Impact of vertical mixing on sea surface pCO2 in temperate seasonally stratified shelf seas

A key parameter in determining the exchange of CO2 across the ocean-atmosphere interface is the sea surface partial pressure of carbon dioxide (pCO2). Temperate seasonally stratified shelf seas represent a significant sink for atmospheric CO2. Here an analytical model is used to quantify the impact of vertical mixing across the seasonal thermocline on pCO2. The model includes the impacts of the resultant dissolved inorganic carbon, heat, salt, and alkalinity fluxes on the solubility of CO2 and the effect of the inorganic carbon sink created by the primary production fuelled by the flux of limiting nutrient. The results indicate that diapycnal mixing drives a modest but continuous change in pCO2 of order 1–10 µatm d−1. In quantifying the individual impacts of the fluxes of the different parameters, we find that the impact of the fluxes of DIC and nitrate fluxes dominate. In consequence, both the direction and magnitude of the change in pCO2 are strongly dependent on the C:N uptake ratio in primary production. While the smaller impacts of the heat and salt fluxes tend to compensate for each other at midshelf locations, the heat flux dominates close to the shelf break. The analysis highlights the importance of the accurate parameterization of the C:N uptake ratio, the surface-mixed layer depth, and the TKE dissipation rate within the seasonal thermocline in models to be used to predict the air-sea exchange of carbon dioxide in these regimes. The results implicate storms as key periods of pCO2 perturbation

Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K

The crystal structure of orthorhombic Bovine Pancreatic Ribonuclease A has been determined to 0.85 Å resolution using low temperature, 100 K, synchrotron X-ray data collected at 16000 keV (λ = 0.77 Å). This is the first ultra-high-resolution structure of a native form of Ribonuclease A to be reported. Refinement carried out with anisotropic displacement parameters, stereochemical restraints, inclusion of H atoms in calculated positions, five SO2−4 moieties, eleven ethanol molecules and 293 water molecules, converged with final R values of R1(Free) = 0.129 (4279 reflections) and R1 = 0.112 (85,346 reflections). The refined structure was deposited in the Protein Data Bank as structure 7p4r. Conserved waters, using four high resolution structures, have been investigated. Cluster analysis identified clusters of water molecules that are associated with the active site of Bovine Ribonuclease A. Particular attention has been paid to making detailed comparisons between the present structure and other high quality Bovine Pancreatic Ribonuclease A X-ray crystal structures with special reference to the deposited classic monoclinic structure 3RN3 Howlin et al. (Acta Crystallogr A 45:851–861, 1989). Detailed studies of various aspects of hydrogen bonding and conformation have been carried out with particular reference to active site residues Lys-1, Lys-7, Gln-11, His-12, Lys-41, Asn-44, Thr-45, Lys-66, His-119 and Ser-123. For the two histidine residues in the active site the initial electron density map gives a clear confirmation that the position of His-12 is very similar in the orthorhombic structure to that in 3RN3. In 3RN3 His-119 exhibited poor electron density which was modelled and refined as two distinct sites, A (65%) and B (35%) but with respect to His-119 in the present ultra-high resolution orthorhombic structure there is clear electron density which was modelled and refined as a single conformation distinct from either conformation A or B in 3RN3. Other points of interest include Serine-32 which is disordered at the end of the sidechain in the present orthorhombic form but has been modelled as a single form in 3RN3. Lysine-66: there is density indicating a possible conformation for this residue. However, the density is relatively weak, and the conformation is unclear. Three types of amino acid representation in the ultra-high resolution electron density are examined: (i) sharp with very clearly resolved features, for example Lys-37; (ii) well resolved but clearly divided into two conformations which are well behaved in the refinement, both having high quality geometry, for example Tyr-76; (iii) poor density and difficult or impossible to model, an example is Lys-31 for which density is missing except for Cβ. The side chains of Gln-11, His-12, Lys-41, Thr-45 and His-119 are generally recognised as being closely involved in the enzyme activity. It has also been suggested that Lys-7, Asp-44, Lys-66, Phe-120, Asp-121 and Ser-123 may also have possible roles in this mechanism. A molecular dynamics study on both structures has investigated the conformations of His-119 which was modelled as two conformations in 3RN3 but is observed to have a single clearly defined conformation in the present orthorhombic structure. MD has also been used to investigate Lys-31, Lys-41 and Ser32. The form of the Ribonuclease A enzyme used in both the present study and in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851–861, 1989) includes a sulphate anion which occupies approximately the same location as the PO2−4 phosphate group in protein nucleotide complexes (Borkakoti et al. in J Mol Biol 169:743–755, 1983). The present structure contains 5 SO2−4 groups SO41151–SO41155 two of which, SO41152 and SO41153 are disordered, SO41152 being in the active site, and 11 EtOH molecules, EOH A 201–EOH A 211 all of which have good geometry. H atoms were built into the EtOH molecules geometrically. Illustrations of these features in the present structure are included here. The sulphates are presumably present in the material purchased for use in the present study. 293 water molecules are included in the present structure compared to 134 in 3RN3 (Howlin et al. in Acta Crystallogr A 45:851–861, 1989)

