DassFow-Shallow, Variational Data Assimilation for Shallow-Water Models: Numerical Schemes, User and Developer Guides

DassFlow is a computational software for free-surface flows includingvariational data assimilation (4D-VAR), sensitivity analysis, calibration features (adjoint method). The code version "shallow" solves shallow-water like models (Saint-Venant's type).The other version (ALE, not detailed in the present document) includes free-surface Stokes like models (low Reynolds, power-law rheology, ALE surface dynamics). All source files are written in Fortran 2003 / MPI. For more details and references, please consult DassFlow website.In the present manuscript, we describe: the equations, the compilation/execution instructions, the input / output files (user guide), the finite volume schemes, few validation test cases included in the archive, and the code structure (developer guide)

New Antarctic gravity anomaly grid for enhanced geodetic and geophysical studies in Antarctica

Gravity surveying is challenging in Antarctica because of its hostile environment and inaccessibility. Nevertheless, many ground-based, airborne, and shipborne gravity campaigns have been completed by the geophysical and geodetic communities since the 1980s. We present the first modern Antarctic-wide gravity data compilation derived from 13 million data points covering an area of 10 million km2, which corresponds to 73% coverage of the continent. The remove-compute-restore technique was applied for gridding, which facilitated leveling of the different gravity data sets with respect to an Earth gravity model derived from satellite data alone. The resulting free-air and Bouguer gravity anomaly grids of 10 km resolution are publicly available. These grids will enable new high-resolution combined Earth gravity models to be derived and represent a major step forward toward solving the geodetic polar data gap problem. They provide a new tool to investigate continental-scale lithospheric structure and geological evolution of Antarctica

A compilation of new airborne magnetic and gravity data across Dronning Maud Land, Antarctica.

The evolution of the South Atlantic region including the Weddell Sea and its adjacent areas is of crucialimportance for understanding the processes of the structure and tectonics of the Antarctic lithosphere, its relation to geodynamic processes, especially to the timing and geometry of the initial stages of the Mesozoic break-up between Africa, Antarctica and South America. For unravelling the geological evolution of Antarctica prior to the break-up of Gondwana, the sub-glacial geology is of utmost importance. Understanding the sub-ice geology allows reconstruction of ancient mountain chains (collision zones) across continents, which are separated by large ocean basins in the presentworld. Since only the peaks of the Dronning Maud Land (DML) mountains can be geologically sampled, geophysical methods are required to uncover the geological structure beneath the ice. Therefore, extensive airborne surveys were conducted across DML between 2001 to 2005 to close data gaps and to improve existing data sets

Structures of bacterial kynurenine formamidase reveal a crowded binuclear zinc catalytic site primed to generate a potent nucleophile

Tryptophan is an important precursor for chemical entities that ultimately support the biosynthesis of key metabolites. The second stage of tryptophan catabolism is catalysed by kynurenine formamidase, an enzyme that is different between eukaryotes and prokaryotes. In the present study, we characterize the catalytic properties and present the crystal structures of three bacterial kynurenine formamidases. The structures reveal a new amidase protein fold, a highly organized and distinctive binuclear Zn2+ catalytic centre in a confined, hydrophobic and relatively rigid active site. The structure of a complex with 2-aminoacetophenone delineates aspects of molecular recognition extending to the observation that the substrate itself may be conformationally restricted to assist binding in the confined space of the active site and for subsequent processing. The cations occupy a crowded environment, and, unlike most Zn2+ -dependent enzymes, there is little scope to increase co-ordination number during catalysis.We propose that the presence of a bridging water/hydroxide ligand in conjunction with the placement of an active site histidine supports a distinctive amidation mechanism.</p

High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility

ERp27 (endoplasmic reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase) localized to the endoplasmic reticulum. ERp27 is predicted to consist of two thioredoxinfold domains homologous with the non-catalytic b and b domains of PDI. The structure in solution of the N-terminal blike domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family. 15N-NMR relaxation data were obtained and ModelFree analysis highlighted limited exchange contributions and slow internal motions, and indicated that the domain has an average order parameter S 2 of 0.79. Comparison of the single-domain structure determined in the present study with the equivalent domain within fulllength ERp27, determined independently by X-ray diffraction, indicated very close agreement. The domain interface inferred from NMR data in solution was much more extensive than that observed in the X-ray structure, suggesting that the domains flex independently and that crystallization selects one specific interdomain orientation. This led us to apply a new rapid method to simulate the flexibility of the full-length protein, establishing that the domains show considerable freedom to flex (tilt and twist) about the interdomain linker, consistent with the NMR data