High-resolution, unstructured meshes for hydrodynamic models of the Great Barrier Reef, Australia

Accuracy and mesh generation are key issues for the high-resolution hydrodynamic modelling of the whole Great Barrier Reef. Our objective is to generate suitable unstructured grids that can resolve topological and dynamical features like tidal jets and recirculation eddies in the wake of islands. A new strategy is suggested to refine the mesh in areas of interest taking into account the bathymetric field and an approximated distance to islands and reefs. Such a distance is obtained by solving an elliptic differential operator, with specific boundary conditions. Meshes produced illustrate both the validity and the efficiency of the adaptive strategy. Selection of refinement and geometrical parameters is discussed. (c) 2006 Elsevier Ltd. All rights reserved.

Consistent approximate models of the global atmosphere: shallow, deep, hydrostatic, quasi-hydrostatic and non-hydrostatic

We study global atmosphere models that are at least as accurate as the hydrostatic primitive equations (HPEs), reviewing known results and reporting some new ones. The HPEs make spherical geopotential and shallow atmosphere approximations in addition to the hydrostatic approximation. As is well known, a consistent application of the shallow atmosphere approximation requires omission of those Coriolis terms that vary as the cosine of latitude and of certain other terms in the components of the momentum equation. An approximate model is here regarded as consistent if it formally preserves conservation principles for axial angular momentum, energy and potential vorticity, and (following R. Müller) if its momentum component equations have Lagrange's form. Within these criteria, four consistent approximate global models, including the HPEs themselves, are identified in a height-coordinate framework. The four models, each of which includes the spherical geopotential approximation, correspond to whether the shallow atmosphere and hydrostatic (or quasi-hydrostatic) approximations are individually made or not made. Restrictions on representing the spatial variation of apparent gravity occur. Solution methods and the situation in a pressure-coordinate framework are discussed. © Crown copyright 2005.

Factors influencing anthropogenic carbon dioxide uptake in the North Atlantic in models of the ocean carbon cycle

The uptake and storage of anthropogenic carbon in the North Atlantic is investigated using different configurations of ocean general circulation/carbon cycle models. We investigate how different representations of the ocean physics in the models, which represent the range of models currently in use, affect the evolution of CO2 uptake in the North Atlantic. The buffer effect of the ocean carbon system would be expected to reduce ocean CO2 uptake as the ocean absorbs increasing amounts of CO2. We find that the strength of the buffer effect is very dependent on the model ocean state, as it affects both the magnitude and timing of the changes in uptake. The timescale over which uptake of CO2 in the North Atlantic drops to below preindustrial levels is particularly sensitive to the ocean state which sets the degree of buffering; it is less sensitive to the choice of atmospheric CO2 forcing scenario. Neglecting physical climate change effects, North Atlantic CO2 uptake drops below preindustrial levels between 50 and 300 years after stabilisation of atmospheric CO2 in different model configurations. Storage of anthropogenic carbon in the North Atlantic varies much less among the different model configurations, as differences in ocean transport of dissolved inorganic carbon and uptake of CO2 compensate each other. This supports the idea that measured inventories of anthropogenic carbon in the real ocean cannot be used to constrain the surface uptake. Including physical climate change effects reduces anthropogenic CO2 uptake and storage in the North Atlantic further, due to the combined effects of surface warming, increased freshwater input, and a slowdown of the meridional overturning circulation. The timescale over which North Atlantic CO2 uptake drops to below preindustrial levels is reduced by about one-third, leading to an estimate of this timescale for the real world of about 50 years after the stabilisation of atmospheric CO2. In the climate change experiment, a shallowing of the mixed layer depths in the North Atlantic results in a significant reduction in primary production, reducing the potential role for biology in drawing down anthropogenic CO2.

Review of theoretical models of electromagnetic NDT and their applications

There is an increasing interest in modelling electromagnetic methods of NDT - particularly eddy currents. A collaboration within the International Institute of Welding led to a survey intended to explain to non mathematicians the present scope of modelling. The present review commences with this survey and then points out some of the developments and some of the outstanding problems in transferring modelling into industry.

