A cell by cell anisotropic adaptive mesh ALE scheme for the numerical solution of the Euler equations

In this paper a cell by cell anisotropic adaptive mesh technique is added to an existing staggered mesh Lagrange plus remap finite element ALE code for the solution of the Euler equations. The quadrilateral finite elements may be subdivided isotropically or anisotropically and a hierarchical data structure is employed. An efficient computational method is proposed, which only solves on the finest level of resolution that exists for each part of the domain with disjoint or hanging nodes being used at resolution transitions. The Lagrangian, equipotential mesh relaxation and advection (solution remapping) steps are generalised so that they may be applied on the dynamic mesh. It is shown that for a radial Sod problem and a two-dimensional Riemann problem the anisotropic adaptive mesh method runs over eight times faster.

Consistent Dirichlet Boundary Conditions for Numerical Solution of Moving Boundary Problems

We consider the imposition of Dirichlet boundary conditions in the finite element modelling of moving boundary problems in one and two dimensions for which the total mass is prescribed. A modification of the standard linear finite element test space allows the boundary conditions to be imposed strongly whilst simultaneously conserving a discrete mass. The validity of the technique is assessed for a specific moving mesh finite element method, although the approach is more general. Numerical comparisons are carried out for mass-conserving solutions of the porous medium equation with Dirichlet boundary conditions and for a moving boundary problem with a source term and time-varying mass.

Structure determination from powder diffraction data

Advances made over the past decade in structure determination from powder diffraction data are reviewed with particular emphasis on algorithmic developments and the successes and limitations of the technique. While global optimization methods have been successful in the solution of molecular crystal structures, new methods are required to make the solution of inorganic crystal structures more routine. The use of complementary techniques such as NMR to assist structure solution is discussed and the potential for the combined use of X-ray and neutron diffraction data for structure verification is explored. Structures that have proved difficult to solve from powder diffraction data are reviewed and the limitations of structure determination from powder diffraction data are discussed. Furthermore, the prospects of solving small protein crystal structures over the next decade are assessed.

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.

Voronoi, Delaunay, and Block-Structured Mesh Refinement for Solution of the Shallow-Water Equations on the Sphere

Alternative meshes of the sphere and adaptive mesh refinement could be immensely beneficial for weather and climate forecasts, but it is not clear how mesh refinement should be achieved. A finite-volume model that solves the shallow-water equations on any mesh of the surface of the sphere is presented. The accuracy and cost effectiveness of four quasi-uniform meshes of the sphere are compared: a cubed sphere, reduced latitude–longitude, hexagonal–icosahedral, and triangular–icosahedral. On some standard shallow-water tests, the hexagonal–icosahedral mesh performs best and the reduced latitude–longitude mesh performs well only when the flow is aligned with the mesh. The inclusion of a refined mesh over a disc-shaped region is achieved using either gradual Delaunay, gradual Voronoi, or abrupt 2:1 block-structured refinement. These refined regions can actually degrade global accuracy, presumably because of changes in wave dispersion where the mesh is highly nonuniform. However, using gradual refinement to resolve a mountain in an otherwise coarse mesh can improve accuracy for the same cost. The model prognostic variables are height and momentum collocated at cell centers, and (to remove grid-scale oscillations of the A grid) the mass flux between cells is advanced from the old momentum using the momentum equation. Quadratic and upwind biased cubic differencing methods are used as explicit corrections to a fast implicit solution that uses linear differencing.

Contributions of labile and resistant organic materials to the immobilization of inorganic soil N when used in the restoration of abandoned agricultural fields

We have examined the contributions sucrose and sawdust make to the net immobilization of inorganic soil N and assimilation of both C and N into microbial biomass when they are used as part of a restoration plan to promote the establishment of indigenous vegetation on abandoned agricultural fields on the Central Hungarian Plain. Both amendments led to net N immobilization. Sucrose addition also led to mobilization of N from the soil organic N pool and its immobilization into microbial biomass, whereas sawdust addition apparently immobilized soil N into a non-biomass compartment or a biomass component that was not detected by the conventional biomass N assay (CHCl3 fumigation and extraction). This suggests that the N was either cycled through the biomass, but not immobilized within it, or that it was immobilized in a protected biomass fraction different to the fraction into which N was immobilized in response to sucrose addition.

