to find matrix elements for transition states among atomic spectra or nuclear shell models.

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

    E-Print Network [OSTI]

    Michael Duerr; Manfred Lindner; Kai Zuber

    2011-11-17

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

  15. Empirical Survey of Neutrinoless Double Beta Decay Matrix Elements

    E-Print Network [OSTI]

    R. G. H. Robertson

    2013-01-07

    Neutrinoless double beta decay has been the subject of intensive theoretical work as it represents the only practical approach to discovering whether neutrinos are Majorana particles or not, and whether lepton number is a conserved quantum number. Available calculations of matrix elements and phase-space factors are reviewed from the perspective of a future large-scale experimental search for neutrinoless double beta decay. Somewhat unexpectedly, a uniform inverse correlation between phase space and the square of the nuclear matrix element emerges. As a consequence, no isotope is either favored or disfavored; all have qualitatively the same decay rate per unit mass for any given value of the Majorana mass.

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

    SciTech Connect (OSTI)

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

    2010-08-15

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

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

    SciTech Connect (OSTI)

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

    2011-11-01

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

  18. Quantum theory of light double-slit diffraction

    E-Print Network [OSTI]

    Xiang-Yao Wu; Hong Li; Bo-Jun Zhang; Ji Ma; Xiao-Jing Liu; Nuo Ba; He Dong; Si-Qi Zhang; Jing Wang; Yi-Heng Wu; Xin-Guo Yin

    2013-05-10

    In this paper, we study the light double-slit diffraction experiment with quantum theory approach. Firstly, we calculate the light wave function in slits by quantum theory of photon. Secondly, we calculate the diffraction wave function with Kirchhoff's law. Thirdly, we give the diffraction intensity of light double-slit diffraction, which is proportional to the square of diffraction wave function. Finally, we compare calculation result of quantum theory and classical electromagnetic theory with the experimental data. We find the quantum calculate result is accordance with the experiment data, and the classical calculation result with certain deviation. So, the quantum theory is more accurately approach for studying light diffraction.

  19. Period doubling, information entropy, and estimates for Feigenbaum's constants

    E-Print Network [OSTI]

    Reginald D. Smith

    2013-08-03

    The relationship between period doubling bifurcations and Feigenbaum's constants has been studied for nearly 40 years and this relationship has helped uncover many fundamental aspects of universal scaling across multiple nonlinear dynamical systems. This paper will combine information entropy with symbolic dynamics to demonstrate how period doubling can be defined using these tools alone. In addition, the technique allows us to uncover some unexpected, simple estimates for Feigenbaum's constants which relate them to log 2 and the golden ratio, phi, as well as to each other.

  20. Double K-shell photoionization of atomic beryllium

    SciTech Connect (OSTI)

    Yip, F. L. [Departamento de Quimica, Modulo 13, Universidad Autonoma de Madrid, E-28049 Madrid (Spain); Martin, F. [Departamento de Quimica, Modulo 13, Universidad Autonoma de Madrid, E-28049 Madrid (Spain); Instituto Madrilen (tilde sign)o de Estudios Avanzados en Nanociencia, Cantoblanco, E-28049 Madrid (Spain); McCurdy, C. W. [Department of Chemistry, University of California, Davis, California 95616 (United States); Lawrence Berkeley National Laboratory, Chemical Sciences, and Ultrafast X-ray Science Laboratory, Berkeley, California 94720 (United States); Rescigno, T. N. [Lawrence Berkeley National Laboratory, Chemical Sciences, and Ultrafast X-ray Science Laboratory, Berkeley, California 94720 (United States)

    2011-11-15

    Double photoionization of the core 1s electrons in atomic beryllium is theoretically studied using a hybrid approach that combines orbital and grid-based representations of the Hamiltonian. The {sup 1} S ground state and {sup 1} P final state contain a double occupancy of the 2s valence shell in all configurations used to represent the correlated wave function. Triply differential cross sections are evaluated, with particular attention focused on a comparison of the effects of scattering the ejected electrons through the spherically symmetric valence shell with similar cross sections for helium, representing a purely two-electron target with an analogous initial-state configuration.