Comparison between observations and models of the Mozambique Channel transport: Seasonal cycle and eddy frequencies

A time series of the observed transport through an array of moorings across the Mozambique Channel is compared with that of six model runs with ocean general circulation models. In the observations, the seasonal cycle cannot be distinguished from red noise, while this cycle is dominant in the transport of the numerical models. It is found, however, that the seasonal cycles of the observations and numerical models are similar in strength and phase. These cycles have an amplitude of 5 Sv and a maximum in September, and can be explained by the yearly variation of the wind forcing. The seasonal cycle in the models is dominant because the spectral density at other frequencies is underrepresented. Main deviations from the observations are found at depths shallower than 1500 m and in the 5/y–6/y frequency range. Nevertheless, the structure of eddies in the models is close to the observed eddy structure. The discrepancy is found to be related to the formation mechanism and the formation position of the eddies. In the observations, eddies are frequently formed from an overshooting current near the mooring section, as proposed by Ridderinkhof and de Ruijter (2003) and Harlander et al. (2009). This causes an alternation of events at the mooring section, varying between a strong southward current, and the formation and passing of an eddy. This results in a large variation of transport in the frequency range of 5/y–6/y. In the models, the eddies are formed further north and propagate through the section. No alternation similar to the observations is observed, resulting in a more constant transport.

Demonstration models of the cost and benefits of BVD and Johne's contol on cattle farms

Demonstration models of the costs of BVD and Johnes in dairy and beef cattle and the costs and benefits of control have been developed. An example applied to BVD in dairy cattle is presented. Downloadable versions of the models, together with supporting material on how to use them are available to veterinarians from a dedicated website.

Demonstration models of the cost and benefits of BVD and Johne's contol on cattle farms

Demonstration models of the costs of BVD and Johnes in dairy and beef cattle and the costs and benefits of control have been developed. An example applied to BVD in dairy cattle is presented. Downloadable versions of the models, together with supporting material on how to use them are available to veterinarians from a dedicated website.

Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes

Motivation: We compare phylogenetic approaches for inferring functional gene links. The approaches detect independent instances of the correlated gain and loss of pairs of genes from species' genomes. We investigate the effect on results of basing evidence of correlations on two phylogenetic approaches, Dollo parsminony and maximum likelihood (ML). We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data. Results: We detect correlated evolution among a test set of pairs of yeast (Saccharomyces cerevisiae) genes, with a case study of 21 eukaryotic genomes and test data derived from known yeast protein complexes. If the rate at which genes are gained is constrained to be low, ML achieves by far the best results at detecting known functional links. The model then has fewer parameters but it is more realistic by preventing genes from being gained more than once. Availability: BayesTraits by M. Pagel and A. Meade, and a script to configure and repeatedly launch it by D. Barker and M. Pagel, are available at http://www.evolution.reading.ac.uk .

Statistical evaluation of alternative models of human evolution

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species approximate to 141 thousand years ago (Kya), an exit out-of-Africa approximate to 51 Kya, and a recent colonization of the Americas approximate to 10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.

Assembling spatially explicit landscape models of pollen and spore dispersal by wind for risk assessment

Models of windblown pollen or spore movement are required to predict gene flow from genetically modified (GM) crops and the spread of fungal diseases. We suggest a simple form for a function describing the distance moved by a pollen grain or fungal spore, for use in generic models of dispersal. The function has power-law behaviour over sub-continental distances. We show that air-borne dispersal of rapeseed pollen in two experiments was inconsistent with an exponential model, but was fitted by power-law models, implying a large contribution from distant fields to the catches observed. After allowance for this 'background' by applying Fourier transforms to deconvolve the mixture of distant and local sources, the data were best fit by power-laws with exponents between 1.5 and 2. We also demonstrate that for a simple model of area sources, the median dispersal distance is a function of field radius and that measurement from the source edge can be misleading. Using an inverse-square dispersal distribution deduced from the experimental data and the distribution of rapeseed fields deduced by remote sensing, we successfully predict observed rapeseed pollen density in the city centres of Derby and Leicester (UK).

Models of shoot apical meristem function

In this review we describe how concepts of shoot apical meristem function have developed over time. The role of the scientist is emphasized, as proposer, receiver and evaluator of ideas about the shoot apical meristem. Models have become increasingly popular over the last 250 years, and we consider their role. They provide valuable grounding for the development of hypotheses, but in addition they have a strong human element and their uptake relies on various degrees of persuasion. The most influential models are probably those that most data support, consolidating them as an insight into reality; but they also work by altering how we see meristems, re-directing us to influence the data we collect and the questions we consider meaningful.