DNA hybridization catalysts and catalyst circuits

Practically all of life's molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalysis of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in DNA nanotechnology as it is in biology. Here we present experimental results on the control of the decay rates of a metastable DNA "fuel". We show that the fuel complex can be induced to decay with a rate about 1600 times faster than it would decay spontaneously. The original DNA hybridization catalyst [15] achieved a maximal speed-up of roughly 30. The fuel complex discussed here can therefore serve as the basic ingredient for an improved DNA hybridization catalyst. As an example application for DNA hybridization catalysts, we propose a method for implementing arbitrary digital logic circuits

Physical origin of the buckling in CuO2_2: Electron-phonon coupling and Raman spectra

It is shown theoretically that the buckling of the CuO$_{2}$ planes in certain cuprate systems can be explained in terms of an electric field across the planes which originates from different valences of atoms above and below the plane. This field results also in a strong coupling of the Raman-active out-of-phase vibration of the oxygen atoms ($B_{1g}$ mode) to the electronic charge transfer between the two oxygens in the CuO$_{2}$ plane. Consequently, the electric field can be deduced from the Fano-type line shape of the $B_{1g}$ phonon. Using the electric field estimated from the electron-phonon coupling the amplitude of the buckling is calculated and found to be in good agreement with the structural data. Direct experimental support for the idea proposed is obtained in studies of YBa$_{2}$Cu$_{3}$O$_{6+x}$ and Bi$_{2}$Sr$_{2}$(Ca$_{1-x}$Y$_{x}$)Cu$_{2}$O$_{8}$ with different oxygen and yttrium doping, respectively, including antiferromagnetic samples. In the latter compound, symmetry breaking by replacing Ca partially by Y leads to an enhancement of the electron-phonon coupling by an order of magnitude.Comment: 12 pages, 4 figures, and 1 tabl

Localization by disorder in the infrared conductivity of (Y,Pr)Ba2Cu3O7 films

The ab-plane reflectivity of (Y{1-x}Prx)Ba2Cu3O7 thin films was measured in the 30-30000 cm-1 range for samples with x = 0 (Tc = 90 K), x = 0.4 (Tc = 35 K) and x = 0.5 (Tc = 19 K) as a function of temperature in the normal state. The effective charge density obtained from the integrated spectral weight decreases with increasing x. The variation is consistent with the higher dc resistivity for x = 0.4, but is one order of magnitude smaller than what would be expected for x = 0.5. In the latter sample, the conductivity is dominated at all temperatures by a large localization peak. Its magnitude increases as the temperature decreases. We relate this peak to the dc resistivity enhancement. A simple localization-by-disorder model accounts for the optical conductivity of the x = 0.5 sample.Comment: 7 pages with (4) figures include

Mineral–water reactions in Earth’s mantle:Predictions from Born theory and ab initio molecular dynamics

Recent studies present compelling evidence that a free aqueous fluid phase exists within the upper mantle. Fluid may be present at depths as great as the transition zone (410–660 km) and possibly beyond. The chemical reactivity of such deep fluids can be predicted from the Born model of solvation. To use the Born model, we need to know the dielectric constant of water under mantle conditions. We have used ab initio molecular dynamics simulations to determine the dielectric constant of water up to a pressure of 30 GPa and a temperature of 3000 K. Increased temperature lowers the dielectric constant and decreases ion solvation, but pressure overcomes this effect. The resulting high dielectric constant suggests that aqueous mantle fluids are highly reactive for ion solvation and mineral dissolution. We tested this by using the Helgeson–Kirkham–Flowers equation of state to estimate free energies of several mineral-solution and ion solvation reactions under mantle conditions. The results support previous estimates of carbonate solubility in the mantle. We also find that mantle fluids may play a key role in transporting ore metals: we evaluated the solubility of chalcopyrite and the complexation of Cu and Fe by Cl under mantle conditions and find that metal complexation is as significant as in ore-forming fluids in the crust. At reasonable conditions of pH and fH2, chalcopyrite is highly soluble. We tentatively hypothesize that exsolved fluids from subducted slabs may extract and mobilize primary sulfides in the mantle, implying potentially deep sources for porphyry copper deposits

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review

Search for supersymmetry in final states with jets, missing transverse momentum and one isolated lepton in sqrt{s} = 7 TeV pp collisions using 1 fb-1 of ATLAS data

We present an update of a search for supersymmetry in final states containing jets, missing transverse momentum, and one isolated electron or muon, using 1.04 fb^-1 of proton-proton collision data at sqrt{s} = 7 TeV recorded by the ATLAS experiment at the LHC in the first half of 2011. The analysis is carried out in four distinct signal regions with either three or four jets and variations on the (missing) transverse momentum cuts, resulting in optimized limits for various supersymmetry models. No excess above the standard model background expectation is observed. Limits are set on the visible cross-section of new physics within the kinematic requirements of the search. The results are interpreted as limits on the parameters of the minimal supergravity framework, limits on cross-sections of simplified models with specific squark and gluino decay modes, and limits on parameters of a model with bilinear R-parity violation.Comment: 18 pages plus author list (30 pages total), 9 figures, 4 tables, final version to appear in Physical Review

‘The Coaching Needs of High Performance Female Athletes within the Coach-Athlete Dyad’

Within the research literature there is little work that has examined how coaches (and coaching) can positively influence female athletes’ continued participation and development in performance sport. With this in mind, utilising a grounded theory approach, this study focused on what are the coaching preferences of female athletes within the elite coachathlete dyad. Through interviews with 27 current high performance female athletes, four major coaching needs were found. These were: to be supported as person as well a performer, coaching to be a joint endeavour, the need for positive communication and finally, recognition of the salience of gender within the coach-athlete dyad. The findings provide evidence that the relational expertise of coaches is at the forefront of these women’s coaching needs. This study also demonstrates that for the participants, the coach-athlete relationship is at the heart of improving athletic training and performance, and that gender is an important influence on this relationship. Furthermore, the research highlights the strength of using an interpretive-qualitative paradigmatic approach to athlete preferences through foregrounding the women’s voices and experiences

Reducing heterotic M-theory to five dimensional supergravity on a manifold with boundary

This paper constructs the reduction of heterotic $M$-theory in eleven dimensions to a supergravity model on a manifold with boundary in five dimensions using a Calabi-Yau three-fold. New results are presented for the boundary terms in the action and for the boundary conditions on the bulk fields. Some general features of dualisation on a manifold with boundary are used to explain the origin of some topological terms in the action. The effect of gaugino condensation on the fermion boundary conditions leads to a `twist' in the chirality of the gravitino which can provide an uplifting mechanism in the vacuum energy to cancel the cosmological constant after moduli stabilisation.Comment: 16 pages, RevTe