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In the second paper of this series, we evaluate two additional well designs for production from permafrost-associated (PA) hydrate deposits. Both designs are within the capabilities of conventional technology. We determine that large volumes of gas can be produced at high rates (several MMSCFD) for long times using either well design. The production approach involves initial fluid withdrawal from the water zone underneath the hydrate-bearing layer (HBL). The production process follows a cyclical pattern, with each cycle composed of two stages: a long stage (months to years) of increasing gas production and decreasing water production, and a short stage (days to weeks) that involves destruction of the secondary hydrate (mainly through warm water injection) that evolves during the first stage, and is followed by a reduction in the fluid withdrawal rate. A well configuration with completion throughout the HBL leads to high production rates, but also the creation of a secondary hydrate barrier around the well that needs to be destroyed regularly by water injection. However, a configuration that initially involves heating of the outer surface of the wellbore and later continuous injection of warm water at low rates (Case C) appears to deliver optimum performance over the period it …

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Current practice in the nuclear industry and elsewhere is to specify the seismic input to design calculations at the surface of the site, rather than at bedrock. This paper investigates the implications of such a specification by comparing the site response of a surface specification to the site response of a corresponding bedrock specification. The investigation considered six different sites consisting of three soil profiles with average shear wave velocities of 800, 1800, and 5000 ft/sec and two oil depths: 200 ft. and 400 ft. Seismic input to these sites consisted of two synthetic accelerograms: one corresponding to Blume's statistically averaged surface response spectrum taken as surface input, the other accelerogram was, in our judgment, a typical bedrock acceleration time history related to the surface synthetic accelerogram. The site response was calculated using the program SHAKE. The deconvolution results indicate that Blume's statistically averaged surface response spectrum envelops all the spectra from lower levels for hard and intermediate sites. When the corresponding bedrock acceleration is used as input for a convolution, the surface acceleration can be greater than Blume's surface spectral acceleration. It is very difficult to calculate physically meaningful results for the soft sites for both convolution and deconvolution. …

Cooking, heat processing, and pyrolysis of protein-rich foods induce the formation of structurally related heterocyclic aromatic amines that have been found to be mutagenic in bacteria, mammalian cells in culture and mice. All these compounds are potent mutagens and most are active below 1 ng/plate, in Ames/Salmonella tester strain TA1538 in the presence of S9 liver microsomal preparations from rat, mouse, or hamster. They are also potent in strains TA98, TA97, moderately active in TA1537, weakly active in TA100, and virtually inactive in TA1535 and TA102. Thus, they show powerful frameshift activity in reverting specific GC-rich sequences, but do not cause base substitution mutations or revert an AT-rich sequence. They are 100-fold less active in the uvrB+, repair-proficient strain TA1978, and in the case of IQ, cause insertions and large deletions not seen in TA1538.

We prove a general theorem on the relation between the bulk topological quantum number and the edge states in two dimensional insulators. It is shown that whenever there is a topological order in bulk, characterized by a non-vanishing Chern number, even if it is defined for a non-conserved quantity such as spin in the case of the spin Hall effect, one can always infer the existence of gapless edge states under certain twisted boundary conditions that allow tunneling between edges. This relation is robust against disorder and interactions, and it provides a unified topological classification of both the quantum (charge) Hall effect and the quantum spin Hall effect. In addition, it reconciles the apparent conflict between the stability of bulk topological order and the instability of gapless edge states in systems with open boundaries (as known happening in the spin Hall case). The consequences of time reversal invariance for bulk topological order and edge state dynamics are further studied in the present framework.

AmiGO is a web application that allows users to query, browse, and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium; it can also be downloaded and installed to browse local ontologies and annotations. AmiGO is free open source software developed and maintained by the GO Consortium.

We report hole-doping dependence of the in-plane resistivity {rho}{sub ab} in a cuprate superconductor La{sub 2-x}Sr{sub x}CuO{sub 4}, carefully examined using a series of high-quality single crystals. Our detailed measurements find a tendency towards charge ordering at particular rational hole doping fractions of 1/16, 3/32, 1/8, and 3/16. This observation appears to suggest a specific form of charge order and is most consistent with the recent theoretical prediction of the checkerboard-type ordering of the Cooper pairs at rational doping fractions x = (2m + 1)/2{sup n}, with integers m and n.

