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

    2015-01-01T23:59:59.000Z

    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]

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

    2015-01-01T23:59:59.000Z

    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...

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

    SciTech Connect (OSTI)

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

    2011-04-01T23:59:59.000Z

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

  4. Protein Bridges DNA Base and Nucleotide Excision Repair Pathways

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

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

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

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

    double helix. A protein called DNA polymerase does most of this work, adding nucleotides complementary to the template's nucleotides. But before polymerase builds the...

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

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2009-01-01T23:59:59.000Z

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

  7. Probing Protein-DNA Interactions by Unzipping a Single DNA Double Helix

    E-Print Network [OSTI]

    Wang, Michelle

    ., 2000; Bianco et al., 2001; Dohoney and Gelles, 2001; Strick et al., 2000), as well as the investigation

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

    E-Print Network [OSTI]

    Xiaoling Lei; Wenpeng Qi; Haiping Fang

    2013-03-13T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    1996-01-01T23:59:59.000Z

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

  10. Helix coupling

    DOE Patents [OSTI]

    Ginell, W.S.

    1982-03-17T23:59:59.000Z

    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.

  11. Helix coupling

    DOE Patents [OSTI]

    Ginell, W.S.

    1989-04-25T23:59:59.000Z

    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.

  12. 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

  13. Helical Disruptions in Small Loops of DNA

    E-Print Network [OSTI]

    Zoli, Marco

    2015-01-01T23:59:59.000Z

    The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings along the double helix are essential to biological functions such as transcription and replication of the genetic information. Helix unwinding and bubble formation patterns are computed in circular sequences with variable radius in order to analyze the interplay between molecule size and appearance of helical disruptions. The latter are found in minicircles with $100$ base pairs and appear as a strategy to soften the stress due to the bending and torsion of the helix.

  14. Behavior of Supercoiled DNA T. R. Strick, J.-F. Allemand, D. Bensimon, and V. Croquette

    E-Print Network [OSTI]

    Croquette, Vincent

    . The over- wound or underwound double helix can assume exotic forms known as plectonemes (like the braided contain 3 m of DNA, divided into 46 chromosomes. If these chromosomes were in the form of a random coil it to be over- wound and underwound from its natural state. Today we know that DNA is topologically polymorphic

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

    E-Print Network [OSTI]

    Cai, Long

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

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

    2006-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2013-05-07T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2005-10-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Ghosh, Indraneel

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

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

    SciTech Connect (OSTI)

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

    2008-02-18T23:59:59.000Z

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

  2. DNA . DNA

    E-Print Network [OSTI]

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

  3. Extrusion of an Imperfect Palindrome to a Cruciform in Superhelical DNA: Complete Determination of

    E-Print Network [OSTI]

    Benham, Craig J.

    of Energetics Using a Statistical Mechanical Model Craig J. Benham1 , Anne G. Savitt2 and William R. Bauer2 * 1 at the base of an imperfect cruciform can successfully compete with extension of the cruciform arms. # 2002 that structures more com- plex than the standard DNA double helix are bio- logically important. These include

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

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Leonor Saiz; Jose M. G. Vilar

    2006-02-10T23:59:59.000Z

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

  6. DNA DNA DNA (d)DNA DNA DNA

    E-Print Network [OSTI]

    Hagiya, Masami

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

  7. 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

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

    SciTech Connect (OSTI)

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

    2014-01-27T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2009-07-21T23:59:59.000Z

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

  10. DNA DNA . DNA

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

    J. Tothova; B. Brutovsky; V. Lisy

    2005-09-15T23:59:59.000Z

    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.

  12. Synthesis of DNA

    DOE Patents [OSTI]

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

    2008-11-18T23:59:59.000Z

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

  13. 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 Ų.; Voulgarakis, Nikolaos K.

    2015-03-12T23:59:59.000Z

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

  14. Absence of zero-temperature transmission rate of a double-chain tight-binding model for DNA with random sequence of nucleotides in thermodynamic limit

    E-Print Network [OSTI]

    Gang Xiong; X. R. Wang

    2005-12-16T23:59:59.000Z

    The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While the whole spectrum tends to zero in thermodynamic limit, regardless of the strength of inter-chain coupling. It is also shown that a more faithful model for real DNA with periodic sugar-phosphate chains in backbone structures can be mapped into the above simple double-chain tight-binding model. Combined with above results, the transmission rate of real DNA with long random sequence of nucleotides is expected to be poor.

  15. DNA -DNA--

    E-Print Network [OSTI]

    Glykos, Nikolaos

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

  16. Inhibition of DNA Supercoiling-dependent Transcriptional Activation by a Distant B-DNA to Z-DNA Transition*

    E-Print Network [OSTI]

    Benham, Craig J.

    that a supercoiling-dependent, DNA structural transmission mechanism of this type is responsible for the integration over other alterna- tives, primarily because the change from right-handed helix to left-handed helix). In this way one can alter the destabilization characteristics of other local regions without changing

  17. Design and Construction of Double-Decker Tile as a Route to Three-Dimensional Periodic Assembly of DNA

    E-Print Network [OSTI]

    Reif, John H.

    of DNA Urmi Majumder§ , Abhijit Rangnekar§|| , Kurt V Gothelf || , John H Reif§* and Thomas H LaBean water and letting it cool down slowly in an insulated (styrofoam) box over 16 hours, followed

  18. The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle stabilized by zinc

    E-Print Network [OSTI]

    Tullius, Thomas D.

    The solution structure of the amino-terminal HHCC domain of HIV-2 integrase: a three-helix bundle to phosphates in the target DNA. Three domains have been identified in HIV integrase: an amino-terminal domain, a central catalytic core and a carboxy- terminal DNA-binding domain. The amino-terminal region is the only

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

    E-Print Network [OSTI]

    Schubert, Christian Reinhold

    2009-01-01T23:59:59.000Z

    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 ...

  20. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2010-06-29T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

  3. Pliable DNA Conformation of Response Elements Bound to Transcription Factor p63

    SciTech Connect (OSTI)

    Chen, Chen; Gorlatova, Natalia; Herzberg, Osnat (Maryland)

    2012-05-02T23:59:59.000Z

    We show that changes in the nucleotide sequence alter the DNA conformation in the crystal structures of p63 DNA-binding domain (p63DBD) bound to its response element. The conformation of a 22-bp canonical response element containing an AT spacer between the two half-sites is unaltered compared with that containing a TA spacer, exhibiting superhelical trajectory. In contrast, a GC spacers abolishes the DNA superhelical trajectory and exhibits less bent DNA, suggesting that increased GC content accompanies increased double helix rigidity. A 19-bp DNA, representing an AT-rich response element with overlapping half-sites, maintains superhelical trajectory and reveals two interacting p63DBD dimers crossing one another at 120{sup o}. p63DBD binding assays to response elements of increasing length complement the structural studies. We propose that DNA deformation may affect promoter activity, that the ability of p63DBD to bind to superhelical DNA suggests that it is capable of binding to nucleosomes, and that overlapping response elements may provide a mechanism to distinguish between p63 and p53 promoters.

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

    E-Print Network [OSTI]

    Kwak, Juhyoun

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

  5. Differences in Electrostatic Potential Around DNA Fragments Containing Guanine and 8-oxo-Guanine

    SciTech Connect (OSTI)

    Haranczyk, Maciej; Gutowski, Maciej S.

    2007-02-01T23:59:59.000Z

    hanges of electrostatic potential (EP) around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through large scale density functional theory computations. Quantum mechanical structural optimizations of DNA fragments with three pairs of nucleotoides and accompanying counteractions were performed with a B3LYP exchange-correlation functional and 6-31G** basis sets. The “intact” DNA fragment contained guanine in the middle layer, while the “damaged” fragment had the guanine replaced with 8-oxo-guanine. The electrostatic potential around these DNA fragments was projected on a surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were analyzed to identify these modifications of EP that result from the occurrence of 8-oxo-guanine. It was found that distortions of the phosphate groups and displacements of the accompanying countercations are clearly reflected in the EP maps.

  6. . DNA, RNA, Protein

    E-Print Network [OSTI]

    Yoo, SukIn

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

  7. 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 (

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

    SciTech Connect (OSTI)

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

    2011-12-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Tentner, Andrea R. (Andrea Ruth)

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    J. L. Gornall; E. M. Terentjev

    2006-03-05T23:59:59.000Z

    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.

  11. Method for assaying clustered DNA damages

    DOE Patents [OSTI]

    Sutherland, Betsy M.

    2004-09-07T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

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

  14. 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

  15. 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

  16. Kinetically driven helix formation during the homopolymer collapse process

    E-Print Network [OSTI]

    Sid Ahmed Sabeur; Fatima Hamdache; Friederike Schmid

    2008-03-07T23:59:59.000Z

    Using Langevin simulations, we find that simple 'generic' bead-and-spring homopolymer chains in a sufficiently bad solvent spontaneously develop helical order during the process of collapsing from an initially stretched conformation. The helix formation is initiated by the unstable modes of the straight chain, which drive the system towards a long-lived metastable transient state. The effect is most pronounced if hydrodynamic interactions are screened.

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

    SciTech Connect (OSTI)

    Horton, John R.; Borgaro, Janine G.; Griggs, Rose M.; Quimby, Aine; Guan, Shengxi; Zhang, Xing; Wilson, Geoffrey G.; Zheng, Yu; Zhu, Zhenyu; Cheng, Xiaodong (Emory-MED); (NE Biolabs)

    2014-07-03T23:59:59.000Z

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

  18. 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 onYou are now leaving Energy.gov You are now leaving Energy.gov You are beingZealand Jump to: navigation, searchOfRose Bend < MHK ProjectsFlagship <Helix < MHK Technologies Jump

  19. 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

  20. Towards 3D modeling of interacting TM helix pairs based on

    E-Print Network [OSTI]

    Nebel, Jean-Christophe

    % of currently known protein structures are from TM proteins [2]. Thus, the lack of experimental structures. Spatial structures of transmembrane proteins are difficult to obtain either experimentally of many transmembrane proteins, is essential in the modeling. Majority of helix-helix interactions

  1. DNA microarray (spot) .

    E-Print Network [OSTI]

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

  2. Mitigating security issues in the evolving DNA synthesis industry

    E-Print Network [OSTI]

    Turlington, Ralph Donald, III

    2013-01-01T23:59:59.000Z

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

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

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

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

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

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

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

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

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

    Print Proofreading Ensures Functional Proteins Genes encoded in DNA are made up of nucleotides wound into a double helix of complementary nucleotide, or base, pairs. Converting...

  6. Shear Unzipping of DNA

    E-Print Network [OSTI]

    Buddhapriya Chakrabarti; David R. Nelson

    2009-04-09T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Kowalczykowski, Stephen C.

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

  8. DNA Computing Hamiltonian path

    E-Print Network [OSTI]

    Hagiya, Masami

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

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

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

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

  10. Elevated temperature triggers human respiratory syncytial virus F protein six-helix bundle formation

    SciTech Connect (OSTI)

    Yunus, Abdul S.; Jackson, Trent P.; Crisafi, Katherine; Burimski, Irina; Kilgore, Nicole R.; Zoumplis, Dorian; Allaway, Graham P.; Wild, Carl T. [Panacos Pharmaceuticals, Inc., 209 Perry Parkway, Suite 7, Gaithersburg, MD 20877 (United States); Salzwedel, Karl, E-mail: salzwedelkd@niaid.nih.go [Panacos Pharmaceuticals, Inc., 209 Perry Parkway, Suite 7, Gaithersburg, MD 20877 (United States)

    2010-01-20T23:59:59.000Z

    Human respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infection in infants, immunocompromised patients, and the elderly. The RSV fusion (F) protein mediates fusion of the viral envelope with the target cell membrane during virus entry and is a primary target for antiviral drug and vaccine development. The F protein contains two heptad repeat regions, HR1 and HR2. Peptides corresponding to these regions form a six-helix bundle structure that is thought to play a critical role in membrane fusion. However, characterization of six-helix bundle formation in native RSV F protein has been hindered by the fact that a trigger for F protein conformational change has yet to be identified. Here we demonstrate that RSV F protein on the surface of infected cells undergoes a conformational change following exposure to elevated temperature, resulting in the formation of the six-helix bundle structure. We first generated and characterized six-helix bundle-specific antibodies raised against recombinant peptides modeling the RSV F protein six-helix bundle structure. We then used these antibodies as probes to monitor RSV F protein six-helix bundle formation in response to a diverse array of potential triggers of conformational changes. We found that exposure of 'membrane-anchored' RSV F protein to elevated temperature (45-55 deg. C) was sufficient to trigger six-helix bundle formation. Antibody binding to the six-helix bundle conformation was detected by both flow cytometry and cell-surface immunoprecipitation of the RSV F protein. None of the other treatments, including interaction with a number of potential receptors, resulted in significant binding by six-helix bundle-specific antibodies. We conclude that native, untriggered RSV F protein exists in a metastable state that can be converted in vitro to the more stable, fusogenic six-helix bundle conformation by an increase in thermal energy. These findings help to better define the mechanism of RSV F-mediated membrane fusion and have important implications for the identification of therapeutic strategies and vaccines targeting RSV F protein conformational changes.

  11. 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

  12. DNA Copyright

    E-Print Network [OSTI]

    Torrance, Andrew W.

    2011-01-01T23:59:59.000Z

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

  13. The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

    SciTech Connect (OSTI)

    Mak, Amanda Nga-Sze; Bradley, Philip; Cernadas, Raul A.; Bogdanove, Adam J.; Stoddard, Barry L. (FHCRC); (Iowa State)

    2012-02-10T23:59:59.000Z

    DNA recognition by TAL effectors is mediated by tandem repeats, each 33 to 35 residues in length, that specify nucleotides via unique repeat-variable diresidues (RVDs). The crystal structure of PthXo1 bound to its DNA target was determined by high-throughput computational structure prediction and validated by heavy-atom derivatization. Each repeat forms a left-handed, two-helix bundle that presents an RVD-containing loop to the DNA. The repeats self-associate to form a right-handed superhelix wrapped around the DNA major groove. The first RVD residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific contact to the DNA sense strand. Two degenerate amino-terminal repeats also interact with the DNA. Containing several RVDs and noncanonical associations, the structure illustrates the basis of TAL effector-DNA recognition.

  14. DNA demethylation by DNA repair

    E-Print Network [OSTI]

    Gehring, Mary

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

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

    E-Print Network [OSTI]

    Giunta, Simona

    2010-11-16T23:59:59.000Z

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

  16. 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)

    2008-04-29T23:59:59.000Z

    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.

  17. Coil-helix transition of polypeptide at water-lipid interface

    E-Print Network [OSTI]

    Ganga P. Sharma; Yana K. Reshetnyak; Oleg A. Andreev; Michael Karbach; Gerhard Müller

    2015-01-08T23:59:59.000Z

    We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\\alpha$-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coil-helix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of order parameter. Our model is constructed as a system of statistically interacting quasiparticles that are activated from the helix pseudo-vacuum. The particles represent links between adjacent residues in coil conformation that form a self-avoiding random walk in two dimensions. Explicit results are presented for helicity, entropy, heat capacity, and the average numbers and sizes of both coil and helix segments.

