Structure determination from powder data : Mogul and CASTEP

When solving the crystal structure of complex molecules from powder data, accurately locating the global minimum can be challenging, particularly where the number of internal degrees of freedom is large. The program Mogul provides a convenient means to access typical torsion angle ranges for fragments related to the molecule of interest. The impact that the application of modal torsion angle constraints has on the structure determination process of two structure solution attempts using DASH is presented. Once solved, accurate refinement of a molecular structure against powder data can also present challenges. Geometry optimisation using density functional theory in CASTEP is shown to be an effective means to locate hydrogen atom positions reliably and return a more accurate description of molecular conformation and intermolecular interactions than global optimisation and Rietveld refinement alone

Earth materials and earth dynamics

In the project ''Earth Materials and Earth Dynamics'' we linked fundamental and exploratory, experimental, theoretical, and computational research programs to shed light on the current and past states of the dynamic Earth. Our objective was to combine different geological, geochemical, geophysical, and materials science analyses with numerical techniques to illuminate active processes in the Earth. These processes include fluid-rock interactions that form and modify the lithosphere, non-linear wave attenuations in rocks that drive plate tectonics and perturb the earth's surface, dynamic recrystallization of olivine that deforms the upper mantle, development of texture in high-pressure olivine polymorphs that create anisotropic velocity regions in the convecting upper mantle and transition zone, and the intense chemical reactions between the mantle and core. We measured physical properties such as texture and nonlinear elasticity, equation of states at simultaneous pressures and temperatures, magnetic spins and bonding, chemical permeability, and thermal-chemical feedback to better characterize earth materials. We artificially generated seismic waves, numerically modeled fluid flow and transport in rock systems and modified polycrystal plasticity theory to interpret measured physical properties and integrate them into our understanding of the Earth. This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL)

GDASH: a grid-enabled program for structure solution from powder diffraction data

The simulated annealing approach to structure solution from powder diffraction data, as implemented in the DASH program, is easily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can therefore be achieved by distributing individual DASH runs over a network of computers. The GDASH program achieves this by packaging DASH in a form that enables it to run under the Univa UD Grid MP system, which harnesses networks of existing computing resources to perform calculations

MDASH: a multi-core-enabled program for structure solution from powder diffraction data

The simulated annealing approach to structure solution from powder diffraction data, as implemented in the DASH program, is easily amenable to parallelization at the individual run level. Modest increases in speed of execution can therefore be achieved by executing individual DASH runs on the individual cores of CPUs

Radio Observations of HD 80606 Near Planetary Periastron

This paper reports Very Large Array observations at 325 and 1425 MHz (90cm and 20cm) during and near the periastron passage of HD 80606b on 2007 November 20. We obtain flux density limits (3-sigma) of 1.7 mJy and 48 microJy at 325 and 1425 MHz, respectively, equivalent to planetary luminosity limits of 2.3 x 10^{24} erg/s and 2.7 x 10^{23} erg/s. These are well above the Jovian value (at 40 MHz) of 2 x 10^{18} erg/s. The motivation for these observations was that the planetary magnetospheric emission is driven by a stellar wind-planetary magnetosphere interaction so that the planetary luminosity would be elevated. Near periastron, HD 80606b might be as much as 3000 times more luminous than Jupiter. Recent transit observations of HD 80606b provide stringent constraints on the planetary mass and radius, and, because of the planet's highly eccentric orbit, its rotation period is likely to be "pseudo-synchronized" to its orbital period, allowing a robust estimate of the former. We are able to make robust estimates of the emission frequency of the planetary magnetospheric emission and find it to be around 60--90 MHz. We compare HD 80606b to other high-eccentricity systems and assess the detection possibilities for both near-term and more distant future systems. Of the known high eccentricity planets, only HD 80606b is likely to be detectable, as HD 20782B b and HD 4113b are both likely to have weaker magnetic field strengths. Both the forthcoming "EVLA low band" system and the Low Frequency Array may be able to improve upon our limits for HD 80606b, and do so at a more optimum frequency. If the low-frequency component of the Square Kilometre Array (SKA-lo) and a future lunar radio array are able to approach their thermal noise limits, they should be able to detect an HD 80606b-like planet, unless the planet's luminosity increases by substantially less than a factor of 3000.Comment: 9 pages; accepted for publication in A

Mitotic cell cycle proteins increase in podocytes despite lack of proliferation

Mitotic cell cycle proteins increase in podocytes despite lack of proliferation.BackgroundPodocyte proliferation is an uncommon response to glomerular injury and its lack may underlie the development of glomerulosclerosis. However, whether podocytes have the capacity to enter and finish mitosis and cytokinesis is not known.MethodsThe expression of mitotic cell cycle proteins (phosphorylated Histone 3, Cdc2, cyclin B1 and B2) was examined by immunohistochemistry in kidneys of embryonal mice, transgenic HIV-mice, and rats with experimental membranous nephropathy (passive Heymann nephritis, PHN). Mitotic proteins also were measured by Western blot in glomerular protein from PHN-rats and the activity of mitotic cyclins was quantified by histone kinase assay.ResultsMitotic proteins were increased in embryonal mouse glomeruli during the S- and comma-shaped stages and were absent at the capillary loop stage and in mature rodent glomeruli. There was an increase in podocyte expression of Cdc2, cyclin B1 and B2 and phosphorylated histone 3 in PHN rats, and in HIV transgenic mice.ConclusionsPodocytes have the ability to increase cell cycle proteins required for mitosis. Without obvious differences in the expression of the major mitotic proteins in PHN- and HIV-nephropathy, a regulatory disturbance in cytokinesis might be responsible for the development of polynucleated cells and a lack of podocyte proliferation in experimental glomerular disease

Workshop on exploration for hot dry rock geothermal systems

Separate abstracts were prepared for fifteen papers. (MHR

p35, the non-cyclin activator of Cdk5, protects podocytes against apoptosis in vitro and in vivo

Cyclin-dependent kinase-5 is widely expressed and predominantly regulated by the non-cyclin activator p35. Since we recently showed that expression of p35 in the kidney is restricted to podocytes, we examined here its function in mice in which p35 was genetically deleted. The mice did not exhibit kidney abnormalities during glomerular development or during adult life. Conditionally immortalized cultured podocytes, derived from these null mice, did not have any change in their morphology, differentiation, or proliferation. However, when these cultured podocytes were exposed to UV-C irradiation, serum depletion, puromycin aminonucleoside, or transforming growth factor-β-1, they showed increased apoptosis compared to those from wild-type mice. Levels of Bcl-2 were decreased in these null podocytes but increased after transduction with human p35. Restoration of p35 or the ectopic expression of Bcl-2 reduced the susceptibility of p35-null podocytes to apoptosis. Experimental glomerulonephritis, characterized by podocyte apoptosis and subsequent crescent formation, was utilized to test these findings in vivo. Podocyte apoptosis was significantly increased in diseased p35-null compared with wild-type mice, accompanied by increased glomerulosclerosis and decreased renal function. Our study shows that p35 does not affect glomerulogenesis but controls podocyte survival following injury, in part, by regulating Bcl-2 expression