At present, the only solid material believed to be a viable option for plasma-facing components (PFCs) in a fusion reactor is tungsten. Operated at the lower temperatures typical of present-day fusion experiments, tungsten is known to suffer from surface degradation during long-term exposure to helium-containing plasmas, leading to reduced thermal conduction to the bulk, and enhanced erosion. Existing alloys are also quite brittle at temperatures under 700oC. However, at a sufficiently high operating temperature (700 - 1000 oC), tungsten is selfannealing and it is expected that surface damage will be reduced to the point where tungsten PFCs will have an acceptable lifetime in a reactor environment. The existence of only one potentially viable option for solid PFCs, though, constitutes one of the most significant restrictions on design space for DEMO and follow-on fusion reactors. In contrast, there are several candidates for liquid metal-based PFCs, including gallium, tin, lithium, and tin-lithium eutectics. We will discuss options for liquid metal walls in tokamaks, looking at both high and low recycling materials. We will then focus in particular on one of the candidate liquids, lithium. Lithium is known to have a high chemical affinity for hydrogen, and has been shown in test stands1 …

Spatial and temporal expression patterns of the sorghum SBEI, SBEIIA and SBEIIB genes, encoding, respectively, starch branching enzyme (SBE) I, IIA and IIB, in the developing endosperm of sorghum (Sorghum bicolor) were studied. Full-length genomic and cDNA clones for sorghum was cloned and the SBEIIA cDNA was used together with gene-specific probes for sorghum SBEIIB and SBEI. In contrast to sorghum SBEIIB, which was expressed primarily in endosperm and embryo, SBEIIA was expressed also in vegetative tissues. All three genes shared a similar temporal expression profile during endosperm development, with a maximum activity at 15-24 days after pollination. This is different from barley and maize where SBEI gene activity showed a significantly later onset compared to that of SBEIIA and SBEIIB. Expression of the three SBE genes in the sorghum endosperm exhibited a diurnal rhythm during a 24-h cycle.

The spin Hall effect depends crucially on the intrinsic spin-orbit coupling of the energy band. Because of the smaller spin-orbit coupling in silicon, the spin Hall effect is expected to be much reduced. We show that the electric field in p-doped silicon can induce a dissipationless orbital current in a fashion reminiscent of the spin Hall effect. The vertex correction due to impurity scattering vanishes and the effect is therefore robust against disorder. The orbital Hall effect can lead to the accumulation of local orbital momentum at the edge of the sample, and can be detected by the Kerr effect.

We present a theory for two recent experiments in bulk strained semiconductors and show that a new, previously overlooked, strain spin-orbit coupling term may play a fundamental role. We propose simple experiments that could clarify the origin of strain-induced spin-orbit coupling terms in inversion asymmetric semiconductors. We predict that a uniform magnetization parallel to the electric field will be induced in the samples studied in for specific directions of the applied electric field. We also propose special geometries to detect spin currents in strained semiconductors.

Quantum Monte-Carlo (QMC) simulations involving fermions have the notorious sign problem. Some well-known exceptions of the auxiliary field QMC algorithm rely on the factorizibility of the fermion determinant. Recently, a fermionic QMC algorithm has been found in which the fermion determinant may not necessarily factorizable, but can instead be expressed as a product of complex conjugate pairs of eigenvalues, thus eliminating the sign problem for a much wider class of models. In this paper, we present general conditions for the applicability of this algorithm and point out that it is deeply related to the time reversal symmetry of the fermion matrix. We apply this method to various models of strongly correlated systems at all doping levels and lattice geometries, and show that many novel phases can be simulated without the sign problem.