  18. 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

  19. Using Loop Length Variants to Dissect the Folding Pathway of a Four-helix-bundle Protein

    E-Print Network [OSTI]

    Mochrie, Simon

    . These observations show that loop alteration may be useful as a general tech- nique for dissecting protein folding pathways. # 1999 Academic Press Keywords: protein folding; kinetics; Rop; loops; four-helix-bundle*Corresponding author Introduction A frequently debated question in the ®eld of protein folding is the importance

  20. Characterization of folding the four-helix bundle protein Rop by real-time NMR

    E-Print Network [OSTI]

    Mochrie, Simon

    -loop-helix monomers. Protein folding moni- tored by stopped-flow fluorescence or CD exhibits biphasic kinetics when: protein folding/real-time NMR Introduction Rop is an RNA-binding protein that is involved in the regu of the effect on protein folding of the length of the connecting loop between the helices, led us to suggest

  1. Helix Stabilization Precedes Aqueous and Bilayer-Catalyzed Fiber Formation in Islet

    E-Print Network [OSTI]

    Miranker, Andrew

    ; received in revised form 12 July 2009; accepted 27 July 2009 Available online 30 July 2009 Islet amyloid-terminal disulfide bond (Cys2­Cys7) decreases the extent of helix formed throughout this region. Through manipulation microglobulin in the joints of end-stage renal disease patients, and islet amyloid polypeptide (IAPP

  2. Type 2 Ryanodine Receptor Domain A Contains a Unique and Dynamic -Helix That

    E-Print Network [OSTI]

    Ikura, Mitsuhiko

    Type 2 Ryanodine Receptor Domain A Contains a Unique and Dynamic -Helix That Transitions/or indirect Ca2+ sensitivity, propagating sarcoplasmic reticulum luminal Ca2+ release in the process of excitation­contraction coupling. There are three human RyR subtypes, and several debilitating diseases

  3. DNA Pendant

    E-Print Network [OSTI]

    Hacker, Randi; Tsutsui, William

    2007-11-14T23:59:59.000Z

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

  4. Chromosome doubling method

    DOE Patents [OSTI]

    Kato, Akio

    2006-11-14T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Leydesdorff, Loet

    2010-01-01T23:59:59.000Z

    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...

  6. Testing the helix model for protein folding on four simple proteins

    E-Print Network [OSTI]

    Pierpaolo Bruscolini

    1997-08-19T23:59:59.000Z

    We test a simplified, local version of the helix model on two synthetic and two natural proteins, to study its efficiency in predicting the native secondary structure. The results we obtain are very good for the synthetic sequences, poorer for the two natural ones. This suggests that non-local terms play a fundamental role in determining the secondary structure, even if in some cases local terms alone may be sufficient.

  7. 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

    1996-12-31T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

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

  10. DNA adsorption at liquid/solid interfaces

    E-Print Network [OSTI]

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

    2008-09-26T23:59:59.000Z

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

  11. (gene expression) DNA (DNA microarrays).

    E-Print Network [OSTI]

    Athens, University of

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

  12. Double Beta Decay: Scintillators

    E-Print Network [OSTI]

    Mark C. Chen

    2008-10-20T23:59:59.000Z

    Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into scintillators or can be loaded into scintillators. Experimental programs developing liquid xenon, inorganic crystals, and Nd-loaded liquid scintillator are described in this review. Experiments with 48Ca and 150Nd benefit from their high endpoint which places the neutrinoless double beta decay signal above most backgrounds from natural radioactivity.

  13. The role of histones and histone modifying enzymes in ribosomal dna silencing in saccharomyces cerevisiae

    E-Print Network [OSTI]

    Li, Chonghua

    2009-05-15T23:59:59.000Z

    DNA silencing. We found that, unlike Sir2 that represses both Pol II transcription and recombination, histone H1 only represses recombination at the rDNA. The hyperrecombination defect at the rDNA is more severe in sir2? hho1? double mutant than in either single...

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

    E-Print Network [OSTI]

    Hohng, Sung Chul

    DNA cleavage and opening reactions of human topoisomerase II are regulated via Mg2ž- mediated dynamic bending of gate-DNA Sanghwa Leea,b,1 , Seung-Ryoung Junga,b,1 , Kang Heoa,b , Jo Ann W. Bylc intrinsic topological problems of double- stranded DNA. As part of its essential cellular functions, the en

  15. ##### SAT Engine ####### _ ############ DNA ###### _

    E-Print Network [OSTI]

    Hagiya, Masami

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

  16. Double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2006-02-22T23:59:59.000Z

    The present status of double beta decay experiments are reviewed. The results of the most sensitive experiments, NEMO-3 and CUORICINO, are discussed. Proposals for future double beta decay experiments are considered. In these experiments sensitivity for the effective neutrino mass will be on the level of (0.1-0.01) eV.

  17. Double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2011-07-28T23:59:59.000Z

    The present status of double beta decay experiments is reviewed. The results of the most sensitive experiments are discussed. Proposals for future double beta decay experiments with a sensitivity to the $$ at the level of (0.01--0.1) eV are considered.

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

    E-Print Network [OSTI]

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

  19. DNA Topology: Fundamentals

    E-Print Network [OSTI]

    Mirkin, Sergei

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

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

    E-Print Network [OSTI]

    Shaikh, Faisal

    2008-10-10T23:59:59.000Z

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

  1. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    SciTech Connect (OSTI)

    Storrs, R.W.

    1992-08-01T23:59:59.000Z

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by [sup 31]P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 [Angstrom] of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an [alpha]-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  2. Structural studies of polypeptides: Mechanism of immunoglobin catalysis and helix propagation in hybrid sequence, disulfide containing peptides

    SciTech Connect (OSTI)

    Storrs, R.W.

    1992-08-01T23:59:59.000Z

    Catalytic immunoglobin fragments were studied Nuclear Magnetic Resonance spectroscopy to identify amino acid residues responsible for the catalytic activity. Small, hybrid sequence peptides were analyzed for helix propagation following covalent initiation and for activity related to the protein from which the helical sequence was derived. Hydrolysis of p-nitrophenyl carbonates and esters by specific immunoglobins is thought to involve charge complementarity. The pK of the transition state analog P-nitrophenyl phosphate bound to the immunoglobin fragment was determined by {sup 31}P-NMR to verify the juxtaposition of a positively charged amino acid to the binding/catalytic site. Optical studies of immunoglobin mediated photoreversal of cis, syn cyclobutane thymine dimers implicated tryptophan as the photosensitizing chromophore. Research shows the chemical environment of a single tryptophan residue is altered upon binding of the thymine dimer. This tryptophan residue was localized to within 20 {Angstrom} of the binding site through the use of a nitroxide paramagnetic species covalently attached to the thymine dimer. A hybrid sequence peptide was synthesized based on the bee venom peptide apamin in which the helical residues of apamin were replaced with those from the recognition helix of the bacteriophage 434 repressor protein. Oxidation of the disufide bonds occured uniformly in the proper 1-11, 3-15 orientation, stabilizing the 434 sequence in an {alpha}-helix. The glycine residue stopped helix propagation. Helix propagation in 2,2,2-trifluoroethanol mixtures was investigated in a second hybrid sequence peptide using the apamin-derived disulfide scaffold and the S-peptide sequence. The helix-stop signal previously observed was not observed in the NMR NOESY spectrum. Helical connectivities were seen throughout the S-peptide sequence. The apamin/S-peptide hybrid binded to the S-protein (residues 21-166 of ribonuclease A) and reconstituted enzymatic activity.

  3. Studies of the Twin Helix Parametric-resonance Ionization Cooling Channel with COSY INFINITY

    SciTech Connect (OSTI)

    J.A. Maloney, K.B. Beard, R.P. Johnson, A. Afanasev, S.A. Bogacz, Y.S. Derbenev, V.S. Morozov, B. Erdelyi

    2012-07-01T23:59:59.000Z

    A primary technical challenge to the design of a high luminosity muon collider is an effective beam cooling system. An epicyclic twin-helix channel utilizing parametric-resonance ionization cooling has been proposed for the final 6D cooling stage. A proposed design of this twin-helix channel is presented that utilizes correlated optics between the horizontal and vertical betatron periods to simultaneously focus transverse motion of the beam in both planes. Parametric resonance is induced in both planes via a system of helical quadrupole harmonics. Ionization cooling is achieved via periodically placed wedges of absorbing material, with intermittent rf cavities restoring longitudinal momentum necessary to maintain stable orbit of the beam. COSY INFINITY is utilized to simulate the theory at first order. The motion of particles around a hyperbolic fixed point is tracked. Comparison is made between the EPIC cooling channel and standard ionization cooling effects. Cooling effects are measured, after including stochastic effects, for both a single particle and a distribution of particles.

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

    E-Print Network [OSTI]

    Carl H. Gibson; Rudolph E. Schild

    2007-11-02T23:59:59.000Z

    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.

  5. Nucleotide-dependent displacement and dynamics of the ?-1 helix in kinesin revealed by site-directed spin labeling EPR

    SciTech Connect (OSTI)

    Yasuda, Satoshi; Yanagi, Takanori [Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan)] [Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan); Yamada, Masafumi D. [Division of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577 (Japan)] [Division of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577 (Japan); Ueki, Shoji [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Shido 1314-1, Samuki, Kagawa 769-2193 (Japan)] [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Shido 1314-1, Samuki, Kagawa 769-2193 (Japan); Maruta, Shinsaku [Division of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577 (Japan)] [Division of Bioengineering, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577 (Japan); Inoue, Akio [Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan)] [Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan); Arata, Toshiaki, E-mail: arata@bio.sci.osaka-u.ac.jp [Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan)] [Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 (Japan)

    2014-01-17T23:59:59.000Z

    Highlights: •Dipolar EPR detects the distance between the spin-labeled kinesin ?-1 and ?-2 helices. •The distance has at least two populations: 1.5 nm (in crystal form: 20%) and >2.5 nm. •The short distance conformer was populated 40% in the apo state with microtubules. •ATP analog or ADP binding caused the 1.5 nm distance to be less populated (?20%). •The ?-1 helix moves closer to the neck-linker (away from ?-2) to facilitate docking. -- Abstract: In kinesin X-ray crystal structures, the N-terminal region of the ?-1 helix is adjacent to the adenine ring of the bound nucleotide, while the C-terminal region of the helix is near the neck-linker (NL). Here, we monitor the displacement of the ?-1 helix within a kinesin monomer bound to microtubules (MTs) in the presence or absence of nucleotides using site-directed spin labeling EPR. Kinesin was doubly spin-labeled at the ?-1 and ?-2 helices, and the resulting EPR spectrum showed dipolar broadening. The inter-helix distance distribution showed that 20% of the spins have a peak characteristic of 1.4–1.7 nm separation, which is similar to what is predicted from the X-ray crystal structure, albeit 80% were beyond the sensitivity limit (>2.5 nm) of the method. Upon MT binding, the fraction of kinesin exhibiting an inter-helix distance of 1.4–1.7 nm in the presence of AMPPNP (a non-hydrolysable ATP analog) and ADP was 20% and 25%, respectively. In the absence of nucleotide, this fraction increased to 40–50%. These nucleotide-induced changes in the fraction of kinesin undergoing displacement of the ?-1 helix were found to be related to the fraction in which the NL undocked from the motor core. It is therefore suggested that a shift in the ?-1 helix conformational equilibrium occurs upon nucleotide binding and release, and this shift controls NL docking onto the motor core.

  6. A model for melting of confined DNA

    E-Print Network [OSTI]

    Werner, E; Ambjörnsson, T; Mehlig, B

    2015-01-01T23:59:59.000Z

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

  7. Double field theory

    E-Print Network [OSTI]

    Hull, Chris

    The zero modes of closed strings on a torus — the torus coordinates plus dual coordinates conjugate to winding number — parameterize a doubled torus. In closed string field theory, the string field depends on all zero-modes ...

  8. Neutrinoless double beta decay

    E-Print Network [OSTI]

    K. Zuber

    2012-01-23T23:59:59.000Z

    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.

  9. Double Beta Decay

    E-Print Network [OSTI]

    Steven R. Elliott; Petr Vogel

    2002-02-27T23:59:59.000Z

    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.

  10. DNA polymerase with modified processivity

    DOE Patents [OSTI]

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

    1999-01-01T23:59:59.000Z

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

  11. 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...

  12. A two length scale polymer theory for RNA loop free energies and helix stacking Daniel P. Aalberts and Nagarajan Nandagopal

    E-Print Network [OSTI]

    Aalberts, Daniel P.

    A two length scale polymer theory for RNA loop free energies and helix stacking Daniel P. Aalberts). The reliability of RNA secondary structure predictions is subject to the accuracy of the underly- ing free energy formulation of loop free energies, particularly for multibranch loops. RNA loops contain single

  13. Advance the DNA computing 

    E-Print Network [OSTI]

    Qiu, Zhiquan Frank

    2004-09-30T23:59:59.000Z

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

  14. Algorithms and statistics for advanced DNA analysis For the first time in history, humankind has the ability to easily read and write DNA sequence, a code

    E-Print Network [OSTI]

    University of Technology, Sydney

    , humankind has the ability to easily read and write DNA sequence, a code which describes the very essence of life itself. Global DNA sequencing operations currently generate 30TB data every day and the rate of this data generation more than doubles every year, outpacing Moore's Law. Sequence analysis has entered

  15. Effects of Sequence Disorder on DNA Looping and Cyclization

    E-Print Network [OSTI]

    Yuri O. Popov; Alexei V. Tkachenko

    2007-06-08T23:59:59.000Z

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

  16. DNA encoding a DNA repair protein

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

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

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

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

    2014-10-15T23:59:59.000Z

    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 andmore »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.« less

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

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

    Sun, Jingchuan [Brookhaven National Laboratory (BNL), Upton, NY (United States); Li, Huilin [Brookhaven National Laboratory (BNL), Upton, NY (United States); Stony Brook Univ., Stony Brook, NY (United States); Fernandez-Cid, Alejandra [Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group; Riera, Alberto [Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre; Tognetti, Sivia [Imperial College Faculty of Medicine, London (United Kingdom). MRC Clinical Sciences Centre; Yuan, Zuanning [Stony Brook Univ., Stony Brook, NY (United States); Stillman, Bruce [Cold Spring Harbor Lab., NY (United States); Speck, Christian [Imperial College Faculty of Medicine, London (United Kingdom). DNA Replication Group

    2014-10-15T23:59:59.000Z

    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.

  19. Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Heinrich Päs; Werner Rodejohann

    2015-07-01T23:59:59.000Z

    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.

  20. Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Päs, Heinrich

    2015-01-01T23:59:59.000Z

    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.

  1. DOUBLE MAJORS Imaging Science + ...

    E-Print Network [OSTI]

    Zanibbi, Richard

    DOUBLE MAJORS Imaging Science + ... Applied Mathematics Biomedical Sciences Computer Science Undergraduate Research Internships and Cooperative Education (Co-op) (optional) Study Abroad WHY IMAGING SCIENCE Science: BS, MS, PhD Color Science: MS, PhD BS + MS/PhD Combos HUMAN VISION BIO- MEDICAL ASTRO- PHYSICS

  2. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, D.R.