  1. 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

  2. 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

  3. 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

  4. 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 ...

  5. 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 ...

  6. 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 ...

  7. 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

  8. 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...

  9. 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...

  10. 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 ...

  11. 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 ...

  12. 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 ...

  13. 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)

  14. 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 ...

  15. 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 ...

  16. 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

  17. 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...

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. Computer code for double beta decay QRPA based calculations

    SciTech Connect (OSTI)

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

    2014-11-11

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

  7. Neutrinoless double beta decay mediated by the neutrino magnetic moment

    E-Print Network [OSTI]

    Marek Gó?d?; Wies?aw A. Kami?ski

    2014-11-07

    We present a new channel of the neutrinoless double beta decay. In this scenario neutrinos not only oscillate inside the nucleus but also interact with an external non-uniform magnetic field. We assume that the field rotates about the direction of motion of the neutrino and show, that for a certain speed of rotation the half-life of the $0\

  8. DOUBLE DUCTED FAN (DDF) Cengiz Camci and Ali Akturk

    E-Print Network [OSTI]

    Camci, Cengiz

    DOUBLE DUCTED FAN (DDF) By Cengiz Camci and Ali Akturk A technology description document a novel ducted fan inlet flow conditioning concept that will significantly improve the performance" and many other ducted fan based systems. The new concept that will significantly reduce the inlet lip

  9. Specific heats of quantum double-well systems

    E-Print Network [OSTI]

    Hideo Hasegawa

    2012-11-26

    Specific heats of quantum systems with symmetric and asymmetric double-well potentials have been calculated. In numerical calculations of their specific heats, we have adopted the combined method which takes into account not only eigenvalues of $\\epsilon_n$ for $0 \\leq n \\leq N_m$ obtained by the energy-matrix diagonalization but also their extrapolated ones for $N_m+1 \\leq n specific heats are shown to be rather different from counterparts of a harmonic oscillator. In particular, specific heats of symmetric double-well systems at very low temperatures have the Schottky-type anomaly, which is rooted to a small energy gap in low-lying two-level eigenstates induced by a tunneling through the potential barrier. The Schottky-type anomaly is removed when an asymmetry is introduced into the double-well potential. It has been pointed out that the specific-heat calculation of a double-well system reported by Feranchuk, Ulyanenkov and Kuz'min [Chem. Phys. 157, 61 (1991)] is misleading because the zeroth-order operator method they adopted neglects crucially important off-diagonal contributions.

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

    SciTech Connect (OSTI)

    Washenfelder, Dennis J.

    2014-04-10

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

  11. Tunneling of Graphene Massive Dirac Fermions through a Double Barrier

    E-Print Network [OSTI]

    Hocine Bahlouli; El Bouazzaoui Choubabi; Ahmed Jellal; Miloud Mekkaoui

    2011-10-04

    We study the tunneling of Dirac fermions in graphene through a double barrier potential allowing the carriers to have an effective mass inside the barrier as generated by a lattice miss-match with the boron nitride substrate. The consequences of this gap opening on the transmission are investigated. The realization of resonant tunneling conditions is also analyzed.

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

    SciTech Connect (OSTI)

    STAEHR, T.W.

    1999-05-12

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

  13. Contributors xix DOUBLE-NEGATIVE (DNG) METAMATERIALS 1

    E-Print Network [OSTI]

    CONTENTS Preface xv Contributors xix PART I DOUBLE-NEGATIVE (DNG) METAMATERIALS 1 SECTION I THREE-DIMENSIONAL VOLUMETRIC DNG METAMATERIALS 3 CHAPTER 1 INTRODUCTION, HISTORY, AND SELECTED TOPICS IN FUNDAMENTAL THEORIES OF METAMATERIALS 5 Richard W. Ziolkowski and Nader Engheta 1.1 Introduction 5 1.2 Wave Parameters in DNG Media 9 1

  14. Double Beta Decay and the Absolute Neutrino Mass Scale

    E-Print Network [OSTI]

    Carlo Giunti

    2003-08-20

    After a short review of the current status of three-neutrino mixing, the implications for the values of neutrino masses are discussed. The bounds on the absolute scale of neutrino masses from Tritium beta-decay and cosmological data are reviewed. Finally, we discuss the implications of three-neutrino mixing for neutrinoless double-beta decay.