Results are presented of single crystal structural, thermodynamic, and reflectivity measurements of the double-perovskite Ba{sub 2}NaOsO{sub 6}. These characterize the material as a 5d1 ferromagnetic Mott insulator with an ordered moment of {approx} 0.2 {micro}B per formula unit and T{sub C} = 6.8(3) K. The magnetic entropy associated with this phase transition is close to Rln2, indicating that the quartet groundstate anticipated from consideration of the crystal structure is split, consistent with a scenario in which the ferromagnetism is associated with orbital ordering.

Sr3(Ru1-xMnx)2O7, in which 4d-Ru is substituted by the more localized 3d-Mn, is studied by x-ray dichroism and spin-resolved density functional theory. We find that Mn impurities do not exhibit the same 4+ valence of Ru, but act as 3+ acceptors; the extra eg electron occupies the in-plane 3dx2-y2 orbital instead of the expected out-of-plane 3d3z2-r2. We propose that the 3d-4d interplay, via the ligand oxygen orbitals, is responsible for this crystal-field level inversion and the material's transition to an antiferromagnetic, possibly orbitally ordered, low-temperature state.

In recent years concern has grown over the contribution of nitrogen (N) fertilizer use to nitrate (NO{sub 3}{sup -}) water pollution and nitrous oxide (N{sub 2}O), nitric oxide (NO), and ammonia (NH{sub 3}) atmospheric pollution. Characterizing soil N effluxes is essential in developing a strategy to mitigate N leaching and emissions to the atmosphere. In this paper, a previously described and tested mechanistic N cycle model (TOUGHREACT-N) was successfully tested against additional observations of soil pH and N{sub 2}O emissions after fertilization and irrigation, and before plant emergence. We used TOUGHREACT-N to explain the significantly different N gas emissions and nitrate leaching rates resulting from the different N fertilizer types, application methods, and soil properties. The N{sub 2}O emissions from NH{sub 4}{sup +}-N fertilizer were higher than from urea and NO{sub 3}{sup -}-N fertilizers in coarse-textured soils. This difference increased with decreases in fertilization application rate and increases in soil buffering capacity. In contrast to methods used to estimate global terrestrial gas emissions, we found strongly non-linear N{sub 2}O emissions as a function of fertilizer application rate and soil calcite content. Speciation of predicted gas N flux into N{sub 2}O and N{sub 2} depended on pH, fertilizer form, and soil …

We study the effects of spin-orbit coupling in the d-density wave (DDW) phase. In the low-temperature orthorhombic phase of La{sub 2-x}Ba{sub x}CuO{sub 4}, we find that spin-orbit coupling induces ferromagnetic moments in the DDW phase, which are polarized along the [110] direction with a considerable magnitude. This effect does not exist in the superconducting phase. On the other hand, if the d-density wave order does not exist at zero field, a magnetic field along the [110] direction always induces such a staggered orbital current. We discuss experimental constraints on the DDW states in light of our theoretical predictions.

The quantum Hall liquid is a novel state of matter with profound emergent properties such as fractional charge and statistics. Existence of the quantum Hall effect requires breaking of the time reversal symmetry caused by an external magnetic field. In this work, we predict a quantized spin Hall effect in the absence of any magnetic field, where the intrinsic spin Hall conductance is quantized in units of 2 e/4{pi}. The degenerate quantum Landau levels are created by the spin-orbit coupling in conventional semiconductors in the presence of a strain gradient. This new state of matter has many profound correlated properties described by a topological field theory.

Persistent infection of the gastric mucosa by Helicobacter pylori, can initiate an inflammatory cascade that progresses into atrophic gastritis, a condition associated with reduced capacity for secretion of gastric acid and an increased risk in developing gastric cancer. The role of H. pylori as an initiator of inflammation is evident but the mechanism for development into gastric cancer has not yet been proven. A reduced capacity for gastric acid secretion allows survival and proliferation of other microbes that normally are killed by the acidic environment. It has been postulated that some of these species may be involved in the development of gastric cancer, however their identities are poorly defined. In this study, the gastric microbiota from ten patients with gastric cancer was characterized and compared with five dyspeptic controls using the molecular profiling approach, terminal-restriction fragment length polymorphism (T-RFLP), in combination with 16S rRNA gene cloning and sequencing. T-RFLP analysis revealed a complex bacterial community in the cancer patients that was not significantly different from the controls. Sequencing of 140 clones revealed 102 phylotypes, with representatives from five bacterial phyla (Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria). The data revealed a relatively low abundance of H. pylori and showed that the …