    1982-09-23T23:59:59.000Z

    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.

  3. Double resonator cantilever accelerometer

    DOE Patents [OSTI]

    Koehler, Dale R. (Albuquerque, NM)

    1984-01-01T23:59:59.000Z

    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.

  4. Neutrinoless double beta decay

    E-Print Network [OSTI]

    Petr Vogel

    2006-11-17T23:59:59.000Z

    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\

  5. WHY SEARCH FOR DOUBLE BETA DECAY?

    E-Print Network [OSTI]

    Kayser, B.

    2010-01-01T23:59:59.000Z

    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

  6. Double field theory at order ??

    E-Print Network [OSTI]

    Hohm, Olaf

    We investigate ?? corrections of bosonic strings in the framework of double field theory. The previously introduced “doubled ??-geometry” gives ??-deformed gauge transformations arising in the Green-Schwarz anomaly ...

  7. The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3; end of 16S rRNA

    SciTech Connect (OSTI)

    Tu, Chao; Zhou, Xiaomei; Tarasov, Sergey G.; Tropea, Joseph E.; Austin, Brian P.; Waugh, David S.; Court, Donald L.; Ji, Xinhua (NCI)

    2012-03-26T23:59:59.000Z

    Era, composed of a GTPase domain and a K homology domain, is essential for bacterial cell viability. It is required for the maturation of 16S rRNA and assembly of the 30S ribosomal subunit. We showed previously that the protein recognizes nine nucleotides (1531{sup AUCACCUCC}1539) near the 3{prime} end of 16S rRNA, and that this recognition stimulates GTP-hydrolyzing activity of Era. In all three kingdoms of life, the 1530{sup GAUCA}1534 sequence and helix 45 (h45) (nucleotides 1506-1529) are highly conserved. It has been shown that the 1530{sup GA}1531 to 1530{sup AG}1531 double mutation severely affects the viability of bacteria. However, whether Era interacts with G1530 and/or h45 and whether such interactions (if any) contribute to the stimulation of Era's GTPase activity were not known. Here, we report two RNA structures that contain nucleotides 1506-1542 (RNA301), one in complex with Era and GDPNP (GNP), a nonhydrolysable GTP-analogue, and the other in complex with Era, GNP, and the KsgA methyltransferase. The structures show that Era recognizes 10 nucleotides, including G1530, and that Era also binds h45. Moreover, GTPase assay experiments show that G1530 does not stimulate Era's GTPase activity. Rather, A1531 and A1534 are most important for stimulation and h45 further contributes to the stimulation. Although G1530 does not contribute to the intrinsic GTPase activity of Era, its interaction with Era is important for binding and is essential for the protein to function, leading to the discovery of a new cold-sensitive phenotype of Era.

  8. Quantitative DNA fiber mapping

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Rossmann, Michael G.

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

  11. 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)

    2010-07-20T23:59:59.000Z

    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.

  12. 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

  13. Double Beta Decay Experiments

    SciTech Connect (OSTI)

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

    2011-11-23T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    1998-12-08T23:59:59.000Z

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

  16. Derivatized versions of ligase enzymes for constructing DNA sequences

    DOE Patents [OSTI]

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

    2006-08-15T23:59:59.000Z

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

  17. Interpretation of the Helix Planetary Nebula using Hydro-Gravitational Theory

    E-Print Network [OSTI]

    Carl H. Gibson; Rudolph E. Schild

    2003-06-25T23:59:59.000Z

    Wide angle Hubble Space Telescope (HST/ACS) images of the Helix Planetary Nebula (NGC 7293) are interpreted using the hydro-gravitational theory (HGT) of Gibson 1996-2000 that predicts the baryonic dark matter and interstellar medium (ISM) consists of Mars-mass primordial-fog-particle (PFP) frozen H-He planets. The new ACS images confirm and extend the O'Dell and Handron 1996 WFPC2 images showing thousands of cometary globules, which we suggest are cocoons of PFP and Jupiter frozen-gas-planets evaporated by powerful beamed radiation from the hot central white dwarf and its companion. The atmosphere mass of the largest cometary globules is ~ 3x10^{25} kg with spacing ~ 10^{14} m, supporting the prediction of HGT that the mass density of the ISM in Galaxy star forming regions should match the large baryonic primordial value at the time of first structure formation (10^{12} s or 30,000 years), with \\rho ~ (3-1)x 10^{-17} kg m^{-3}.

  18. Natural DNA sequencing by synthesis

    E-Print Network [OSTI]

    Roller, Eric E.

    2011-01-01T23:59:59.000Z

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

  19. Helix Unwinding and Base Flipping Enable Human MTERF1 to Terminate Mitochondrial Transcription

    SciTech Connect (OSTI)

    Yakubovskaya, E.; Mejia, E; Byrnes, J; Hambardjieva, E; Garcia-Diaz, M

    2010-01-01T23:59:59.000Z

    Defects in mitochondrial gene expression are associated with aging and disease. Mterf proteins have been implicated in modulating transcription, replication and protein synthesis. We have solved the structure of a member of this family, the human mitochondrial transcriptional terminator MTERF1, bound to dsDNA containing the termination sequence. The structure indicates that upon sequence recognition MTERF1 unwinds the DNA molecule, promoting eversion of three nucleotides. Base flipping is critical for stable binding and transcriptional termination. Additional structural and biochemical results provide insight into the DNA binding mechanism and explain how MTERF1 recognizes its target sequence. Finally, we have demonstrated that the mitochondrial pathogenic G3249A and G3244A mutations interfere with key interactions for sequence recognition, eliminating termination. Our results provide insight into the role of mterf proteins and suggest a link between mitochondrial disease and the regulation of mitochondrial transcription.

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

    E-Print Network [OSTI]

    Cox, Michael M.

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

  1. DNA conjugation andDNA conjugation and reversibility onreversibility on

    E-Print Network [OSTI]

    Rubloff, Gary W.

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

  2. Double Beta Decay

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

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract ManagementDiscovering HowAna Moore Anne Jones DevensforDouble Beta

  3. Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA

    SciTech Connect (OSTI)

    Xing, G.; Kirouac, K.; Shin, Y.J.; Bell, S.D.; Ling, H.; (UWO); (Sir W.Dunn)

    2009-09-16T23:59:59.000Z

    DNA polymerases are co-ordinated by sliding clamps (PCNA/{beta}-clamp) in translesion synthesis. It is unclear how these enzymes assemble on PCNA with geometric and functional compatibility. We report the crystal structure of a full-length Y-family polymerase, Dpo4, in complex with heterodimeric PCNA1-PCNA2 at 2.05 {angstrom} resolution. Dpo4 exhibits an extended conformation that differs from the Dpo4 structures in apo- or DNA-bound form. Two hinges have been identified in Dpo4, which render the multidomain polymerase flexible conformations and orientations relative to PCNA. Dpo4 binds specifically to PCNA1 on the conserved ligand binding site. The C-terminal peptide of Dpo4 becomes structured with a 3{sub 10} helix and dominates the specific binding. The Y-family polymerase also contacts PCNA1 with its finger, thumb and little finger domains, which are conformation-dependent protein-protein interactions that diversify the binding mode of Dpo4 on PCNA. The structure reveals a molecular model in which substrate/partner binding-coupled multiple conformations of a Y-family polymerase facilitate its recruitment and co-ordination on the sliding clamp. The conformational flexibility would turn the error-prone Y-family polymerase off when more efficient high-fidelity DNA polymerases work on undamaged DNA and turn it onto DNA templates to perform translesion synthesis when replication forks are stalled by DNA lesions.

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

    E-Print Network [OSTI]

    Reif, John H.

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

  5. Quantitive DNA Fiber Mapping

    E-Print Network [OSTI]

    Lu, Chun-Mei

    2009-01-01T23:59:59.000Z

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

  6. DNA Sequencing apparatus

    DOE Patents [OSTI]

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

    1992-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Potsdam, Universität

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

  8. 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

  9. Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs

    E-Print Network [OSTI]

    Wu, Yuan-Yan; Zhang, Xi; Tan, Zhi-Jie

    2015-01-01T23:59:59.000Z

    Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5 to 50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ~6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ~29nm to ~45nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ~6 bps at each helix end have...

  10. Hole interactions with molecular vibrations on DNA

    E-Print Network [OSTI]

    A. Omerzu; M. Licer; T. Mertelj; V. V. Kabanov; D. Mihailovic

    2004-05-13T23:59:59.000Z

    We report on a study of the interactions between holes and molecular vibrations on dry DNA using photoinduced infrared absorption spectroscopy. Laser photoexcited (PE) holes are found to have a room-temperature lifetime in excess of 1 ms, clearly indicating the presence of localization. However, from a quantitative model analysis of the frequency shifts of vibrational modes caused by the PE holes, we find the holevibrational coupling constant to be relatively small, 0.2. This interaction leads to a change in the conformational energy of 0.015 eV, which is too small to cause selftrapping at room temperature. We conclude that, at least in the dry (A) form, DNA is best understood in terms of a double chain of coupled quantum dots arising from the pseudo-random chain sequence of base pairs, in which Anderson localization prevents the formation of a metallic state.

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

    SciTech Connect (OSTI)

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

    2002-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Hagiya, Masami

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

  13. An unprecedented nucleic acid capture mechanism for excision of DNA damage

    SciTech Connect (OSTI)

    Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.; Gold, Barry; Eichmanbrand, Brandt F. (Pitt); (Vanderbilt); (Penn)

    2010-11-18T23:59:59.000Z

    DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.

  14. Double acting bit holder

    DOE Patents [OSTI]

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

    1994-01-01T23:59:59.000Z

    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.

  15. Double Chooz: Latest results

    E-Print Network [OSTI]

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

    2014-12-11T23:59:59.000Z

    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.

  16. DNA ELECTROPHORESIS AT SURFACES

    SciTech Connect (OSTI)

    RAFAILOVICH, MIRIAM; SOKOLOV, JONATHAN; GERSAPPE, DILIP

    2003-09-01T23:59:59.000Z

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

  17. Multiprotein DNA looping

    E-Print Network [OSTI]

    Jose M. G. Vilar; Leonor Saiz

    2006-06-19T23:59:59.000Z

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

  18. Neutrinoless Double Beta-Decay

    E-Print Network [OSTI]

    S. M. Bilenky

    2010-01-12T23:59:59.000Z

    The neutrinoless double $\\beta$-decay of nuclei is reviewed. We discuss neutrino mixing and 3x3 PMNS neutrino mixing matrix. Basic theory of neutrinoless double $\\beta$-decay is presented in some details. Results of different calculations of nuclear matrix element are discussed. Experimental situation is considered. The Appendix is dedicated to E. Majorana (brief biography and his paper in which the theory of Majorana particles is given)

  19. Visualizing DNA What is it?

    E-Print Network [OSTI]

    Rose, Michael R.

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

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

    SciTech Connect (OSTI)

    SUTHERLAND, B.M.

    2001-07-26T23:59:59.000Z

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

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

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

  2. amphipathic helix-like TBP-associated factor homology domain The acute myeloid leukemia fusion protein AML1-ETO targets E proteins via a paired

    E-Print Network [OSTI]

    Ikura, Mitsuhiko

    amphipathic helix-like TBP-associated factor homology domain The acute myeloid leukemia fusion. Roeder, May 10, 2006 Up to 15% of acute myeloid leukemias (AMLs) are characterized by the abnormal that is frequently mutated in acute myeloid leukemias (AMLs) (1, 2). In up to 15% of AML cases, a translocation

  3. LEE, K., SHLIR.M.. L ~ E .K.w.,VU,T., ROBERTS, P . and HELIX. M.: 'A new interpretation of 'end' resistance measurements', IEEE

    E-Print Network [OSTI]

    lowering effect with bias in quantum wells Y. Xu, A. Shakouri, A. Yariv, T. Krabach and S. DejewskiReferences LEE, K., SHLIR.M.. L ~ E .K.w.,VU,T., ROBERTS, P . and HELIX. M.: 'A new interpretation.w.: 'A floating-gate transmission-line model technique for measuring source resistance in heterostructure

  4. Conformational plasticity of the influenza A M2 transmembrane helix in lipid bilayers under varying pH, drug binding, and membrane thickness

    E-Print Network [OSTI]

    Hong, Mei

    Conformational plasticity of the influenza A M2 transmembrane helix in lipid bilayers under varying cues, thus conformational plasticity is important for function. The influenza A M2 protein forms spectroscopy to examine the conformational plasticity of membrane-bound transmembrane domain of M2 (M2TM). 13 C

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

    SciTech Connect (OSTI)

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

    2012-05-21T23:59:59.000Z

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

  6. 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

    1995-02-08T23:59:59.000Z

    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.

  7. DNA-PK assay

    DOE Patents [OSTI]

    Anderson, Carl W.; Connelly, Margery A.

    2004-10-12T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Hagiya, Masami

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

  9. Focus: DNA probes

    SciTech Connect (OSTI)

    Not Available

    1986-11-01T23:59:59.000Z

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

  10. New Double Soft Emission Theorems

    E-Print Network [OSTI]

    Freddy Cachazo; Song He; Ellis Ye Yuan

    2015-03-16T23:59:59.000Z

    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

  11. Predicting Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

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

    2005-07-12T23:59:59.000Z

    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.

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

    SciTech Connect (OSTI)

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

    2009-06-08T23:59:59.000Z

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

  13. Attosecond Double-Slit Experiment

    SciTech Connect (OSTI)

    Lindner, F.; Schaetzel, M.G.; Baltuska, A.; Goulielmakis, E. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Walther, H. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet Muenchen, 85748 Garching (Germany); Krausz, F. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet Muenchen, 85748 Garching (Germany); Institut fuer Photonik, Technische Universitaet Wien, Gusshausstr. 27, A-1040 Vienna (Austria); Milosevic, D.B. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, 71000 Sarajevo (Bosnia and Herzegowina); Bauer, D. [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); Becker, W. [Max-Born-Institut, Max-Born-Str. 2a, 12489 Berlin (Germany); Paulus, G.G. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet Muenchen, 85748 Garching (Germany); Department of Physics, Texas A and M University, College Station, Texas 77843-4242 (United States)

    2005-07-22T23:59:59.000Z

    A new scheme for a double-slit experiment in the time domain is presented. Phase-stabilized few-cycle laser pulses open one to two windows (slits) of attosecond duration for photoionization. Fringes in the angle-resolved energy spectrum of varying visibility depending on the degree of which-way information are measured. A situation in which one and the same electron encounters a single and a double slit at the same time is observed. The investigation of the fringes makes possible interferometry on the attosecond time scale. From the number of visible fringes, for example, one derives that the slits are extended over about 500 as.

  14. Double beta decay: present status

    E-Print Network [OSTI]

    A. S. Barabash

    2008-07-18T23:59:59.000Z

    The present status of double beta decay experiments (including the search for $2\\beta^{+}$, EC$\\beta^{+}$ and ECEC processes) are reviewed. The results of the most sensitive experiments are discussed. Average and recommended half-life values for two-neutrino double beta decay are presented. Conservative upper limits on effective Majorana neutrino mass and the coupling constant of the Majoron to the neutrino are established as $ beta decay experiments with a sensitivity for the $$ at the level of (0.01-0.1) eV are considered.