  15. Effects of New Gravitational Interactions on Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    H. V. Klapdor--Kleingrothaus; H. Päs; U. Sarkar

    2000-04-13

    It has recently been proposed that violations of Lorentz invariance or violations of the equivalence principle can be constrained from the non-observation of neutrinoless double beta decay. We generalize this analysis to all possible new gravitational interactions and discuss briefly the constraints for different cases.

  16. Bound states in a hyperbolic asymmetric double-well

    SciTech Connect (OSTI)

    Hartmann, R. R.

    2014-01-15

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

  17. Neutrinoless Double Beta Decay with R-parity Violation

    E-Print Network [OSTI]

    Yosuke Uehara

    2002-06-26

    We consider recently observed neutrinoless double beta decay in the context of the minimal supersymmetric standard model with R-parity violating couplings lambda^{'}. We observe that most of the current experimental bounds on the R-parity violating couplings do not exclude the possibility that the neutrinoless double beta decay is caused by R-parity violation. But if we consider K-bar{K} oscillation, we observe that we have to make the R-parity violating couplings generation-dependent to accomodate with the observed neutrinoless double beta decay. And furthermore, we need some mechanism to cancel the contribution to K-bar{K} mixing from a large R-parity violating coupling. We realized this cancellation by assuming that the first- and the second- generation of quark sector do not couple with the first-generation lepton sector by R-parity violating couplings except the term W=lambda_{111}^{'} L_{1} Q_{1} D_{1}^{c}, which is responsible for the observed neutrinoless double beta decay.

  18. Double beta decay to the excited states: experimental review

    E-Print Network [OSTI]

    A. S. Barabash

    2007-10-11

    A brief review on double beta decay to excited states of daughter nuclei is given. The ECEC(ov) transision to the excited states are discussed in association with a possible enhancement of the decay rate by several orders of magnitude.

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

    SciTech Connect (OSTI)

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

    2011-01-01

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

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

    Broader source: Energy.gov [DOE]

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

  1. Dynamic fluctuation phenomena in double membrane films E. I. Kats*)

    E-Print Network [OSTI]

    Lebedev, Vladimir

    1 is satisfied where g T/ , T is the temperature, and is the bending modulus . The corresponding fluctuations of the membrane lead to the logarithmic renormalization of the bending modulus , which . In this paper we will examine the dynamic properties of such double membrane films. The main peculiarity

  2. Scaling factor inconsistencies in neutrinoless double beta decay

    SciTech Connect (OSTI)

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

    2006-02-15

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

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

    SciTech Connect (OSTI)

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

    2006-12-15

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

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

    SciTech Connect (OSTI)

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

    2005-10-12

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

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

    SciTech Connect (OSTI)

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

    2006-12-15

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

  6. New Advances in Neutrinoless Double Beta Decay Matrix Elements

    SciTech Connect (OSTI)

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

    2010-08-04

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

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

    E-Print Network [OSTI]

    Alicja Joniec; Marek Zralek

    2005-12-30

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

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

    SciTech Connect (OSTI)

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

    2009-11-09

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

  9. Scaling Factor Inconsistencies in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    S. Cowell

    2005-12-05

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

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

    SciTech Connect (OSTI)

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

    2006-02-01

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

  11. First experiment with the double solenoid RIBRAS system

    SciTech Connect (OSTI)

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

    2013-05-06

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

  12. Neutrinoless double beta decay mediated by the neutrino magnetic moment

    E-Print Network [OSTI]

    Gó?d?, Marek

    2014-01-01

    We present a new channel of the neutrinoless double beta decay. In this scenario neutrinos not only oscillate inside the nucleus but also interact with an external non-uniform magnetic field. We assume that the field rotates about the direction of motion of the neutrino and show, that for a certain speed of rotation the half-life of the $0\

  13. Resumming double logarithms in the QCD evolution of color dipoles

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

    Iancu, E.; Madrigal, J.D.; Mueller, A.H.; Soyez, G.; Triantafyllopoulos, D.N.