We show that the dissipationless spin current in the ground state of the Rashba model gives rise to a reactive coupling between the spin and charge propagation, which is formally identical to the coupling between the electric and the magnetic fields in the 2 + 1 dimensional Maxwell equation. This analogy leads to a remarkable prediction that a density packet can spontaneously split into two counter propagation packets, each carrying the opposite spins. In a certain parameter regime, the coupled spin and charge wave propagates like a transverse 'photon'. We propose both optical and purely electronic experiments to detect this effect.

Employing a recently developed Monte Carlo model, we study the fission of {sup 240}Pu induced by neutrons with energies from thermal to just below the threshold for second chance fission. Current measurements of the mean number of prompt neutrons emitted in fission, together with less accurate measurements of the neutron energy spectra, place remarkably fine constraints on predictions of microscopic calculations. In particular, the total excitation energy of the nascent fragments must be specified to within 1 MeV to avoid disagreement with measurements of the mean neutron multiplicity. The combination of the Monte Carlo fission model with a statistical likelihood analysis also presents a powerful tool for the evaluation of fission neutron data. Of particular importance is the fission spectrum, which plays a key role in determining reactor criticality. We show that our approach can be used to develop an estimate of the fission spectrum with uncertainties several times smaller than current experimental uncertainties for outgoing neutron energies of less than 2 MeV.

A simple conceptual model has been recently developed for analyzing pressure and temperature data from flowing fluid temperature logging (FFTL) in unsaturated fractured rock. Using this conceptual model, we developed an analytical solution for FFTL pressure response, and a semianalytical solution for FFTL temperature response. We also proposed a method for estimating fracture permeability from FFTL temperature data. The conceptual model was based on some simplifying assumptions, particularly that a single-phase airflow model was used. In this paper, we develop a more comprehensive numerical model of multiphase flow and heat transfer associated with FFTL. Using this numerical model, we perform a number of forward simulations to determine the parameters that have the strongest influence on the pressure and temperature response from FFTL. We then use the iTOUGH2 optimization code to estimate these most sensitive parameters through inverse modeling and to quantify the uncertainties associated with these estimated parameters. We conclude that FFTL can be utilized to determine permeability, porosity, and thermal conductivity of the fracture rock. Two other parameters, which are not properties of the fractured rock, have strong influence on FFTL response. These are pressure and temperature in the borehole that were at equilibrium with the fractured rock formation …

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The local structure of aqueous metal ions on solid surfaces is central to understanding many chemical and biological processes in soil and aquatic environments. Here, the local coordination structure of hydrated Zn(II) at water-TiO{sub 2} interfaces was identified by extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectroscopy combined with density functional theory (DFT) calculations. A nonintegral coordination number of average {approx}4.5 O atoms around a central Zn atom was obtained by EXAFS analysis. DFT calculations indicated that this coordination structure was consistent with the mixture of 4-coordinated bidentate binuclear (BB) and 5-coordinated bidentate mononuclear (BM) metastable equilibrium adsorption (MEA) states. The BB complex has 4-coordinated Zn, while the monodentate mononuclear (MM) complex has 6-coordinated Zn, and a 5-coordinated adsorbed Zn was found in the BM adsorption mode. DFT calculated energies showed that the lower-coordinated BB and BM modes were thermodynamically more favorable than the higher-coordinated MM MEA state. The experimentally observed XANES fingerprinting provided additional direct spectral evidence of 4- and 5-coordinated Zn-O modes. The overall spectral and computational evidence indicated that Zn(II) can occur in 4-, 5-, and 6-oxygen coordinated sites in different MEA states due to steric hindrance effects, and the coexistence of …