  15. Neutrinoless double beta decay experiments

    E-Print Network [OSTI]

    K. Zuber

    2006-10-04T23:59:59.000Z

    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.

  16. Neutrinoless Double Beta Decay Constraints

    E-Print Network [OSTI]

    Hiroaki Sugiyama

    2003-07-25T23:59:59.000Z

    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.

  17. -DNA 1217 BK21-IT,

    E-Print Network [OSTI]

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

  18. Quadratic $?'$-Corrections to Heterotic Double Field Theory

    E-Print Network [OSTI]

    Kanghoon Lee

    2015-04-01T23:59:59.000Z

    We investigate $\\alpha'$-corrections of heterotic double field theory up to quadratic order in the language of supersymmetric O(D,D+dim G) gauged double field theory. After introducing double-vielbein formalism with a parametrization which reproduces heterotic supergravity, we show that supersymmetry for heterotic double field theory up to leading order $\\alpha'$-correction is obtained from supersymmetric gauged double field theory. We discuss the necessary modifications of the symmetries defined in supersymmetric gauged double field theory. Further, we construct supersymmetric completion at quadratic order in $\\alpha'$.

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

    E-Print Network [OSTI]

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

    2015-01-05T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2011-01-05T23:59:59.000Z

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

  1. Constraining neutrinoless double beta decay

    E-Print Network [OSTI]

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

    2011-11-23T23:59:59.000Z

    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.

  2. Strandwise translocation of a DNA glycosylase on undamaged DNA

    SciTech Connect (OSTI)

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

    2012-05-14T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    M Langelier; J Planck; S Roy; J Pascal

    2011-12-31T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Bahcall, John N.

    2009-01-01T23:59:59.000Z

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

  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)

    1997-01-01T23:59:59.000Z

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

  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.

    1997-05-27T23:59:59.000Z

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

  7. Coarse-graining DNA for simulations of DNA nanotechnology

    E-Print Network [OSTI]

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

    2013-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2010-01-06T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Tao Hu; B. I. Shklovskii

    2008-06-20T23:59:59.000Z

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

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

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

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

  11. ap2-integrase dna binding: Topics by E-print Network

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

    Ser-142 (14). Ser-129 is believed to be a substrate for glycogen synthase kinase 3 Brownfield, Mark S. 156 An Unusual Helix Turn Helix Motif in the Catalytic Core of HIV-1...

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

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

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

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

    DOE Patents [OSTI]

    Tabor, S.; Richardson, C.

    1997-03-25T23:59:59.000Z

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

  14. Neutrinoless Double Beta Decay Experiments

    E-Print Network [OSTI]

    Garfagnini, Alberto

    2014-01-01T23:59:59.000Z

    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.

  15. Neutrinoless Double Beta Decay Experiments

    E-Print Network [OSTI]

    Alberto Garfagnini

    2014-08-11T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2014-04-10T23:59:59.000Z

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

  17. 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, ...

  18. Pair extended coupled cluster doubles

    E-Print Network [OSTI]

    Henderson, Thomas M; Scuseria, Gustavo E

    2015-01-01T23:59:59.000Z

    The accurate and efficient description of strongly correlated systems remains an important challenge for computational methods. Doubly occupied configuration interaction (DOCI), in which all electrons are paired and no correlations which break these pairs are permitted, can in many cases provide an accurate account of strong correlations, albeit at combinatorial computational cost. Recently, there has been significant interest in a method we refer to as pair coupled cluster doubles (pCCD), a variant of coupled cluster doubles in which the electrons are paired. This is simply because pCCD provides energies nearly identical to those of DOCI, but at mean-field computational cost (disregarding the cost of the two-electron integral transformation). Here, we introduce the more complete pair extended coupled cluster doubles (pECCD) approach which, like pCCD, has mean-field cost and reproduces DOCI energetically. We show that unlike pCCD, pECCD also reproduces the DOCI wave function with high accuracy. Moreoever, pEC...

  19. 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)

    2011-10-15T23:59:59.000Z

    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.

  20. 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

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

    E-Print Network [OSTI]

    Ralf Metzler; Tobias Ambjoernsson

    2005-08-20T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

    Ovchinnikov, Victor, E-mail: ovchinnv@georgetown.edu [Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138 (United States)] [Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138 (United States); Karplus, Martin, E-mail: marci@tammy.harvard.edu [Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138 (United States) [Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138 (United States); Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg (France)

    2014-05-07T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Cai, Long

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

  4. Fleet DNA (Presentation)

    SciTech Connect (OSTI)

    Walkokwicz, K.; Duran, A.

    2014-06-01T23:59:59.000Z

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

  5. Tops and Writhing DNA

    E-Print Network [OSTI]

    Joseph Samuel; Supurna Sinha

    2010-11-30T23:59:59.000Z

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

  6. DNA waves and water

    E-Print Network [OSTI]

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

    2010-12-23T23:59:59.000Z

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

  7. Double perovskite catalysts for oxidative coupling

    DOE Patents [OSTI]

    Campbell, K.D.

    1991-01-01T23:59:59.000Z

    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.

  8. Review of double beta decay experiments

    E-Print Network [OSTI]

    A. S. Barabash

    2014-03-12T23:59:59.000Z

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

  9. Operator Analysis of Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Kiwoon Choi; Kwang Sik Jeong; Wan Young Song

    2002-07-19T23:59:59.000Z

    We study the effective operators of the standard model fields which would yield an observable rate of neutrinoless double beta decay. We particularly focus on the possibility that neutrinoless double beta decay is dominantly induced by lepton-number-violating higher dimensional operators other than the Majorana neutrino mass. Our analysis can be applied to models in which neutrinoless double beta decay is induced either by a strong dynamics or by quantum gravity effects at a fundamental scale near the TeV scale as well as the conventional models in which neutrinoless double beta decay is induced by perturbative renormalizable interactions.

  10. Neutrinoless Double Beta Decay: Present and Future

    E-Print Network [OSTI]

    Oliviero Cremonesi

    2002-10-04T23:59:59.000Z

    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\

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

    SciTech Connect (OSTI)

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

    2013-09-20T23:59:59.000Z

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

  12. The tropical double description method

    E-Print Network [OSTI]

    Allamigeon, Xavier; Goubault, Eric

    2010-01-01T23:59:59.000Z

    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.

  13. 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)

    2005-11-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Gates, Kent. S.

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

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

    SciTech Connect (OSTI)

    Hingerty, B.E.

    1992-07-01T23:59:59.000Z

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

  16. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1988-10-11T23:59:59.000Z

    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.

  17. Double beta decay: experiments and theory review

    E-Print Network [OSTI]

    A. Nucciotti

    2007-07-28T23:59:59.000Z

    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.

  18. Neutrinoless double beta decay and neutrino physics

    E-Print Network [OSTI]

    Werner Rodejohann

    2012-08-20T23:59:59.000Z

    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.

  19. DNA attachment to support structures

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

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

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

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

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

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

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

  2. Controlling DNA Methylation

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

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

  3. Instability limits for spontaneous double layer formation

    SciTech Connect (OSTI)

    Carr, J. Jr. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States) [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Department of Physics, Texas Lutheran University, Seguin, Texas 78155 (United States); Galante, M. E.; McCarren, D.; Scime, E. E.; Sears, S.; VanDervort, R. W. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States)] [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Magee, R. M. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States) [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); TriAlpha Energy, Inc., Foothill Ranch, California 92610 (United States); Reynolds, E. [Department of Physics and Engineering, West Virginia Wesleyan, Buckhannon, West Virginia 26201 (United States)] [Department of Physics and Engineering, West Virginia Wesleyan, Buckhannon, West Virginia 26201 (United States)

    2013-11-15T23:59:59.000Z

    We present time-resolved measurements that demonstrate that large amplitude electrostatic instabilities appear in pulsed, expanding helicon plasmas at the same time as particularly strong double layers appear in the expansion region. A significant cross-correlation between the electrostatic fluctuations and fluctuations in the number of ions accelerated by the double layer electric field is observed. No correlation is observed between the electrostatic fluctuations and ions that have not passed through the double layer. These measurements confirm that the simultaneous appearance of the electrostatic fluctuations and the double layer is not simple coincidence. In fact, the accelerated ion population is responsible for the growth of the instability. The double layer strength, and therefore, the velocity of the accelerated ions, is limited by the appearance of the electrostatic instability.

  4. Reliability Estimation for Double Containment Piping

    SciTech Connect (OSTI)

    L. Cadwallader; T. Pinna

    2012-08-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Podgornik, Rudolf

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

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

    SciTech Connect (OSTI)

    Suh, Myungkoo

    1995-12-06T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Murayama, Hitoshi

    2009-01-01T23:59:59.000Z

    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

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

    E-Print Network [OSTI]

    Bryant, Adam Douglas

    2010-01-01T23:59:59.000Z

    A Search for Neutrinoless Double Beta Decay of Te by AdamA Search for Neutrinoless Double Beta Decay of CopyrightA Search for Neutrinoless Double Beta Decay of Te by Adam

  9. 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)

    2014-05-01T23:59:59.000Z

    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.

  10. Dynamic Phase Shifts in Nanoscale Distance Measurements by Double...

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

    by Double Electron Electron Resonance (DEER)† . Abstract: The off-resonant pump pulse used in double electron electron resonance (DEER) measurements produces dynamic...

  11. antigen doubling time: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  12. acute double blockade: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  13. albicans double infection: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  14. air double contrast: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  15. ammonium lanthanide double: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  16. 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...

  17. Neutrinoless Double Beta Decay and Neutrino Masses

    E-Print Network [OSTI]

    Michael Duerr

    2012-06-04T23:59:59.000Z

    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.

  18. Condensation of circular DNA

    E-Print Network [OSTI]

    E. L. Starostin

    2013-04-05T23:59:59.000Z

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

  19. The Double-Dark Portal

    E-Print Network [OSTI]

    David Curtin; Yuhsin Tsai

    2014-12-04T23:59:59.000Z

    In most models of the dark sector, dark matter is charged under some new symmetry to make it stable. We explore the possibility that not just dark matter, but also the force carrier connecting it to the visible sector is charged under this symmetry. This dark mediator then acts as a Double-Dark Portal. We realize this setup in the \\emph{dark mediator Dark matter} model (dmDM), featuring a fermionic DM candidate $\\chi$ with Yukawa couplings to light scalars $\\phi_i$. The scalars couple to SM quarks via the operator $\\bar q q \\phi_i^* \\phi_j/\\Lambda_{ij}$. This can lead to large direct detection signals via the $2\\rightarrow3$ process $\\chi N \\rightarrow \\chi N \\phi$ if one of the scalars has mass $ \\lesssim 10$ keV. For dark matter Yukawa couplings $y_\\chi \\sim 10^{-3} - 10^{-2}$, dmDM features a thermal relic dark matter candidate while also implementing the SIDM scenario for ameliorating inconsistencies between dwarf galaxy simulations and observations. We undertake the first systematic survey of constraints on light scalars coupled to the SM via the above operator. The strongest constraints are derived from a detailed examination of the light mediator's effects on stellar astrophysics. LHC experiments and cosmological considerations also yield important bounds. Observations of neutron star cooling exclude the minimal model with one dark mediator, but a scenario with two dark mediators remains viable and can give strong direct detection signals. We explore the direct detection consequences of this scenario and find that a heavy $\\mathcal{O}(100)$ GeV dmDM candidate fakes different $\\mathcal{O}(10)$ GeV WIMPs at different experiments. Large regions of dmDM parameter space are accessible above the irreducible neutrino background.

  20. Formation of double-$?$ hypernuclei at PANDA

    E-Print Network [OSTI]

    T. Gaitanos; A. B. Larionov; H. Lenske; U. Mosel

    2012-01-17T23:59:59.000Z

    We study the formation of single- and double-$\\Lambda$ hypernuclei in antiproton-induced reactions relevant for the forthcoming PANDA experiment at FAIR. We use the Giessen Boltzmann-Uehling-Uhlenbeck (GiBUU) transport model with relativistic mean-fields for the description of non-equilibrium dynamics and the statistical multifragmentation model (SMM) for fragment formation. This combined approach describes the dynamical properties of strangeness and fragments in low energy $\\bar{p}$-induced reactions fairly well. We then focus on the formation of double-$\\Lambda$ hypernuclei in high energy $\\bar{p}$-nucleus collisions on a primary target including the complementary $\\Xi$-induced reactions to a secondary one, as proposed by the PANDA collaboration. Our results show that a copious production of double-$\\Lambda$ hyperfragments is possible at PANDA. In particular, we provide first theoretical estimations on the double-$\\Lambda$ production cross section, which strongly rises with decreasing energy of the secondary $\\Xi$-beam.

  1. Double field theory of type II strings

    E-Print Network [OSTI]

    Hohm, Olaf

    We use double field theory to give a unified description of the low energy limits of type IIA and type IIB superstrings. The Ramond-Ramond potentials fit into spinor representations of the duality group O(D, D) and ...

  2. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

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

    2015-02-25T23:59:59.000Z

    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

    2015-05-01T23:59:59.000Z

    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. Probing neutrinoless double beta decay with SNO+

    E-Print Network [OSTI]

    Arushanova, Evelina

    2015-01-01T23:59:59.000Z

    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\

  5. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    Gómez-Cadenas, J J

    2015-01-01T23:59:59.000Z

    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.

  6. Double layer capacitors : automotive applications and modeling

    E-Print Network [OSTI]

    New, David Allen, 1976-

    2004-01-01T23:59:59.000Z

    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 ...

  7. Double bevel construction of a diamond anvil

    DOE Patents [OSTI]

    Moss, W.C.

    1987-02-06T23:59:59.000Z

    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.

  8. Double Importance Sampling Val'erie Ventura

    E-Print Network [OSTI]

    Double Importance Sampling Val'erie Ventura Department of Statistics Carnegie Mellon University (Newton and Geyer, 1994, Ventura, 1998), where estimation must be made with respect to many first

  9. CP Violation in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    T. Fukuyama; K. Matsuda; H. Nishiura

    1997-08-19T23:59:59.000Z

    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.

  10. Engineering & Technology January 2012 www.EandTmagazine.com 68 InformatIon technology SYNTHETIC BIOLOGY

    E-Print Network [OSTI]

    Winfree, Erik

    that interact by strand- displacement (see box, right) in a kind of computational soup. The project to build `velcro' that binds the two strands of the DnA double helix together. Methods to exploit this phenomenon strand-displacement. The researchers made four fully-connected artificial neurons from these elements

  11. Wavelength-doubling optical parametric oscillator

    DOE Patents [OSTI]

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

    2007-07-24T23:59:59.000Z

    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.

  12. Double shell tank waste analysis plan

    SciTech Connect (OSTI)

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

    1994-12-15T23:59:59.000Z

    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.

  13. Neutrinoless double beta decay with scalar bilinears

    E-Print Network [OSTI]

    H. V. Klapdor-Kleingrothaus; U. Sarkar

    2002-11-18T23:59:59.000Z

    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.

  14. Searches for neutrinoless double beta decay

    E-Print Network [OSTI]

    B. Schwingenheuer

    2012-01-24T23:59:59.000Z

    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.

