A calibrated, non-invasive method for measuring the internal interface height field at high resolution in the rotating, two-layer annulus

We describe a remote sensing method for measuring the internal interface height field in a rotating, two-layer annulus laboratory experiment. The method is non-invasive, avoiding the possibility of an interaction between the flow and the measurement device. The height fields retrieved are accurate and highly resolved in both space and time. The technique is based on a flow visualization method developed by previous workers, and relies upon the optical rotation properties of the working liquids. The previous methods returned only qualitative interface maps, however. In the present study, a technique is developed for deriving quantitative maps by calibrating height against the colour fields registered by a camera which views the flow from above. We use a layer-wise torque balance analysis to determine the equilibrium interface height field analytically, in order to derive the calibration curves. With the current system, viewing an annulus of outer radius 125 mm and depth 250 mm from a distance of 2 m, the inferred height fields have horizontal, vertical and temporal resolutions of up to 0.2 mm, 1 mm and 0.04 s, respectively.

Jupiter's and Saturn's convectively driven banded jets in the laboratory

The banded patterns of cloud and wind are among the most striking features of the atmospheres of Jupiter and Saturn, but their dynamical origin remains poorly understood. Most approaches towards understanding zonation so far (also in the terrestrial oceans) have used highly idealized models to show that it might originate from dynamical anisotropy in a shallow turbulent fluid layer due to the planetary β-effect. Here we report the results of laboratory experiments, conducted on a 14-m diameter turntable, which quantitatively confirm that multiple zonal jets may indeed be generated and maintained by this mechanism in the presence of deep convection and a topographic β-effect. At the very small values of Ekman number (≤2 × 10−5) and large local Reynolds numbers (≥2000, based on jet scales) achieved, the kinetic energy spectra suggest the presence of both energy-cascading and enstrophy-cascading inertial ranges in addition to the zonation near twice the Rhines wave number.

Spontaneous generation and impact of inertia-gravity waves in a stratified, two-layer shear flow

Inertia-gravity waves exist ubiquitously throughout the stratified parts of the atmosphere and ocean. They are generated by local velocity shears, interactions with topography, and as geostrophic (or spontaneous) adjustment radiation. Relatively little is known about the details of their interaction with the large-scale flow, however. We report on a joint model/laboratory study of a flow in which inertia-gravity waves are generated as spontaneous adjustment radiation by an evolving large-scale mode. We show that their subsequent impact upon the large-scale dynamics is generally small. However, near a potential transition from one large-scale mode to another, in a flow which is simultaneously baroclinically-unstable to more than one mode, the inertia-gravity waves may strongly influence the selection of the mode which actually occurs.

The role of nonhydrostatic dynamics in controlling development of a surface ocean front

Numerical studies of surface ocean fronts forced by inhomogeneous buoyancy loss show nonhydrostatic convective plumes coexisting with baroclinic eddies. The character of the vertical overturning depends sensitively on the treatment of the vertical momentum equation in the model. It is less well known how the frontal evolution over scales of O(10 km) is affected by these dynamics. Here, we compare highly resolved numerical experiments using nonhydrostatic and hydrostatic models and the convective-adjustment parametrization. The impact of nonhydrostatic processes on average cross-frontal transfer is weak compared to the effect of the O(1 km) scale baroclinic motions. For water-mass distribution and formation rate nonhydrostatic dynamics have similar influence to the baroclinic eddies although adequate resolution of the gradients in forcing fluxes is more important. The overall implication is that including nonhydrostatic surface frontal dynamics in ocean general circulation models will have only a minor effect on scales of O(1 km) and greater.