    2015-05-01

    The higher-order perturbative corrections, beyond leading logarithmic accuracy, to the BFKL evolution in QCD at high energy are well known to suffer from a severe lack-of-convergence problem, due to radiative corrections enhanced by double collinear logarithms. Via an explicit calculation of Feynman graphs in light cone (time-ordered) perturbation theory, we show that the corrections enhanced by double logarithms (either energy-collinear, or double collinear) are associated with soft gluon emissions which are strictly ordered in lifetime. These corrections can be resummed to all orders by solving an evolution equation which is non-local in rapidity. This equation can be equivalently rewritten inmore »local form, but with modified kernel and initial conditions, which resum double collinear logs to all orders. We extend this resummation to the next-to-leading order BFKL and BK equations. The first numerical studies of the collinearly-improved BK equation demonstrate the essential role of the resummation in both stabilizing and slowing down the evolution.« less

  14. G8 Hokkaido-Toyako Summit Double Jeopardy

    E-Print Network [OSTI]

    Sadoulet, Elisabeth

    G8 Hokkaido-Toyako Summit Double Jeopardy: Responding to High Food and Fuel Prices July 2, 2008 World Bank #12;SUGGESTED ACTION ITEMS ON FOOD PRICES FOR CONSIDERATION BY THE G8 A New Deal for Global-fuels in the G8 countries: 7. Agree on action in the US and Europe to ease subsidies, mandates and tariffs on bio

  15. Generator Coordinate Method framework for Double Beta Decay

    E-Print Network [OSTI]

    Andrzej Bobyk; Wies?aw A. Kami?ski

    2014-11-10

    We propose a consistent prescription for the derivation of the particle number and angular momentum projected QRPA (PQRPA) equation in the Generator Coordinate Method (GCM) framework for calculation of NME's of double-beta decay of axially deformed nuclei. We derive closed formulae for the calculation of excitation energies and wave functions of the intermediate nucleus.

  16. Coherent control of atomic spin currents in a double well

    E-Print Network [OSTI]

    Chu, Shih-I; Ng, H. T.

    2012-02-27

    We propose a method for controlling the atomic currents of a two-component Bose-Einstein condensate in a double well by applying an external field to the atoms in one of the potential wells. We study the ground-state properties of the system...

  17. Chemical Shielding Tensors for a Silicon-Carbon Double Bond

    E-Print Network [OSTI]

    Apeloig, Yitzhak

    Chemical Shielding Tensors for a Silicon-Carbon Double Bond Jarrod J. Buffy, Robert West,*, Michael of NMR chemical shielding tensors (CST) have been important in aiding the understanding of the nature shielding tensors have been reported and interpreted for compounds containing SidSi,1 PdP,2 SndSn,3 Cd

  18. Jet schemes of rational double point singularities Hussein MOURTADA

    E-Print Network [OSTI]

    Jet schemes of rational double point singularities Hussein MOURTADA September 30, 2012 Abstract We prove that for m N, m big enough, the number of irreducble components of the schemes of m-jets centered of the jet schemes of an E6 singularity to its "minimal" embedded resolutions of singularities. 1

  19. Jet schemes of rational double point singularities Hussein Mourtada

    E-Print Network [OSTI]

    Bodin, Arnaud

    Jet schemes of rational double point singularities Hussein Mourtada Abstract. We prove that for m N, m big enough, the number of irreducible compo- nents of the schemes of m-jets centered at a point on the minimal reso- lution of the singularity. We also relate some irreducible components of the jet schemes

  20. Nuclear Matrix Elements for Double-Beta Decay

    E-Print Network [OSTI]

    Engel, Jonathan

    2015-01-01

    Recent progress in nuclear-structure theory has been dramatic. I describe recent and future applications of ab initio calculations and the generator coordinate method to double-beta decay. I also briefly discuss the old and vexing problem of the renormalization of the weak nuclear axial-vector coupling constant "in medium" and plans to resolve it.