  15. Neutrinoless Double Beta Decay and CP Violation

    E-Print Network [OSTI]

    Patrick J. O'Donnell; Utpal Sarkar

    1993-05-27T23:59:59.000Z

    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).

  16. DNA Twist Elasticity: Mechanics and Thermal Fluctuations

    E-Print Network [OSTI]

    Supurna Sinha; Joseph Samuel

    2010-11-30T23:59:59.000Z

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

  17. The Structure of a High Fidelity DNA Polymerase Bound to a Mismatched Nucleotide Reveals an ;Ajar; Intermediate Conformation in the Nucleotide Selection Mechanism

    SciTech Connect (OSTI)

    Wu, Eugene Y.; Beese, Lorena S. (Duke)

    2011-10-10T23:59:59.000Z

    To achieve accurate DNA synthesis, DNA polymerases must rapidly sample and discriminate against incorrect nucleotides. Here we report the crystal structure of a high fidelity DNA polymerase I bound to DNA primer-template caught in the act of binding a mismatched (dG:dTTP) nucleoside triphosphate. The polymerase adopts a conformation in between the previously established 'open' and 'closed' states. In this 'ajar' conformation, the template base has moved into the insertion site but misaligns an incorrect nucleotide relative to the primer terminus. The displacement of a conserved active site tyrosine in the insertion site by the template base is accommodated by a distinctive kink in the polymerase O helix, resulting in a partially open ternary complex. We suggest that the ajar conformation allows the template to probe incoming nucleotides for complementarity before closure of the enzyme around the substrate. Based on solution fluorescence, kinetics, and crystallographic analyses of wild-type and mutant polymerases reported here, we present a three-state reaction pathway in which nucleotides either pass through this intermediate conformation to the closed conformation and catalysis or are misaligned within the intermediate, leading to destabilization of the closed conformation.

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

    SciTech Connect (OSTI)

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

    2011-08-10T23:59:59.000Z

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

  19. Force-induced rupture of a DNA duplex

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

  20. Sequence independent amplification of DNA

    DOE Patents [OSTI]

    Bohlander, Stefan K. (Chicago, IL)

    1998-01-01T23:59:59.000Z

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

  1. Normalized cDNA libraries

    DOE Patents [OSTI]

    Soares, M.B.; Efstratiadis, A.

    1997-06-10T23:59:59.000Z

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

  2. Normalized cDNA libraries

    DOE Patents [OSTI]

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

    1997-01-01T23:59:59.000Z

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

  3. DNA UPTAKE BY TRANSFORMABLE BACTERIA

    SciTech Connect (OSTI)

    LACKS,S.A.

    1999-09-07T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2012-10-16T23:59:59.000Z

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

  5. 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

    2014-10-07T23:59:59.000Z

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

  6. 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 Enriched Xenon Observatory for neutrinoless double beta decay (EXO) will search for the rare decays

  7. Transcriptional Control of DNA-Based Nanomachines

    E-Print Network [OSTI]

    Ludwig-Maximilians-Universität, München

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

  8. Unnatural nucleotides for DNA sequencing

    E-Print Network [OSTI]

    Jacutin, Swanee E

    1997-01-01T23:59:59.000Z

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

  9. Mammalian DNA Repair. Final Report

    SciTech Connect (OSTI)

    None

    2003-01-24T23:59:59.000Z

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

  10. Excited states and energy transfer among DNA bases in double helices

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    spectroscopy. The present article points out contentious questions regarding the nature of the excited states at the University of Stockholm (Sweden) in 1988. He joined CNRS in 1991 where he is presently research director. He a PhD in Chemistry from the University of Bern (Switzerland). He worked in the field of gas phase

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

    E-Print Network [OSTI]

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

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

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

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

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

    E-Print Network [OSTI]

    Shapiro, Beth

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

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

    E-Print Network [OSTI]

    Reif, John H.

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

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

    E-Print Network [OSTI]

    Reif, John H.

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

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

    E-Print Network [OSTI]

    Wang, Wei Hua

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

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

    E-Print Network [OSTI]

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

  18. DNA polymorphism identity determination using flow cytometry

    DOE Patents [OSTI]

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

    2001-01-01T23:59:59.000Z

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

  19. Cellular responses to environmental DNA damage

    SciTech Connect (OSTI)

    Not Available

    1994-08-01T23:59:59.000Z

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

  20. The search for neutrinoless double beta decay

    E-Print Network [OSTI]

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

    2012-01-16T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Woodruff, Rachel Van Etten

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

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

    2011-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

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

  4. 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

    2014-08-15T23:59:59.000Z

    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.

  5. Double hadron leptoproduction in the nuclear medium

    E-Print Network [OSTI]

    Airapetian, A; Akopov, Z; Amarian, M; Andrus, A; Aschenauer, E C; Augustyniak, W; Avakian, R; Avetisian, A; Avetissian, E; Bailey, P; Belostotskii, S; Bianchi, N; Blok, H P; Böttcher, Helmut B; Borisov, A; Borysenko, A; Brüll, A; Bryzgalov, V; Capiluppi, M; Capitani, G P; Ciullo, G; Contalbrigo, M; Dalpiaz, P F; Deconinck, W; De Leo, R; Demey, M; De Nardo, L; De Sanctis, E; Devitsin, E G; Diefenthaler, M; Di Nezza, P; Dreschler, J; Düren, M; Ehrenfried, M; Elalaoui-Moulay, A; Elbakian, G; Ellinghaus, F; Elschenbroich, U; Fabbri, R; Fantoni, A; Felawka, L; Frullani, S; Funel, A; Gapienko, G; Gapienko, V; Garibaldi, F; Garrow, K; Gavrilov, G; Karibian, V; Giordano, F; Grebenyuk, O; Gregor, I M; Griffioen, K; Guler, H; Hadjidakis, C; Hartig, M; Hasch, D; Hasegawa, T; Hesselink, W H A; Hillenbrand, A; Hoek, M; Holler, Y; Hommez, B; Hristova, I; Iarygin, G; Ivanilov, A; Izotov, A; Jackson, H E; Jgoun, A; Kaiser, R; Keri, T; Kinney, E; Kiselev, A; Kobayashi, T; Kopytin, M; Korotkov, V; Kozlov, V; Krauss, B; Kravchenko, P; Krivokhizhin, V G; Lagamba, L; Lapikas, L; Lenisa, P; Liebing, P; Linden-Levy, L A; Lorenzon, W; Lü, J; Lu, S; Ma, B Q; Maiheu, B; Makins, N C R; Mao, Y; Marianski, B; Marukyan, H; Masoli, F; Mexner, V; Meyners, N; Michler, T; Miklukho, O; Miller, C A; Miyachi, Y; Muccifora, V; Murray, M; Nagaitsev, A; Nappi, E; Naryshkin, Yu; Negodaev, M; Nowak, Wolf-Dieter; Ohsuga, H; Osborne, A; Perez-Benito, R; Pickert, N; Raithel, M; Reggiani, D; Reimer, P E; Reischl, A; Reolon, A R; Riedl, C; Rith, K; Rosner, G; Rostomyan, A; Rubacek, L; Rubin, J; Ryckbosch, D; Salomatin, Y; Sanjiev, I; Savin, I; Schäfer, A; Schnell, G; Schüler, K P; Seele, J; Seidl, R; Seitz, B; Shearer, C; Shibata, T A; Shutov, V; Sinram, K; Stancari, M; Statera, M; Steffens, E; Steijger, J J M; Stenzel, H; Stewart, J; Stinzing, F; Streit, J; Tait, P; Tanaka, H; Taroian, S P; Tchuiko, B; Terkulov, A R; Trzcinski, A; Tytgat, M; Vandenbroucke, A; Van der Nat, P B; van der Steenhoven, G; Van Haarlem, Y; Veretennikov, D; Vikhrov, V; Vogel, C; Wang, S; Ye, Y; Ye, Z; Yen, S; Zihlmann, B; Zupranski, P

    2006-01-01T23:59:59.000Z

    First measurement of double-hadron production in deep-inelastic scattering has been measured with the HERMES spectrometer at HERA using a 27.6 GeV positron beam with deuterium, nitrogen, krypton and xenon targets. The influence of the nuclear medium on the ratio of double-hadron to single-hadron yields has been investigated. Nuclear effects are clearly observed but with substantially smaller magnitude and reduced $A$-dependence compared to previously measured single-hadron multiplicity ratios. The data are in fair agreement with models based on partonic or pre-hadronic energy loss, while they seem to rule out a pure absorptive treatment of the final state interactions. Thus, the double-hadron ratio provides an additional tool for studying modifications of hadronization in nuclear matter.

  6. Phenomenology of neutrinoless double beta decay

    E-Print Network [OSTI]

    M. Hirsch

    2006-09-15T23:59:59.000Z

    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.

  7. Recent Results in Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Lisa J. Kaufman

    2013-05-14T23:59:59.000Z

    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.

  8. The double-beta decay: Theoretical challenges

    SciTech Connect (OSTI)

    Horoi, Mihai [Department of Physics, Central Michigan University, Mount Pleasant, Michigan, 48859 (United States)

    2012-11-20T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Marchetti, Francesco

    2008-01-01T23:59:59.000Z

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

  11. DNA repair is the target of novel antibiotics

    E-Print Network [OSTI]

    Gunderson, Carl Wayne

    2007-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Noh, Hyunwoo

    2013-01-01T23:59:59.000Z

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

  13. Neutrino oscillations and neutrinoless double beta decay

    E-Print Network [OSTI]

    D. Falcone; F. Tramontano

    2001-03-16T23:59:59.000Z

    The relation between neutrino oscillation parameters and neutrinoless double beta decay is studied, assuming normal and inverse hierarchies for Majorana neutrino masses. For normal hierarchy the crucial dependence on U_{e3} is explored. The link with tritium beta decay is also briefly discussed.

  14. Scale evolution of double parton correlations

    E-Print Network [OSTI]

    Tomas Kasemets

    2014-11-17T23:59:59.000Z

    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. Double layer capacitor prospects look good

    SciTech Connect (OSTI)

    NONE

    1995-07-01T23:59:59.000Z

    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.

  16. Double tracks test site characterization report

    SciTech Connect (OSTI)

    NONE

    1996-05-01T23:59:59.000Z

    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).

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

    E-Print Network [OSTI]

    Younger, John G.

    2005-01-01T23:59:59.000Z

    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).

  18. Neutrinoless double beta decay in seesaw models

    E-Print Network [OSTI]

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

    2014-05-12T23:59:59.000Z

    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.

  19. 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)

    2007-03-28T23:59:59.000Z

    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.

  20. Double Tracks revegetation and monitoring plan

    SciTech Connect (OSTI)

    NONE

    1997-07-01T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Reif, John H.

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

  3. Micropatterned cell arrays for detecting DNA damage

    E-Print Network [OSTI]

    Mittal, Sukant

    2008-01-01T23:59:59.000Z

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

  4. Towards Privacy Preserving of Forensic DNA Databases

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14T23:59:59.000Z

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

  5. 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...

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

    E-Print Network [OSTI]

    Smith, Wendy Marie

    1987-01-01T23:59:59.000Z

    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 ...

  7. Diapycnal advection by double diffusion and turbulence in the ocean

    E-Print Network [OSTI]

    St. Laurent, Louis C

    1999-01-01T23:59:59.000Z

    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 ...

  8. The spacetime of double field theory: Review, remarks, and outlook

    E-Print Network [OSTI]

    Hohm, Olaf

    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 ...

  9. Progress Towards Doubling the Beam Power at Fermilab's Accelerator Complex

    SciTech Connect (OSTI)

    Kourbanis, ioanis

    2014-06-01T23:59:59.000Z

    After a 14 month shutdown accelerator modifications and upgrades are in place to allow us doubling of the Main Injector beam power. We will discuss the past MI high power operation and the current progress towards doubling the power.

  10. Amplification of chromosomal DNA in situ

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

  11. DNA Microarrays An R Tutorial

    E-Print Network [OSTI]

    Qiu, Weigang

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

  12. Chromosome specific repetitive DNA sequences

    DOE Patents [OSTI]

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

    1991-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Podgornik, Rudolf

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

  14. The Neutrinoless Double Beta Decay: The Case for Germanium Detectors

    E-Print Network [OSTI]

    A. Morales; J. Morales

    2002-11-21T23:59:59.000Z

    An overview of the current status of Neutrinoless Double Beta Decay is presented, emphasizing on the case of Germanium Detectors.

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

    E-Print Network [OSTI]

    Frank F. Deppisch; Martin Hirsch; Heinrich Päs

    2012-08-03T23:59:59.000Z

    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.

  16. Probe and method for DNA detection

    SciTech Connect (OSTI)

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

    2013-07-02T23:59:59.000Z

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

  17. DNA Sequencing via Electron Tunneling Michael Zwolak

    E-Print Network [OSTI]

    Zwolak, Michael

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

  18. Antibody specific for a DNA repair protein

    DOE Patents [OSTI]

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

    2006-07-11T23:59:59.000Z

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

  19. Homotopy BV-algebra structure on the double cobar construction

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Homotopy BV-algebra structure on the double cobar construction Alexandre Quesney Abstract We show that the double cobar construction, 2C(X), of a simplicial set X is a homotopy BV-algebra if X is a double.2 The bar and cobar constructions . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 1.3 Hopf algebras

  20. Double Beta Decay Experiments Department of Physics and Astronomy

    E-Print Network [OSTI]

    Piepke, Andreas G.

    1 Double Beta Decay Experiments A. Piepkea a Department of Physics and Astronomy University. The experimen- tal investigation of the nuclear double beta decay is one of the key techniques for solving, such as the evaluation of the beta spec- tra near their endpoint, or neutrinoless double beta decay. The latter technique

  1. 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

  2. Sensitivity of CUORE to Neutrinoless Double-Beta Decay

    E-Print Network [OSTI]

    Alessandria, F.

    2013-01-01T23:59:59.000Z

    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 .

  3. DNA and the Genetic Code June 14, 2011

    E-Print Network [OSTI]

    Guevara-Vasquez, Fernando

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

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

    SciTech Connect (OSTI)

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

    2011-06-01T23:59:59.000Z

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

  5. JUNO and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Ge, Shao-Feng

    2015-01-01T23:59:59.000Z

    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.

  6. JUNO and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Shao-Feng Ge; Werner Rodejohann

    2015-07-20T23:59:59.000Z

    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.

  7. Importance of neutrinoless double beta decay

    E-Print Network [OSTI]

    Utpal Sarkar

    2007-12-17T23:59:59.000Z

    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.

  8. 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)

    2010-10-08T23:59:59.000Z

    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.

  9. 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)

    1984-01-01T23:59:59.000Z

    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.

  10. Neutrinoless Double Beta Decay in Particle Physics

    E-Print Network [OSTI]

    Werner Rodejohann

    2010-11-22T23:59:59.000Z

    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.

  11. Neutrinoless Double Beta Decay and its "Inverse"

    E-Print Network [OSTI]

    Clemens A. Heusch; Peter Minkowski

    1996-11-18T23:59:59.000Z

    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.