Exploiting Lexical Conceptual Structure for paraphrase generation

Abstract. Lexical Conceptual Structure (LCS) represents verbs as semantic structures with a limited number of semantic predicates. This paper attempts to exploit how LCS can be used to explain the regularities underlying lexical and syntactic paraphrases, such as verb alternation, compound word decomposition, and lexical derivation. We propose a paraphrase generation model which transforms LCSs of verbs, and then conduct an empirical experiment taking the paraphrasing of Japanese light-verb constructions as an example. Experimental results justify that syntactic and semantic properties of verbs encoded in LCS are useful to semantically constrain the syntactic transformation in paraphrase generation.

Evaluation of the potential for significant ammonia releases from Hanford waste tanks

Ammonia is ubiquitous as a component of the waste stored in the Hanford Site single-shell tanks (SSTs) and double-shell tanks (DSTs). Because ammonia is both flammable and toxic, concerns have been raised about the amount of ammonia stored in the tanks and the possible mechanisms by which it could be released from the waste into the head space inside the tanks as well as into the surrounding atmosphere. Ammonia is a safety issue for three reasons. As already mentioned, ammonia is a flammable gas and may contribute to a flammability hazard either directly, if it reaches a high enough concentration in the tank head space, or by contributing to the flammability of other flammable gases such as hydrogen (LANL 1994). Ammonia is also toxic and at relatively low concentrations presents a hazard to human health. The level at which ammonia is considered Immediately Dangerous to Life or Health (IDLH) is 300 ppm (WHC 1993, 1995). Ammonia concentrations at or above this level have been measured inside the head space in a number of SSTs. Finally, unlike hydrogen and nitrous oxide, ammonia is highly soluble in aqueous solutions, and large amounts of ammonia can be stored in the waste as dissolved gas. Because of its high solubility, ammonia behaves in a qualitatively different manner from hydrogen or other insoluble gases. A broader range of scenarios must be considered in modeling ammonia storage and release

Stochastic processes with finite correlation time: modeling and application to the generalized Langevin equation

The kangaroo process (KP) is characterized by various forms of the covariance and can serve as a useful model of random noises. We discuss properties of that process for the exponential, stretched exponential and algebraic (power-law) covariances. Then we apply the KP as a model of noise in the generalized Langevin equation and simulate solutions by a Monte Carlo method. Some results appear to be incompatible with requirements of the fluctuation-dissipation theorem because probability distributions change when the process is inserted into the equation. We demonstrate how one can construct a model of noise free of that difficulty. This form of the KP is especially suitable for physical applications.Comment: 22 pages (RevTeX) and 4 figure

The response function of a sphere in a viscoelastic two-fluid medium

In order to address basic questions of importance to microrheology, we study the dynamics of a rigid sphere embedded in a model viscoelastic medium consisting of an elastic network permeated by a viscous fluid. We calculate the complete response of a single bead in this medium to an external force and compare the result to the commonly-accepted, generalized Stokes-Einstein relation (GSER). We find that our response function is well approximated by the GSER only within a particular frequency range determined by the material parameters of both the bead and the network. We then discuss the relevance of this result to recent experiments. Finally we discuss the approximations made in our solution of the response function by comparing our results to the exact solution for the response function of a bead in a viscous (Newtonian) fluid.Comment: 12 pages, 2 figure

Dynamical properties of liquid Al near melting. An orbital-free molecular dynamics study

The static and dynamic structure of liquid Al is studied using the orbital free ab-initio molecular dynamics method. Two thermodynamic states along the coexistence line are considered, namely T = 943 K and 1323 K for which X-ray and neutron scattering data are available. A new kinetic energy functional, which fulfills a number of physically relevant conditions is employed, along with a local first principles pseudopotential. In addition to a comparison with experiment, we also compare our ab-initio results with those obtained from conventional molecular dynamics simulations using effective interionic pair potentials derived from second order pseudopotential perturbation theory.Comment: 15 pages, 12 figures, 2 tables, submitted to PR

Schottky levels and thermodynamic contributions of light lanthanide sesquisulfides having the Th3P4 structure

Heat capacity measurements were made by adiabatic calorimetry over the range 7-350 K on [gamma] phase preparations of four lanthanide sesquisulfides, and the heat capacities were resolved into lattice, magnetic, Schottky and other components. The entropy at 298.15 K for La2S3 which is written as S[deg]/R is 19.51 while values of S[deg] -- S[deg](7 K) for Ce2S3, Nd2S3, Gd2S3 and Dy2S3 are 21.34, 22.38, 20.05 and 22.58 respectively. IR and visible optical spectra of La2S3, Ce2S3, Nd2S3 and Dy2S3 and lattice sum crystal field splitting calculations for Nd2S3, Ce2S3 and Dy2S3 are compared with Raman scattering data and Schottky contributions derived from calorimetry.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25086/1/0000517.pd

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