Improving the worthiness of the Elder problem as a benchmark for buoyancy driven convection models

An important trapping mechanism associated with the geosequestration of CO~2~ is that of dissolution into the formation water. Although supercritical CO~2~ is significantly less dense than water, experimental data reported in the literature show that the density of an aqueous solution of CO~2~ could be slightly greater. Under normal situations, the transfer of gas to solution is largely controlled by the relatively slow process of molecular diffusion. However, the presence of variable densities can trigger off gravity instabilities leading to much larger-scale convection processes. Such processes can potentially enhance rates of dissolution by an order of magnitude. Consequently there is a need for future performance assessment models to incorporate buoyancy driven convection (BDC). A major issue associated with BDC models is that of grid convergence when benchmarking to the Elder problem. The Elder problem originates from a heat convection experiment whereby a rectangular Hele-Shaw cell was heated over the central half of its base. A quarter of the way through the experiment, Elder (1967) observed six plumes, with four narrow plumes in the center and two larger plumes at the edges. As the experiment progressed, only four plumes remained. The issue is that depending on the grid resolution used when seeking to model this problem, modelers have found that different schemes yield steady states with either one, two or three plumes. The aim of this paper is to clarify and circumvent the issue of multiple steady state solutions in the Elder problem using a pseudospectral method

Natural handicaps in Dutch agricultural areas : assessment of less favoured areas based on economic criteria

Smit en Brouwer (2009) hebben bodems met een landbouwkundige handicap geselecteerd aan de hand van biofysische criteria. De relevante biofysische criteria waren gerelateerd aan bodemeigenschappen: drainage, textuur, aanwezigheid van stenen en chemische eigenschappen. Textuur en aanwezigheid van stenen zijn onderverdeeld in verschillende klassen: grof materiaal, grof en middelgrof zand, zware klei, veengronden, zwel en krimpverschijnselen en het opkomen van stenen uit de ondergrond. Verzilting is de enige chemische eigenschap die relevant is voor Nederland. Naast een selectie van gebieden op grond van biofysische eigenschappen, moet ook een verfijnde selectie worden uitgevoerd. Deze verfijnde selectie is gebaseerd op de verschillen in saldo per hectare tussen gebieden met en zonder de landbouwkundige gevolgen van de biofysische eigenschappen. De belangrijkste landbouwkundige gevolgen voor de verschillende categorieën waren de gevoeligheid voor winderosie bij grof en middelgrof zand; de beperkingen van de bewerkbaarheid van de grond en de beperkingen in het bouwplan op de zware kleigronden en lagere netto productie en de onmogelijkheid om maïs te verbouwen op veengronde

Structure of turbulence in temporal planar jets

A detailed analysis of the structure of turbulence in a temporal planar turbulent jet is reported. Instantaneous snapshots of the flow and three-dimensional spatial correlation functions are considered. It is found that the flow is characterized by large-scale spanwise vortices whose motion is felt in the entire flow field. Superimposed to this large-scale motion, a hierarchy of turbulent structures is present. The most coherent ones take the form of quasi-streamwise vortices and high and low streamwise velocity streaks. The topology of these interacting structures is analyzed by quantitatively addressing their shape and size in the different flow regions. Such information is recognized to be relevant for a structural description of the otherwise disorganized motion in turbulent free-shear flows and can be used for the assessment of models based on coherent structure assumptions. Finally, the resulting scenario provides a phenomenological description of the elementary processes at the basis of turbulence in free-shear flows

Noord-Hollands koolbedrijf van 28 ha op kleigrond

Met deze voorbeeldberekening wordt aan de oriënterende ondernemer inzicht gegeven in de financiële verandering tijdens en na het omschakelen naar een biologische bedrijfsvoering. In dit voorbeeld gaat het om een gespecialiseerd (sluit)koolbedrijf met een bedrijfsgrootte van 18 hectare eigen grond en daarnaast nog 10 hectare huurland voor de koolteelt. Door de flexibiliteit van huurland en het hanteren van een 'slim en kort omschakeltraject' komt het bouwplansaldo alleen in het eerste omschakeljaar iets lager uit dan in de gangbare situatie

Spatially evolving cascades in temporal planar jets

Starting from an alternative decomposition of the turbulent field, a multi-dimensional statistical formalism for the description and understanding of turbulence in free-shear flows is proposed and applied to the symmetries of planar temporal jets. The theoretical framework is based on the exact equation for the second-order moment of the two-point velocity increment and allows us to trace, for the first time, the spatially evolving cascade processes at the basis of turbulence mixing and entrainment. Fascinating reverse energy cascade mechanisms are found to be responsible for the generation of long and wide structures in the interface region. Analogously to two-dimensional turbulence, the energy provided by these spatially ascending reverse cascades is found to be eventually dissipated by viscosity at large scales through friction shearing processes involving a thin cross-flow layer of these large-scale structures. Finally, the external non-turbulent region of the jet is also found to be active from an energetic point of view. It is found that pressure-mediated non-local phenomena of displacement of almost quiescent fluid give rise to non-turbulent fluctuations that in time, through transitional mechanisms, would contribute to the growth of the turbulent jet. Overall, the unexpected paths taken by the scale-energy flux in the combined physical/scale space, which are a substantial novelty with respect to known descriptions of turbulent mixing and entrainment, may have major repercussions on our theoretical understanding and modelling, as anticipated here by reduced equations capable of giving a simple scale-dependent description of the rich dynamics of the flow