  12. Method for sequencing DNA base pairs

    DOE Patents [OSTI]

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

    1993-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Artusa, D. R.

    2014-01-01T23:59:59.000Z

    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-

  14. Double-Difference Tomography for Sequestration MVA

    SciTech Connect (OSTI)

    Westman, Erik

    2008-12-31T23:59:59.000Z

    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. 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)

    2011-12-16T23:59:59.000Z

    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.

  16. Microfluidic DNA sample preparation method and device

    DOE Patents [OSTI]

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

    2002-01-01T23:59:59.000Z

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

  17. Fleet DNA Project (Fact Sheet)

    SciTech Connect (OSTI)

    Not Available

    2012-10-01T23:59:59.000Z

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

  18. Particle sizer and DNA sequencer

    DOE Patents [OSTI]

    Olivares, Jose A.; Stark, Peter C.

    2005-09-13T23:59:59.000Z

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

  19. Channel plate for DNA sequencing

    DOE Patents [OSTI]

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

    1998-01-13T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Jumpathong, Watthanachai

    2014-01-01T23:59:59.000Z

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

  1. 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. (NWU); (Stanford-MED)

    2014-10-02T23:59:59.000Z

    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.

  2. Complete characterization of double photoionization processes

    SciTech Connect (OSTI)

    Ivanov, I. A.; Kheifets, A. S. [Research School of Physical Sciences, Australian National University, Canberra ACT 0200 (Australia)

    2011-06-15T23:59:59.000Z

    We analyze correlated photoelectron spectra of single-photon two-electron ionization [double photoionization (DPI)] of helium to reconstruct the phase of the spectral amplitude of this process. The phase can be reconstructed reliably in a wide range of photoelectron momenta, thus allowing one to retrieve information about the wave function of the DPI process and its temporal evolution. Our simulation indicates that the proposed phase reconstruction technique can be applied in experiment to trace dynamics of the DPI process with attosecond precision.

  3. Simulated progress in double-beta decay

    SciTech Connect (OSTI)

    Miley, H.S.; Arthur, R.J. [Pacific Northwest Lab., Richland, WA (United States); Avignone, F.T. [South Carolina Univ., Columbia, SC (United States)] [and others

    1993-09-01T23:59:59.000Z

    A Monte Carlo code has been developed to accurately simulate double-beta decay measurements. Coincident gamma rays, beta spectra, and angular correlations have been added to adequately simulate a complete {sup 100}Mo nuclear decay and provide corrections to experimentally determined detector efficiencies. This code has been used to strip certain low-background spectra obtained in the Homestake gold mine in Lead, SD, for the purpose of extremely sensitive materials assay for the construction of new, large, enriched germanium detectors. Assays as low as 9 {mu}Bq/g of {sup 210}Pb in lead shielding were obtained.

  4. Neutrinoless double beta decay and neutrino masses

    SciTech Connect (OSTI)

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

    2012-07-27T23:59:59.000Z

    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.

  5. Neutrinoless double beta decay and QCD corrections

    E-Print Network [OSTI]

    Namit Mahajan

    2014-01-30T23:59:59.000Z

    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.

  6. Double acting stirling engine phase control

    DOE Patents [OSTI]

    Berchowitz, David M. (Scotia, NY)

    1983-01-01T23:59:59.000Z

    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.

  7. 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministration Donald6,Double Coil

  8. DNA Bubble Life Time in Denaturation

    E-Print Network [OSTI]

    Zh. S. Gevorkian; Chin-Kun Hu

    2010-10-11T23:59:59.000Z

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

  9. Assembling semiconductor nanocomposites using DNA replication technologies.

    SciTech Connect (OSTI)

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

    2005-11-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Shrivastav, Nidhi

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

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

    E-Print Network [OSTI]

    Ng, Jin Kiat

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

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

    E-Print Network [OSTI]

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

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

    E-Print Network [OSTI]

    Tse, Pui Wah

    2011-01-01T23:59:59.000Z

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

  14. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18T23:59:59.000Z

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

  15. DNA: The Strand that Connects Us All

    SciTech Connect (OSTI)

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

    2011-03-29T23:59:59.000Z

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

  16. SnapShot: DNA Polymerases II Mammals

    E-Print Network [OSTI]

    Foti, James J.

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

  17. DNA sequencing using fluorescence background electroblotting membrane

    DOE Patents [OSTI]

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

    1992-01-01T23:59:59.000Z

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

  18. Nucleotide capacitance calculation for DNA sequencing

    SciTech Connect (OSTI)

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

    2008-01-01T23:59:59.000Z

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

  19. DNA-guided nanoparticle assemblies

    DOE Patents [OSTI]

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

    2013-07-16T23:59:59.000Z

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

  20. DNA

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

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

  1. DNA

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

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

  2. Neutrinoless Double Beta Decay in Supersymmetric Seesaw model

    E-Print Network [OSTI]

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

    2002-09-26T23:59:59.000Z

    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.

  3. Results of the NEMO-3 Double Beta Decay Experiment

    E-Print Network [OSTI]

    Mathieu BONGRAND for the NEMO-3 Collaboration

    2011-05-12T23:59:59.000Z

    The NEMO-3 experiment is searching for neutrinoless double beta decay for 2 main isotopes (100Mo and 82Se) and is studying the two-neutrino double beta decay of seven isotopes. The experiment has been taking data since 2003 and, up to the end of 2009, showed no evidence for neutrinoless double beta decay. Two 90 % CL lower limits on the half-lives of the transitions were obtained : T_{1/2}^{0\

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

    E-Print Network [OSTI]

    Irina Nasteva; for the NEMO 3 Collaboration

    2008-10-03T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    Zornitza Daraktchieva

    2009-01-18T23:59:59.000Z

    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

  6. 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)

    2008-11-23T23:59:59.000Z

    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.

  7. DNA nanotechnology DOI: 10.1002/smll.200500464

    E-Print Network [OSTI]

    Li, Jiali

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

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

    E-Print Network [OSTI]

    Stoltz, Brian M.

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

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

    E-Print Network [OSTI]

    Williams, Loren

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

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

    E-Print Network [OSTI]

    Yuejiao Ren; Zhongzhou Ren

    2015-01-07T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

    V. Barger; K. Whisnant

    1999-04-08T23:59:59.000Z

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

  12. Neutrinoless double beta decay can constrain neutrino dark matter

    E-Print Network [OSTI]

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

    2002-02-26T23:59:59.000Z

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

  13. Surface-plasmons lasing in double-graphene-layer structures

    SciTech Connect (OSTI)

    Dubinov, A. A. [Research Institute for Electrical Communication, Tohoku University, Sendai 980-8577 (Japan); Institute for Physics of Microstructures of Russian Academy of Sciences, and Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603950 (Russian Federation); Aleshkin, V. Ya. [Institute for Physics of Microstructures of Russian Academy of Sciences, and Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod 603950 (Russian Federation); Ryzhii, V. [Research Institute for Electrical Communication, Tohoku University, Sendai 980-8577 (Japan); Center for Photonics and Infrared Engineering, Bauman Moscow State Technical University, Moscow 105005 (Russian Federation); Shur, M. S. [Department of Electrical, Electronics, and System Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180 (United States); Otsuji, T. [Research Institute for Electrical Communication, Tohoku University, Sendai 980-8577 (Japan)

    2014-01-28T23:59:59.000Z

    We consider the concept of injection terahertz lasers based on double-graphene-layer (double-GL) structures with metal surface-plasmon waveguide and study the conditions of their operation. The laser under consideration exploits the resonant radiative transitions between GLs. This enables the double-GL laser room temperature operation and the possibility of voltage tuning of the emission spectrum. We compare the characteristics of the double-GL lasers with the metal surface-plasmon waveguides with those of such laser with the metal-metal waveguides.

  14. 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

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

    E-Print Network [OSTI]

    Deaton, Russell J.

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

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

    SciTech Connect (OSTI)

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

    2009-09-07T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2009-01-01T23:59:59.000Z

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

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

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

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

  19. Single Stranded DNA Induced Assembly of Gold Nanoparticles

    E-Print Network [OSTI]

    Yang, Jun

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

  20. Single molecule analysis of DNA electrophoresis in microdevices

    E-Print Network [OSTI]

    Randall, Greg C

    2006-01-01T23:59:59.000Z

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

  1. DNA topology confers sequence specificity to nonspecific architectural proteins

    E-Print Network [OSTI]

    Swigon, David

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

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

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

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

  3. Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

    E-Print Network [OSTI]

    Dekker, Cees

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

  4. Double Kelvin Wave Cascade in Superfluid Helium

    E-Print Network [OSTI]

    G. Boffetta; A. Celani; D. Dezzani; J. Laurie; S. Nazarenko

    2008-10-20T23:59:59.000Z

    We study the double cascade of energy and wave action in a local model of superfluid vortex filaments. The model is obtained from a truncated expansion of the 2D Local Induction Approximation and it is shown to support six-wave interactions. We argue that, because of the uncertainty in the vortex core profile, this model has the same status of validity as the traditionally used Biot-Savart model with cutoff, but it has advantage of being much simpler. Our minimal model leads to a wave kinetic equation for which we predict existence of two distinct power-law scaling in the spectrum, corresponding to a direct cascade of energy and an inverse one of wave action. Direct numerical simulations confirm the theoretical predictions in the weak turbulence regime.

  5. Double beta decay and neutrino mass models

    E-Print Network [OSTI]

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

    2015-01-01T23:59:59.000Z

    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.

  6. Neutrinoless Double Beta Decay with SNO+

    E-Print Network [OSTI]

    J. Hartnell; for the SNO+ collaboration

    2012-01-30T23:59:59.000Z

    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.

  7. 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)

    2009-11-09T23:59:59.000Z

    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.

  8. The Double Copy Structure of Soft Gravitons

    E-Print Network [OSTI]

    Agustin Sabio Vera; Miguel A. Vazquez-Mozo

    2014-12-11T23:59:59.000Z

    The subleading corrections to factorization theorems for soft bremsstrahlung in nonabelian gauge theories and gravity are investigated. Building on recent results, we write the action of the angular momentum operators on scattering amplitudes as derivatives with respect to the Mandelstam invariants to uncover a double copy structure in the contribution of the soft graviton to the amplitude, both in the leading term and the first correction. Using our approach, we study Gribov's theorem as extended to nonabelian gauge theories and gravity by Lipatov, and find that subleading corrections can be obtained from those to Low's theorem by dropping the terms with derivatives with respect to the center-of-mass energy, which are suppressed at high energies. In this case, the emitted gravitons are not necessarily soft.

  9. Forty kilojoule carbon double layer capacitor

    SciTech Connect (OSTI)

    Evans, D.A. [Evans Co., East Providence, RI (United States)

    1994-10-01T23:59:59.000Z

    Evans was awarded a Small Business Innovation Research (SBIR) grant from the Department of the Navy to determine if carbon double layer capacitor (DLC) technology could be used as a bridge DC power source for submarine computer systems. The Navy is interested in the technology because DLCs have high power density, require no maintenance, and are free of the hazards commonly associated with batteries. The proposed work had three main objectives: First, to design a DLC power source capable of a 15 kw average discharge rate for a minimum of 100 ms. The operating voltage was to be selected by external buss connections at 15 to 120 volts. And, the unit needed to be sealed to prevent contamination and electrolyte loss. Second, to fabricate the device according to this design and third, to measure the electrical characteristics, evaluate power performance, and report the results to the Navy. This article describes the design and performance of the capacitor.

  10. Double Shell Tank (DST) Utilities Specification

    SciTech Connect (OSTI)

    SUSIENE, W.T.

    2000-04-27T23:59:59.000Z

    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.

  11. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-01-01T23:59:59.000Z

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

  12. Recombinant DNA encoding a desulfurization biocatalyst

    DOE Patents [OSTI]

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

    1994-10-18T23:59:59.000Z

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

  13. Dynamics and control of DNA sequence amplification

    SciTech Connect (OSTI)

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

    2014-10-28T23:59:59.000Z

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

  14. DNA Motif Representation with Nucleotide Dependency

    E-Print Network [OSTI]

    Chin, Francis Y.L.

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

  15. Neutrinoless Double Beta Decay in Gauge Theories

    E-Print Network [OSTI]

    J. D. Vergados

    1999-07-12T23:59:59.000Z

    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. Atomic force microscopy of biochemically tagged DNA

    SciTech Connect (OSTI)

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

    1993-05-01T23:59:59.000Z

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

  17. Storing data encoded DNA in living organisms

    DOE Patents [OSTI]

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

    2006-06-06T23:59:59.000Z

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

  18. Elastic and Proton Dynamics of the DNA

    E-Print Network [OSTI]

    V. L. Golo

    2008-03-28T23:59:59.000Z

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

  19. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2011-07-05T23:59:59.000Z

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

  20. Flow cytometric detection method for DNA samples

    DOE Patents [OSTI]

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

    2006-08-01T23:59:59.000Z

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

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

    SciTech Connect (OSTI)

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

    2010-10-01T23:59:59.000Z

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

  2. An improved selective excitation double Mossbauer spectrometer J. van Lieropa)

    E-Print Network [OSTI]

    Ryan, Dominic

    An improved selective excitation double MoØssbauer spectrometer J. van Lieropa) and D. H. Ryan, operation and performance of a selective excitation double MoØssbauer SEDM spectrometer are described circuitry together with Wissel MoØssbauer velocity transducers and electronics supplies energy

  3. Support of Evidence for Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    H. V. Klapdor-Kleingrothaus; A. Dietz; I. V. Krivosheina; Ch. Doerr; C. Tomei

    2003-12-12T23:59:59.000Z

    Indirect support for the evidence of neutrinoless double beta decay reported recently, is obtained by analysis of other Ge double beta experiments, which yield independent information on the background in the region of Q_(beta-beta). Some statistical features as well as background simulations with GEANT 4 of the HEIDELBERG-MOSCOW experiment are discussed which disprove recent criticism.

  4. One Year of Evidence for Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    H. V. Klapdor-Kleingrothaus

    2003-02-26T23:59:59.000Z

    The present experimental status in the search for neutrinoless double beta decay is reviewed, with emphasis on the first indication for neutrinoless double beta decay found in the HEIDELBERG-MOSCOW experiment, giving first evidence for lepton number violation and a Majorana nature of the neutrinos. Future perspectives of the field are briefly outlined.

  5. Experimental research of double beta decay of atomic nuclei

    E-Print Network [OSTI]

    F. A. Danevich

    2011-12-26T23:59:59.000Z

    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 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.

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

    E-Print Network [OSTI]

    Pei-Hong Gu

    2012-09-13T23:59:59.000Z

    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.

  7. 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

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

    E-Print Network [OSTI]

    Gemmen, Gregory John

    2006-01-01T23:59:59.000Z

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

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

    E-Print Network [OSTI]

    Troll, Christopher

    2013-01-01T23:59:59.000Z

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

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

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

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

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

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

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

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

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

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

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

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

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

  14. 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...

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

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

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

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

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

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

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

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

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

  18. DNA Replication via Entanglement Swapping

    E-Print Network [OSTI]

    Onur Pusuluk; Cemsinan Deliduman

    2011-03-31T23:59:59.000Z

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

  19. Abstract DNA-type systems

    E-Print Network [OSTI]

    Diederik Aerts; Marek Czachor

    2005-12-22T23:59:59.000Z

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

  20. Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA

    E-Print Network [OSTI]

    Richardson, Charles C.