The influence of mineral solubility and soil solution concentration on the toxicity of copper to Eisenia fetida Savigny

The OECD 14 d earthworm acute toxicity test was used to determine the toxicity of copper added as copper nitrate (Cu(NO3)(2)), copper sulphate (CuSO4) and malachite (Cu-2(OH)(2)(CO3)) to Eisenia fetida Savigny. Cu(NO3)(2), and CuSO4 were applied in both an aqueous (aq) and solid (s) form, Cu-2(OH)(2)(CO3) was added as a solid. Soil solution was extracted by centrifugation, and analysed for copper. Two extractants [0.01 M CaCl2 and 0.005 M diethylenetriminpentaacetic acid (DTPA)] were used as a proxy of the bioavailable copper fraction in the soil. For bulk soil copper content the calculated copper toxicity decreased in the order nitrate > sulphide > carbonate, the same order as decreasing solubility of the metal compounds. For Cu(NO3)(2) and CuSO4, the LC50s obtained were not significantly different when the compound was added in solution or solid form. There was a significant correlation between the soil solution copper concentration and the percentage earthworm mortality for all 3 copper compounds (P less than or equal to 0.05) indicating that the soil pore water copper concentration is important for determining copper availability and toxicity to E. fetida. In soil avoidance tests the earthworms avoided the soils treated with Cu(NO3)(2) (aq and s) and CuSO4 (aq and s), at all concentrations used (110-8750 mug Cu g(-1), and 600-8750 mug Cu g(-1) respectively). In soils treated with Cu-2(OH2)CO3, avoidance behaviour was exhibited at all concentrations greater than or equal to3500 mug Cu g(-1). There was no significant correlation between the copper extracted by either CaCl2 or DTPA and percentage mortality. These two extractants are therefore not useful indicators of copper availability and toxicity to E. fetida.

Decomposition and phosphorus release from organic residues as affected by residue quality and added inorganic phosphorus

The combined use of organic residue and inorganic fertiliser-phosphorus (P) is appropriate in meeting both the short and long-term P requirement of crops. To assess the influence of added inorganic fertiliser-P on the processes of decomposition and P release from the residue and the relationships with quality, prunings of Gliricidia sepium, Leucaena leucocephela, Senna siamea, Acacia mangium and Paraserienthus falcataria were incubated without and with added inorganic fertiliser-P for 56 days. Soil was added only as inoculum. Decomposition rate and amounts of acid extractable-P (P release) were in the same order: G. sepium > S. siamea > L. leucocepheta > P falcataria > A. mangium. Unlike the other residues, A. mangium released no P despite the loss of half its mass during the 8 weeks of incubation. The residue P content correlated with P release. However, decomposition rate did not correlate with residue P content but with the lignin, polyphenol and cellulose content, and ratios to P. These ratios were negatively correlated with P release suggesting that lignin and polyphenol contents influence P release more when the residue-P content is low. Results suggest that rate of decomposition influences the release of P. The critical residue P content for P release was estimated to be 0.12% < P < 0.19%. Added P had no effect on decomposition and P release from the residues.

Naturally occurring radioactive material (NORM) from a former phosphoric acid processing plant

In recent years there has been an increasing awareness of the radiological impact of non-nuclear industries that extract and/or process ores and minerals containing naturally occurring radioactive material (NORM). These industrial activities may result in significant radioactive contamination of (by-) products, wastes and plant installations. In this study, scale samples were collected from a decommissioned phosphoric acid processing plant. To determine the nature and concentration of NORM retained in pipe-work and associated process plant, four main areas of the site were investigated: (1) the 'Green Acid Plant', where crude acid was concentrated; (2) the green acid storage tanks; (3) the Purified White Acid (PWA) plant, where inorganic impurities were removed; and (4) the solid waste, disposed of on-site as landfill. The scale samples predominantly comprise the following: fluorides (e.g. ralstonite); calcium sulphate (e.g. gypsum); and an assemblage of mixed fluorides and phosphates (e.g. iron fluoride hydrate, calcium phosphate), respectively. The radioactive inventory is dominated by U-238 and its decay chain products, and significant fractionation along the series occurs. Compared to the feedstock ore, elevated concentrations (<= 8.8 Bq/g) of U-238 Were found to be retained in installations where the process stream was rich in fluorides and phosphates. In addition, enriched levels (<= 11 Bq/g) of Ra-226 were found in association with precipitates of calcium sulphate. Water extraction tests indicate that many of the scales and waste contain significantly soluble materials and readily release radioactivity into solution. (c) 2005 Elsevier Ltd. All rights reserved.