Conserved co-expression for candidate disease gene prioritization

Contains fulltext : 71114.pdf ( ) (Open Access)BACKGROUND: Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The evolutionary conservation of co-expression between species can be used to predict protein function more reliably than co-expression in a single species. Here we examine whether co-expression across multiple species is also a better prioritizer of disease genes than is co-expression between human genes alone. RESULTS: We use co-expression data from yeast (S. cerevisiae), nematode worm (C. elegans), fruit fly (D. melanogaster), mouse and human and find that the use of evolutionary conservation can indeed improve the predictive value of co-expression. The effect that genes causing the same disease have higher co-expression than do other genes from their associated disease loci, is significantly enhanced when co-expression data are combined across evolutionarily distant species. We also find that performance can vary significantly depending on the co-expression datasets used, and just using more data does not necessarily lead to better prioritization. Instead, we find that dataset quality is more important than quantity, and using a consistent microarray platform per species leads to better performance than using more inclusive datasets pooled from various platforms. CONCLUSION: We find that evolutionarily conserved gene co-expression prioritizes disease candidate genes better than human gene co-expression alone, and provide the integrated data as a new resource for disease gene prioritization tools.13 p

Potential-enstrophy lengthscale for the turbulent/nonturbulent interface in stratified flow

We study properties of the turbulent/nonturbulent interface (TNTI) between two layers of stratified fluids through direct numerical simulations (DNSs). Zero mean shear forcing creates moderate turbulence in one of the layers with the Taylor microscale Reynolds numbers in the mixed region of Re λ = 35 , 44 . We focus on the similarities and differences of the properties of stratified TNTIs due to two distinct types of forcing: (a) convection due to a boundary heat source and (b) agitation resembling a vertically oscillating grid experiment. Similarly to other stratified flows, the small scale dynamics of the TNTI in the present DNSs differ from what would be expected in comparable yet unstratified TNTIs. The interface cannot be indeed uniquely identified by the commonly used vorticity ω . Instead, the potential enstrophy Π 2 is shown to be the most appropriate marker in these flow cases. It is emphasized that the Kolmogorov lengthscale η K ∼ √ ν / ω is not representative of the small scale dynamics of the interface. Hence, an alternative lengthscale, η Π , is defined, in analogy to the Kolmogorov scale, based on the potential enstrophy, η Π = ( ν 3 / Π ∗ ) 1 / 6 , being Π ∗ = | g / ρ 0 Π | . The conditionally averaged profiles of potential enstrophy Π 2 , enstrophy ω 2 , and turbulent kinetic energy dissipation ε of the two distinctly different turbulence forcing cases collapsed when scaled by η Π at different time instants in each simulation. This implies not only the self-similarity of the small scale statistics of the TNTI in either of the two cases, but also the similarity between the statistics of the two different turbulent flows in the proximity of TNTI

WRF‐TEB: implementation and evaluation of the coupled Weather Research and Forecasting (WRF) and Town Energy Balance (TEB) model

Urban land surface processes need to be represented to inform future urban‐climate and building‐energy projections. Here, the single layer urban canopy model Town Energy Balance (TEB) is coupled to the Weather Research and Forecasting (WRF) model to create WRF‐TEB. The coupling method is described generically, implemented into software, and the issue of scientific reproducibility is addressed by releasing all code and data with a Singularity image. The coupling is implemented modularly and verified by an integration test. Results show no detectable errors in the coupling. Separately, a meteorological evaluation is undertaken using observations from Toulouse, France. The latter evaluation, during an urban canopy layer heat island episode, shows reasonable ability to estimate turbulent heat flux densities and other meteorological quantities. We conclude that new model couplings should make use of integration tests as meteorological evaluations by themselves are insufficient, given that errors are difficult to attribute because of the interplay between observational errors and multiple parameterization schemes (e.g. radiation, microphysics, boundary layer)

Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome

Intragenic homozygous deletions in the Large gene are associated with a severe neuromuscular phenotype in the myodystrophy (myd) mouse. These mutations result in a virtual lack of glycosylation of α-dystroglycan. Compound heterozygous LARGE mutations have been reported in a single human patient, manifesting with mild congenital muscular dystrophy (CMD) and severe mental retardation. These mutations are likely to retain some residual LARGE glycosyltransferase activity as indicated by residual α-dystroglycan glycosylation in patient cells. We hypothesized that more severe LARGE mutations are associated with a more severe CMD phenotype in humans. Here we report a 63-kb intragenic LARGE deletion in a family with Walker-Warburg syndrome (WWS), which is characterized by CMD, and severe structural brain and eye malformations. This finding demonstrates that LARGE gene mutations can give rise to a wide clinical spectrum, similar as for other genes that have a role in the post-translational modification of the α-dystroglycan protein

Prenatal muscle development in a mouse model for the secondary dystroglycanopathies

The defective glycosylation of α-dystroglycan is associated with a group of muscular dystrophies that are collectively referred to as the secondary dystroglycanopathies. Mutations in the gene encoding fukutin-related protein (FKRP) are one of the most common causes of secondary dystroglycanopathy in the UK and are associated with a wide spectrum of disease. Whilst central nervous system involvement has a prenatal onset, no studies have addressed prenatal muscle development in any of the mouse models for this group of diseases. In view of the pivotal role of α-dystroglycan in early basement membrane formation, we sought to determine if the muscle formation was altered in a mouse model of FKRP-related dystrophy