    Acidic C-terminal tail of the ssDNA-binding protein of bacteriophage T7 and ssDNA compete. Prokaryotic ssDNA-binding proteins share a conserved DNA-binding fold and an acidic C-terminal tail. It has been proposed that in the absence of ssDNA, the C-terminal tail contacts the ssDNA-binding cleft

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

    DOE Patents [OSTI]

    Hammond, Mark L. (Angier, NC); Jett, James H. (Los Alamos, NM); Keller, Richard A. (Los Alamos, NM); Marrone, Babetta L. (Los Alamos, NM); Martin, John C. (Los Alamos, NM)

    1996-01-01T23:59:59.000Z

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

  2. Triple Differential Cross sections and Nuclear Recoil in Two-Photon Double Ionization of Helium

    E-Print Network [OSTI]

    Horner, Daniel A.

    2008-01-01T23:59:59.000Z

    Two-Photon Double Ionization of Helium D. A. Horner, 1 C. W.photon double ionization of helium are calculated using theDouble ionization of the helium atom by two XUV photons in

  3. Cross sections for short pulse single and double ionization of helium

    E-Print Network [OSTI]

    Palacios, Alicia; Rescigno, Thomas N.; McCurdy, C. William

    2008-01-01T23:59:59.000Z

    ton double ionization of helium at 20 eV above threshold. 1single and double ionization of helium A. Palacios, 1 T. N.double ionization of helium. In particular it is shown how

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

    E-Print Network [OSTI]

    2003-01-01T23:59:59.000Z

    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-

  5. Method of quantitating dsDNA

    DOE Patents [OSTI]

    Stark, Peter C. (Los Alamos, NM); Kuske, Cheryl R. (Los Alamos, NM); Mullen, Kenneth I. (Los Alamos, NM)

    2002-01-01T23:59:59.000Z

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

  6. , btzhang}@bi.snu.ac.kr Boosted DNA Computing for Evolutionary Graphical Structure Learning

    E-Print Network [OSTI]

    PLM (Probabilistic Library Model PLM PLM DNA bead seperation PCR (Polymerase Chain Reaction) PLM PLM DNA DNA PLM PLM PLM PLM DNA PLM PLM evolutionary graph structure PLM DNA &$$) Jc`" '& Bc" %6 #12

  7. DNA looping: the consequences and its control

    E-Print Network [OSTI]

    Leonor Saiz; Jose M. G. Vilar

    2006-09-26T23:59:59.000Z

    The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of DNA looping in its natural context and how they propagate to the cellular behavior through gene regulation. The results of connecting the molecular properties with cellular physiology indicate that looping of DNA in vivo is much more complex and easier than predicted from current models and reveals a wealth of previously unappreciated details.

  8. Integrated reservoir management doubles Nigerian field reserves

    SciTech Connect (OSTI)

    Akinlawon, Y.; Nwosu, T.; Satter, A.; Jespersen, R.

    1996-10-01T23:59:59.000Z

    An integrated alliance across disciplines, companies and countries enabled Texaco to conduct a comprehensive reservoir analysis of the North Apoi/Funiwa field in Nigeria. Recommendations implemented in 3 months doubled the book reserves of this mature field. The paper discusses the objectives, the integration of organizations, reservoir analysis, and conclusions. The conclusions made from the integrated study are: (1) 3-D seismic data dramatically improved reservoir description. (2) OOIP is considerably more than the booked values and reserves additions are substantial. (3) Significant value has been added to TOPCON`s assets as a result of teamwork and a multidisciplinary approach to evaluating the reservoirs and optimizing the scenarios for reservoir management. (4) Teamwork and integration of professionals, data, technology and tools was critical to the projects success. (5) The study set an example for effective and expeditious technology transfer and applications. (6) Partnering of TOPCON, DPR, NAPIMS, EPTD and SSI resulted in a quick cycle time and set an excellent example of integration and alliance.

  9. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M. (Oak Ridge, TN)

    1995-01-01T23:59:59.000Z

    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.

  10. Double-duct liquid metal magnetohydrodynamic engine

    DOE Patents [OSTI]

    Haaland, Carsten M. (Oak Ridge, TN)

    1997-01-01T23:59:59.000Z

    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.

  11. 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)

    2010-02-01T23:59:59.000Z

    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.

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

    DOE Patents [OSTI]

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

    2013-06-25T23:59:59.000Z

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

  13. aligned double-walled carbon: Topics by E-print Network

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

    Reinhard 2 Atomistic Simulations of Double-Walled Carbon Nanotubes (DWCNTs) as Materials Science Websites Summary: Atomistic Simulations of Double-Walled Carbon Nanotubes...

  14. above-threshold nonsequential double: Topics by E-print Network

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

    Summary: Scintillator detectors can be used in experiments searching for neutrinoless double beta decay. A wide variety of double beta decay candidate isotopes can be made into...

  15. T-581: Novell Access Manager Java Double Literal Denial of Service...

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

    Vulnerability Report: Novell Access Manager 3.x Oracle FPUpdater Tool IMPACT ASSESSMENT: Medium Discussion: The Double.parseDouble method in Java Runtime Environment in Oracle...

  16. Electric Field in a Double Layer and the Imparted Momentum

    SciTech Connect (OSTI)

    Fruchtman, A. [Holon Academic Institute of Technology, 52 Golomb Street, Holon 58102 (Israel)

    2006-02-17T23:59:59.000Z

    It is shown that the net momentum delivered by the large electric field inside a one-dimensional double layer is zero. This is demonstrated through an analysis of the momentum balance in the double layer at the boundary between the ionosphere and the aurora cavity. For the recently observed double layer in a current-free plasma expanding along a divergent magnetic field, an analysis of the evolution of the radially averaged variables shows that the increase of plasma thrust results from the magnetic-field pressure balancing the plasma pressure in the direction of acceleration, rather than from electrostatic pressure.

  17. Increased Upstream Ionization due to Formation of a Double Layer

    SciTech Connect (OSTI)

    Thakur, S. Chakraborty; Harvey, Z.; Biloiu, I. A.; Hansen, A.; Hardin, R. A.; Przybysz, W. S.; Scime, E. E. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506-6315 (United States)

    2009-01-23T23:59:59.000Z

    We report observations that confirm a theoretical prediction that formation of a current-free double layer in a plasma expanding into a chamber of larger diameter is accompanied by an increase in ionization upstream of the double layer. The theoretical model argues that the increased ionization is needed to balance the difference in diffusive losses upstream and downstream of the expansion region. In our expanding helicon source experiments, we find that the upstream plasma density increases sharply at the same antenna frequency at which the double layer appears.

  18. Majorons Without Majorana Masses and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    C. P. Burgess; J. M. Cline

    1992-09-30T23:59:59.000Z

    We explain excess events near the endpoints of the double beta decay spectra of several elements, using the neutrinoless emission of massless Goldstone bosons. Models with scalars carrying lepton number $-2$ are proposed for this purpose so that ordinary neutrinoless double beta decay is forbidden, and we can raise the scale of global symmetry breaking above the 10 keV scale needed for observable emission of conventional Majorons in double beta decay. The electron spectrum has a different shape, and the rate depends on different nuclear matrix elements, than for the emission of ordinary Majorons.

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

    E-Print Network [OSTI]

    Rabindra N. Mohapatra

    1995-07-05T23:59:59.000Z

    The various mechanisms for neutrinoless double beta decay in gauge theories are reviewed and the present experimental data is used to set limits on physics scenarios beyond the standard model. The positive indications for nonzero neutrino masses in various experiments such as those involving solar, atmospheric and accelerator neutrinos are discussed and it is pointed out how some neutrino mass textures consistent with all data can be tested by the ongoing double beta decay experiments. Finally, the outlook for observable neutrinoless double beta decay signal in grand unified theories is discussed.

  20. Fabrication and Measurements of 500 MHz Double Spoke Cavity

    SciTech Connect (OSTI)

    Park, HyeKyoung [JLAB; Hopper, Christopher S. [Old Dominion University; Delayen, Jean R. [Old Dominion University

    2014-12-01T23:59:59.000Z

    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.

  1. Double-$?$ hypernuclei in the relativistic mean-field theory

    E-Print Network [OSTI]

    H. Shen; F. Yang; H. Toki

    2006-02-14T23:59:59.000Z

    We study the properties of double-$\\Lambda$ hypernuclei in the relativistic mean-field theory, which has been successfully used for the description of stable and unstable nuclei. With the meson-hyperon couplings determined by the experimental binding energies of single-$\\Lambda$ hypernuclei, we present a self-consistent calculation of double-$\\Lambda$ hypernuclei in the relativistic mean-field theory, and discuss the influence of hyperons on the nuclear core. The contribution of two mesons with dominant strange quark components (scalar $\\sigma^*$ and vector $\\phi$) to the $\\Lambda\\Lambda$ binding energy of double-$\\Lambda$ hypernuclei is examined.

  2. Matched Slow Pulses Using Double Electromagnetically Induced Transparency

    E-Print Network [OSTI]

    Andrew MacRae; Geoff Campbell; A. I. Lvovsky

    2008-09-29T23:59:59.000Z

    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.

  3. 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

  4. DNA ARRAY DECODING FROM NONLINEAR MEASUREMENTS BY BELIEF PROPAGATION

    E-Print Network [OSTI]

    DNA ARRAY DECODING FROM NONLINEAR MEASUREMENTS BY BELIEF PROPAGATION Mona A. Sheikh, Shriram Compressed Sensing (CS) and demonstrate its utility in DNA array decoding. In a CS DNA microarray, the array spots identify DNA sequences that are shared between multiple organisms, thereby reduc- ing the number

  5. DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications

    E-Print Network [OSTI]

    Weiss, Sharon

    DNA Oligonucleotide Synthesis in Mesoporous Silicon for Biosensing Applications Jenifer L. Lawrie for improving the sensitivity of label-free optical biosensors based on in-situ synthesis of DNA probes within was utilized as the sensor structure. Synthesis of DNA probe, as well as sensing of target DNA, was verified

  6. DNA Deformation Energy as an Indirect Recognition Mechanism in

    E-Print Network [OSTI]

    Lathrop, Richard H.

    DNA Deformation Energy as an Indirect Recognition Mechanism in Protein-DNA Interactions Kimberly A. Senear Abstract--Proteins that bind to specific locations in genomic DNA control many basic cellular. Deformation energy, which models the energy required to bend DNA from its native shape to its shape when bound

  7. DNA Translocation Governed by Interactions with Solid-State Nanopores

    E-Print Network [OSTI]

    Meller, Amit

    DNA Translocation Governed by Interactions with Solid-State Nanopores Meni Wanunu, Jason Sutin, Ben dynamics of individual DNA molecules through solid-state nanopores in the diameter range 2.7­5 nm. Our with DNA length by two power laws: for short DNA molecules, in the range 150­3500 bp, we find an exponent

  8. DNA Compression Challenge Revisited: a Dynamic Programming Approach

    E-Print Network [OSTI]

    Lonardi, Stefano

    DNA Compression Challenge Revisited: a Dynamic Programming Approach Behshad Behzadi and Fabrice Le Fessant LIX, Ecole Polytechnique, Paris, FRANCE June 21 2005 B. Behzadi, F. Le Fessant (LIX) DNA Compression June 21 2005 1 / 38 #12;Outline 1 DNA Compression Challenge 2 Tools and Methods 3 DNA Compression

  9. DNA Computing: A Research University of Western Ontario

    E-Print Network [OSTI]

    Kari, Lila

    31 DNA Computing: A Research Snapshot Lila Kari University of Western Ontario Kalpana Mahalingam ........................................... 31-6 31.5 DNA Memory ................................................... 31-8 Nested Primer Molecular Memory · Organic DNA Memory · Design of DNA Sequences 31.6 Computation in Living Cells

  10. Deoxyribose oxidation chemistry and endogenous DNA adducts

    E-Print Network [OSTI]

    Zhou, Xinfeng

    2006-01-01T23:59:59.000Z

    Endogenous and exogenous oxidants react with cellular macromolecules to generate a variety of electrophiles that react with DNA produce cytotoxic and mutagenic adducts. One source of such electrophiles is deoxyribose in ...

  11. DNA Assembly Line for Nano-Construction

    ScienceCinema (OSTI)

    Oleg Gang

    2010-01-08T23:59:59.000Z

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

  12. Linear Thermodynamics of Rodlike DNA Filtration

    E-Print Network [OSTI]

    Li, Zirui

    Linear thermodynamics transportation theory is employed to study filtration of rodlike DNA molecules. Using the repeated nanoarray consisting of alternate deep and shallow regions, it is demonstrated that the complex ...

  13. Intriguing DNA Editor Has a Structural Trigger

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

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

  14. The Initiation of Bacterial DNA Replication

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

    that the ATP-DnaA active site is in a closed configuration, which allows it to bind nucleotides using conserved residues from neighboring AAA+ protomers. The precise geometry of...

  15. Double, Double Toil and Trouble: Tungsten Burn 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministration Donald6,DoubleDOE

  16. Double, Double Toil and Trouble: Tungsten Burn 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: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOEThe Bonneville Power AdministrationField Campaign:INEA : Papers69 FederalAdministration Donald6,DoubleDOEDOE

  17. RecA acts in trans to allow replication of damaged DNA by DNA polymerase V

    E-Print Network [OSTI]

    Cox, Michael M.

    , Michael M. Cox2 , Roger Woodgate3 & Myron F. Goodman1 The DNA polymerase V (pol V) and RecA proteins

  18. Carbon Nanotube DNA Sensor and Sensing Mechanism

    E-Print Network [OSTI]

    Le Roy, Robert J.

    nanotube (SWNT) DNA sensors and the sensing mechanism. The simple and generic protocol for label for direct label-free detection of DNA hybridization in a biocompatible buffer solution. We also carried out is a field effect device, which has a typical on-current of 3-6 µA at 10 mV source- drain bias and an on-off

  19. Regulation of DNA repair by parkin

    SciTech Connect (OSTI)

    Kao, Shyan-Yuan, E-mail: shyan-yuan_kao@meei.harvard.edu [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)] [Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114 (United States)

    2009-05-01T23:59:59.000Z

    Mutation of parkin is one of the most prevalent causes of autosomal recessive Parkinson's disease (PD). Parkin is an E3 ubiquitin ligase that acts on a variety of substrates, resulting in polyubiquitination and degradation by the proteasome or monoubiquitination and regulation of biological activity. However, the cellular functions of parkin that relate to its pathological involvement in PD are not well understood. Here we show that parkin is essential for optimal repair of DNA damage. Parkin-deficient cells exhibit reduced DNA excision repair that can be restored by transfection of wild-type parkin, but not by transfection of a pathological parkin mutant. Parkin also protects against DNA damage-induced cell death, an activity that is largely lost in the pathological mutant. Moreover, parkin interacts with the proliferating cell nuclear antigen (PCNA), a protein that coordinates DNA excision repair. These results suggest that parkin promotes DNA repair and protects against genotoxicity, and implicate DNA damage as a potential pathogenic mechanism in PD.