Zinc deficiency in selected cultivars of wheat and barley as tested in solution culture

The relative zinc (Zn) efficiencies of 33 wheat and 3 barley cultivars were determined by growing them in chelate-buffered culture solutions. Zn efficiency, determined by growth in a Zn-deficient solution relative to that in a medium containing an adequate concentration of Zn, was found to vary between 10% and 63% among the cultivars tested. Out of the 36 cultivars tested, 12 proved to be Zn efficient, 10 were Zn inefficient, and the remaining 14 varieties were classed as intermediate. The most Zn-efficient cultivars included Bakhtawar, Gatcher S61, Wilgoyne, and Madrigal, and the most Zn inefficient included Durati, Songlen, Excalibur, and Chakwal-86. Zn-efficient cultivars accumulated greater amounts of Zn in their shoots than inefficient cultivars, but the correlation between shoot Zn and shoot dry matter production was poor. All the cultivars accumulated higher concentrations of iron (Fe), copper (Cu), manganese (Mn), and phosphorus (P) at deficient levels of Zn, compared with adequate Zn concentrations. The Zn-inefficient cultivars accumulated higher concentrations of these other elements compared to efficient cultivars.

Results from the Covered Catchment Experiment at Gårdsjön, Sweden, after ten years of clean precipitation treatment

The Covered Catchment Experiment at Gordsjon is a large scale forest ecosystem manipulation, where acid precipitation was intercepted by a 7000 m(2) plastic roof and replaced by 'clean precipitation' sprinkled below the roof for ten years between 1991 and 2001. The treatment resulted in a strong positive response of runoff quality. The runoff sulphate, inorganic aluminium and base cations decreased, while there was a strong increase in runoff ANC and a moderate increase in pH. The runoff continued to improve over the whole duration of the experiment. The achieved quality was, however, after ten years still considerably worse than estimated pre-industrial runoff at the site. Stable isotopes of sulphur were analysed to study the soil sulphur cycling. At the initial years of the experiment, the desorption of SO4 from the mineral soil appeared to control the runoff SO4 concentration. However, as the experiment proceeded, there was growing evidence that net mineralisation of soil organic sulphur in the humus layer was an additional source of SO4 in runoff. This might provide a challenge to current acidification models. The experiment convincingly demonstrated on a catchment scale, that reduction in acid deposition causes an immediate improvement of surface water quality even at heavily acidified sites. The improvement of the runoff appeared to be largely a result of cation exchange processes in the soil due to decreasing concentrations of the soil solution, while any potential change in soil base saturation seemed to be less important for the runoff chemistry over the short time period of one decade. These findings should be considered when interpreting and extrapolating regional trends in surface water chemistry to the terrestrial parts of ecosystems.

Acid-base reactions between an acidic soil and plant residues

The elemental composition of residues of maize (Zea mays), sorghum (S. bicolor), groundnuts (Arachis hypogea), soya beans (Glycine max), leucaena (L. leucocephala), gliricidia (G. sepium), and sesbania (S. sesban) was determined as a basis for examining their alkalinity when incorporated into an acidic Zambian Ferralsol. Potential (ash) alkalinity, available alkalinity by titration to pH 4 and soluble alkalinity (16 It water extract titrated to pH 4) were measured. Potential alkalinity ranged from 3 73 (maize) to 1336 (groundnuts) mmol kg(-1) and was equivalent to the excess of their cation charge over inorganic anion charge. Available alkalinity was about half the potential alkalinity. Cations associated with organic anions are the source of alkalinity. About two thirds of the available alkalinity is soluble. Residue buffer curves were determined by titration with H2SO4 to pH 4. Soil buffer capacity measured by addition of NaOH was 12.9 mmol kg(-1) pH(-1). Soil and residue (10 g:0.25 g) were shaken in solution for 24 h and suspension pH values measured. Soil pH increased from 4.3 to between 4.6 (maize) and 5.2 (soyabean) and the amounts of acidity neutralized (calculated from the rise in pH and the soil buffer capacity) were between 3.9 and 11.5 mmol kg(-1), respectively. The apparent base contributions by the residues (calculated from the buffer curves and the fall in pH) ranged between 105 and 350 mmol kg(-1) of residue, equivalent to 2.6 and 8.8 mmol kg(-1) of soil, respectively. Therefore, in contact with soil acidity, more alkalinity becomes available than when in contact with H2SO4 solution. Available alkalinity (to pH 4) would be more than adequate to supply that which reacts with soil but soluble alkalinity would not. It was concluded that soil Al is able to displace cations associated with organic anions in the residues which are not displaced by H+, or that residue decomposition may have begun in the soil suspension releasing some of the non-available alkalinity. Soil and four of the residues were incubated for 100 days and changes in pH, NH4+ and NO3- concentrations measured. An acidity budget equated neutralized soil acidity with residue alkalinity and base or acid produced by N transformations. Most of the potential alkalinity of soyabean and leucaena had reacted after 14 days, but this only occurred after 100 days for gliricidia, and for maize only the available alkalinity reacted. For gliricidia and leucaena, residue alkalinity was primarily used to react with acidity produced by nitrification. Thus, the ability of residues to ameliorate acidity depends not only on their available and potential alkalinity but also on their potential to release mineral N. (C) 2004 Elsevier B.V. All rights reserved.