  20. DNA Polymerase-Mediated DNA Synthesis on a TNA Template John C. Chaput, Justin K. Ichida, and Jack W. Szostak*

    E-Print Network [OSTI]

    Heller, Eric

    DNA Polymerase-Mediated DNA Synthesis on a TNA Template John C. Chaput, Justin K. Ichida, and Jack TNA is capable of antiparallel, Watson-Crick base-pairing with complementary DNA, RNA, and TNA oligo- nucleotides.2 This property is remarkable, given that the TNA repeat unit is one atom shorter than that of DNA

  1. Classical cutoffs for laser-induced nonsequential double ionization

    SciTech Connect (OSTI)

    Milosevic, D.B. [Faculty of Science, University of Sarajevo, Zmaja od Bosne 35, 71000 Sarajevo (Bosnia and Herzegowina); Max-Born-Institut, Max-Born-Strasse 2a, 12489 Berlin (Germany); Becker, W. [Max-Born-Institut, Max-Born-Strasse 2a, 12489 Berlin (Germany)

    2003-12-01T23:59:59.000Z

    Classical cutoffs for the momenta of electrons ejected in laser-induced nonsequential double ionization are derived for the recollision-impact-ionization scenario. Such simple cutoff laws can aid in the interpretation of the observed electron spectra.

  2. Comparing Control Constructs by Typing Double-barrelled CPS Transforms

    E-Print Network [OSTI]

    Thielecke, Hayo

    Comparing Control Constructs by Typing Double-barrelled CPS Transforms Hayo Thielecke School Kingdom Copyright 2000 ACM 0-89791-88-6/97/05 ..$5.00 the bare essentials of labelling and jumping, so

  3. New expectations and uncertainties on Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Dell'Oro, Stefano; Vissani, Francesco

    2014-01-01T23:59:59.000Z

    The discovery of neutrino oscillations and its implication that neutrinos have mass have boosted the importance of neutrinoless double beta decay. Neutrinoless double beta decay offers unique chances to investigate the nature of the neutrino mass term, giving also information on the absolute scale and the mass hierarchy, assuming that neutrinos are Majorana particles. We study the Majorana Effective Mass, i. e. the crucial parameter that regulates the rate of the neutrinoless double beta decay due to light neutrino exchange. We update the previous estimations of this parameter, using the most recent data analysis, phase space factors and nuclear matrix elements. We evaluate the impact of the quenching in the nuclear medium of the axial vector coupling constant, as discussed by Iachello and collaborators. We provide estimations of the sensitivity of recent and future neutrinoless double beta decay experiments in terms of the Majorana Effective Mass. Finally, we discuss the possibility of taking advantage of th...

  4. Characterization of double walled carbon nanotubes-polyvinylidene fluoride nanocomposites 

    E-Print Network [OSTI]

    Almasri, Atheer Mohammad

    2007-04-25T23:59:59.000Z

    One of the main objectives of this thesis is to disperse double-walled carbon nanotubes (DWNT) in a polyvinylidene fluoride (PVDF) matrix, and to characterize the resulting composite using electrical, thermal, and mechanical ...

  5. Double beta decay experiments: past and present achievements

    E-Print Network [OSTI]

    Alexander Barabash

    2006-08-23T23:59:59.000Z

    A brief history of double beta decay experiments is presented. The best currently running experiments (NEMO-3 and CUORICINO) and their latest results are described. The best measurements and limits for the $2\

  6. Double Beta Decay: Historical Review of 75 Years of Research

    E-Print Network [OSTI]

    A. S. Barabash

    2011-04-25T23:59:59.000Z

    Main achievements during 75 years of research on double beta decay have been reviewed. The existing experimental data have been presented and the capabilities of the next-generation detectors have been demonstrated.

  7. Double Eagle II Airport (AEG) Pavement Condition and Analysis

    E-Print Network [OSTI]

    Cal, Mark P.

    Double Eagle II Airport (AEG) Pavement Condition and Analysis Submitted to: Jane M. Lucero, AICP ...................................................................................................................FWD Analysis 11 .......................................3. Predicted Pavement Conditions Assuming No Maintenance 11 .....................Table 4. Predicted Pavement Conditions (PCI) Assuming no Maintenance 12

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

    E-Print Network [OSTI]

    A. S. Barabash

    2012-09-19T23:59:59.000Z

    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.

  9. 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 ...

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

    SciTech Connect (OSTI)

    BAFUS, R.R.

    2000-11-03T23:59:59.000Z

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

  11. Double Shell Tank (DST) Process Waste Sampling Subsystem Specification

    SciTech Connect (OSTI)

    RASMUSSEN, J.H.

    2000-05-03T23:59:59.000Z

    This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied to the Double-Shell Tank (DST) Process Waste Sampling Subsystem which supports the first phase of Waste Feed Delivery.

  12. Neutrinoless double beta decay, solar neutrinos and mass scales

    E-Print Network [OSTI]

    Per Osland; Geir Vigdel

    2001-09-13T23:59:59.000Z

    We obtain bounds for the neutrino masses by combining atmospheric and solar neutrino data with the phenomenology of neutrinoless double beta decay where hypothetical values of || are envisaged from future 0\

  13. Bounds on Compositeness from Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Orlando Panella; Yogendra N. Srivastava

    1994-11-07T23:59:59.000Z

    Assuming the existence of a heavy Majorana neutral particle arising from a composite model scenario we discuss the constraints imposed by present experimental limits of half-life neutrinoless double beta decay $(0\

  14. Molecular Dynamics Study of the Electrical Double Layer at Silver...

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

    double layer at AgClaqueous electrolyte (KCl) interfaces are presented, accompanied by a new force field and properties of bulk AgCl computed using planewave density functional...

  15. 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

    2002-05-22T23:59:59.000Z

    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.

  16. Towards a double field theory on para-Hermitian manifolds

    SciTech Connect (OSTI)

    Vaisman, Izu [Department of Mathematics, University of Haifa, Haifa (Israel)] [Department of Mathematics, University of Haifa, Haifa (Israel)

    2013-12-15T23:59:59.000Z

    In a previous paper, we have shown that the geometry of double field theory has a natural interpretation on flat para-Kähler manifolds. In this paper, we show that the same geometric constructions can be made on any para-Hermitian manifold. The field is interpreted as a compatible (pseudo-)Riemannian metric. The tangent bundle of the manifold has a natural, metric-compatible bracket that extends the C-bracket of double field theory. In the para-Kähler case, this bracket is equal to the sum of the Courant brackets of the two Lagrangian foliations of the manifold. Then, we define a canonical connection and an action of the field that correspond to similar objects of double field theory. Another section is devoted to the Marsden-Weinstein reduction in double field theory on para-Hermitian manifolds. Finally, we give examples of fields on some well-known para-Hermitian manifolds.

  17. Young's Double Slit Experiment in Quantum Field Theory

    E-Print Network [OSTI]

    Masakatsu Kenmoku; Kenji Kume

    2011-03-01T23:59:59.000Z

    Young's double slit experiment is formulated in the framework of canonical quantum field theory in view of the modern quantum optics. We adopt quantum scalar fields instead of quantum electromagnetic fields ignoring the vector freedom in gauge theory. The double slit state is introduced in Fock space corresponding to experimental setup. As observables, expectation values of energy density and positive frequency part of current with respect to the double slit state are calculated which give the interference term. Classical wave states are realized by coherent double slit states in Fock space which connect quantum particle states with classical wave states systematically. In case of incoherent sources, the interference term vanishes by averaging random phase angles as expected.

  18. additional double bonds: Topics by E-print Network

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

    such as weak-magnetism and pseudoscalar couplings to the amplitude of neutrinoless double beta decay in the mechanisms of light and heavy Majorana neutrino as well as in that...

  19. amplitude double layers: Topics by E-print Network

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

    the nuclear deformation, as generator coordinates in a calculation of the neutrinoless double-beta decay of 76Ge. We work in two oscillator shells, with a Hamiltonian that...

  20. 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 ...

  1. Improved cell cycle synchronization and chromosome doubling methods in cotton

    E-Print Network [OSTI]

    Halfmann, Randal

    2013-02-22T23:59:59.000Z

    Cotton is an economically important crop in the U.S., but is relatively poorly characterized genetically. Unlike other, more researched crops, it is lacking highly effective methods for consistent cell cycle manipulation and chromosome doubling...

  2. Cross sections for short pulse single and double ionization ofhelium

    SciTech Connect (OSTI)

    Palacios, Alicia; Rescigno, Thomas N.; McCurdy, C. William

    2007-11-27T23:59:59.000Z

    In a previous publication, procedures were proposed for unambiguously extracting amplitudes for single and double ionization from a time-dependent wavepacket by effectively propagating for an infinite time following a radiation pulse. Here we demonstrate the accuracy and utility of those methods for describing two-photon single and one-photon double ionization of helium. In particular it is shown how narrow features corresponding to autoionizing states are easily resolved with these methods.

  3. Band Tunneling through Double Barrier in Bilayer Graphene

    E-Print Network [OSTI]

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

    2014-01-20T23:59:59.000Z

    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.

  4. Neutrinoless Double Beta Decay with Negligible Neutrino Mass

    E-Print Network [OSTI]

    Biswajoy Brahmachari; Ernest Ma

    2002-02-27T23:59:59.000Z

    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.

  5. Constraints on neutrinoless double beta decay from neutrino oscillation experiments

    E-Print Network [OSTI]

    S. M. Bilenky; C. Giunti; M. Monteno

    1997-01-15T23:59:59.000Z

    We show that, in the framework of a general model with mixing of three Majorana neutrinos and a neutrino mass hierarchy, the results of the Bugey and Krasnoyarsk reactor neutrino oscillation experiments imply strong limitations for the effective Majorana mass || that characterizes the amplitude of neutrinoless double beta decay. We obtain further limitations on || from the data of the atmospheric neutrino experiments. We discuss the possible implications of the results of the future long baseline neutrino oscillation experiments for neutrinoless double beta decay.

  6. CP Violation in Neutrinoless Double Beta Decay and Neutrino Oscillation

    E-Print Network [OSTI]

    T. Fukuyama; K. Matsuda; H. Nishiura

    1998-03-03T23:59:59.000Z

    Taking account of possible CP violation, we discuss about the constraints on the lepton mixing angles from the neutrinoless double beta decay and from the neutrino oscillation for the three flavour Majorana neutrinos. From the CHORUS oscillation experiment, combined with the data of neutrinoless double beta decay, we show that the large angle solution of (\\theta_{23}) is improbable if the neutrino mass (m_3) of the third generation is a candidate of hot dark matters.

  7. Effect of nuclear deformation on double beta decay

    SciTech Connect (OSTI)

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

    2009-11-09T23:59:59.000Z

    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.

  8. 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

    2008-05-29T23:59:59.000Z

    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\

  9. Energy levels of double triangular graphene quantum dots

    SciTech Connect (OSTI)

    Liang, F. X.; Jiang, Z. T., E-mail: ztjiang616@hotmail.com; Zhang, H. Y.; Li, S. [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Lv, Z. T. [School of Physics, Beijing Institute of Technology, Beijing 100081 (China); School of Physical Science and Information Engineering, Liaocheng University, Liaocheng 252059 (China)

    2014-09-28T23:59:59.000Z

    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.

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

    E-Print Network [OSTI]

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

    2004-04-08T23:59:59.000Z

    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.

  11. 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

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

    E-Print Network [OSTI]

    Tan, Weihong

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

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

    E-Print Network [OSTI]

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

    2015-01-09T23:59:59.000Z

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

  14. 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,Ć, 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

  15. Double-core excitations in formamide can be probed by X-ray double-quantum-coherence spectroscopy

    E-Print Network [OSTI]

    Mukamel, Shaul

    Yu Zhang, Daniel Healion, Jason D. Biggs, and Shaul Mukamel Citation: J. Chem. Phys. 138, 144301 be probed by X-ray double-quantum-coherence spectroscopy Yu Zhang, Daniel Healion, Jason D. Biggs, and Shaul

  16. A Non-SUSY Model for Neutrino Oscillation, Baryogenesis and Neutrinoless Double Beta Decay

    E-Print Network [OSTI]

    Holger Bech Nielsen; Yasutaka Takanishi

    2001-10-09T23:59:59.000Z

    We fitted the neutrino oscillations, baryogenesis and neutrinoless double beta decay using Anti-GUT model.

  17. Grooving Down the Helix http://www.bnl.gov/bnlweb/pubaf/pr/PR_display.asp?prID=1038&template=Today[12/7/2009 9:39:49 AM

    E-Print Network [OSTI]

    Heller, Eric

    &H | Newsroom | Administration | Visitors | Directory search TODAY Archive BNL TODAY Links Brookhaven Home TODAY, NY -- A team of scientists from the U.S. Department of Energy's (DOE) Brookhaven National Laboratory to alter the behavior of DNA-binding proteins, which are responsible for replicating and repairing DNA

  18. Time-resolved measurements of double layer evolution in expanding plasma

    SciTech Connect (OSTI)

    Scime, E. E.; Biloiu, I. A.; Carr, J. Jr.; Thakur, S. Chakraborty; Galante, M.; Hansen, A.; Houshmandyar, S.; Keesee, A. M.; McCarren, D.; Sears, S. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506 (United States); Biloiu, C. [Varian Associates, Gloucester, Massachusetts 01930 (United States); Sun, X. [Tri-Alpha Corporation, Foothill Ranch, California 92610 (United States)

    2010-05-15T23:59:59.000Z

    Observations in steady-state plasmas confirm predictions that formation of a current-free double layer in a plasma expanding into a chamber of larger diameter is accompanied by an increase in ionization upstream of the double layer. The upstream plasma density increases sharply at the same driving frequency at which a double layer appears. For driving frequencies at which no double layer appears, large electrostatic instabilities are observed. Time-resolved measurements in pulsed discharges indicate that the double layer initially forms for all driving frequencies. However, for particularly strong double layers, instabilities appear early in the discharge and the double layer collapses.

  19. Optical selection and collection of DNA fragments

    DOE Patents [OSTI]

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

    1998-01-01T23:59:59.000Z

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

  20. DNA nanotechnology: understanding and optimisation through simulation

    E-Print Network [OSTI]

    Thomas E. Ouldridge

    2014-11-07T23:59:59.000Z

    DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA nanotechnology, highlighting the need for a more detailed understanding of the key processes, both in terms of theoretical modelling and experimental characterisation. I then consider coarse-grained models of DNA, mesoscale descriptions that have the potential to provide great insight into the operation of DNA nanotechnology if they are well designed. In particular, I discuss a number of nanotechnological systems that have been studied with oxDNA, a recently developed coarse-grained model, highlighting the subtle interplay of kinetic, thermodynamic and mechanical factors that can determine behaviour. Finally, new results highlighting the importance of mechanical tension in the operation of a two-footed walker are presented, demonstrating that recovery from an unintended `overstepped' configuration can be accelerated by three to four orders of magnitude by application of a moderate tension to the walker's track. More generally, the walker illustrates the possibility of biasing strand-displacement processes to affect the overall rate.