Stochastic resonance in a nonlinear model of a rotating, stratified shear flow, with a simple stochastic inertia-gravity wave parameterization

We report on a numerical study of the impact of short, fast inertia-gravity waves on the large-scale, slowly-evolving flow with which they co-exist. A nonlinear quasi-geostrophic numerical model of a stratified shear flow is used to simulate, at reasonably high resolution, the evolution of a large-scale mode which grows due to baroclinic instability and equilibrates at finite amplitude. Ageostrophic inertia-gravity modes are filtered out of the model by construction, but their effects on the balanced flow are incorporated using a simple stochastic parameterization of the potential vorticity anomalies which they induce. The model simulates a rotating, two-layer annulus laboratory experiment, in which we recently observed systematic inertia-gravity wave generation by an evolving, large-scale flow. We find that the impact of the small-amplitude stochastic contribution to the potential vorticity tendency, on the model balanced flow, is generally small, as expected. In certain circumstances, however, the parameterized fast waves can exert a dominant influence. In a flow which is baroclinically-unstable to a range of zonal wavenumbers, and in which there is a close match between the growth rates of the multiple modes, the stochastic waves can strongly affect wavenumber selection. This is illustrated by a flow in which the parameterized fast modes dramatically re-partition the probability-density function for equilibrated large-scale zonal wavenumber. In a second case study, the stochastic perturbations are shown to force spontaneous wavenumber transitions in the large-scale flow, which do not occur in their absence. These phenomena are due to a stochastic resonance effect. They add to the evidence that deterministic parameterizations in general circulation models, of subgrid-scale processes such as gravity wave drag, cannot always adequately capture the full details of the nonlinear interaction.

QUAGMIRE v1.3: a quasi-geostrophic model for investigating rotating fluids experiments

QUAGMIRE is a quasi-geostrophic numerical model for performing fast, high-resolution simulations of multi-layer rotating annulus laboratory experiments on a desktop personal computer. The model uses a hybrid finite-difference/spectral approach to numerically integrate the coupled nonlinear partial differential equations of motion in cylindrical geometry in each layer. Version 1.3 implements the special case of two fluid layers of equal resting depths. The flow is forced either by a differentially rotating lid, or by relaxation to specified streamfunction or potential vorticity fields, or both. Dissipation is achieved through Ekman layer pumping and suction at the horizontal boundaries, including the internal interface. The effects of weak interfacial tension are included, as well as the linear topographic beta-effect and the quadratic centripetal beta-effect. Stochastic forcing may optionally be activated, to represent approximately the effects of random unresolved features. A leapfrog time stepping scheme is used, with a Robert filter. Flows simulated by the model agree well with those observed in the corresponding laboratory experiments.

A lightweight balloon-carried cloud charge sensor

Despite the importance of microphysical cloud processes on the climate system, some topics are under-explored. For example, few measurements of droplet charges in nonthunderstorm clouds exist. Balloon carried charge sensors can be used to provide new measurements. A charge sensor is described for use with meteorological balloons, which has been tested over a range of atmospheric temperatures from -60 to 20 degrees C, in cloudy and clear air. The rapid time response of the sensor (to >10 V s(-1)) permits charge densities from 100 fC m(-3) to 1 nC m(-3) to be determined, which is sufficient for it to act as a cloud edge charge detector at weakly charged horizontal cloud boundaries.

The relationship between diffuse spectral reflectance of the soil and its cation exchange capacity is scale-dependent

Diffuse reflectance spectroscopy (DRS) is increasingly being used to predict numerous soil physical, chemical and biochemical properties. However, soil properties and processes vary at different scales and, as a result, relationships between soil properties often depend on scale. In this paper we report on how the relationship between one such property, cation exchange capacity (CEC), and the DRS of the soil depends on spatial scale. We show this by means of a nested analysis of covariance of soils sampled on a balanced nested design in a 16 km × 16 km area in eastern England. We used principal components analysis on the DRS to obtain a reduced number of variables while retaining key variation. The first principal component accounted for 99.8% of the total variance, the second for 0.14%. Nested analysis of the variation in the CEC and the two principal components showed that the substantial variance components are at the > 2000-m scale. This is probably the result of differences in soil composition due to parent material. We then developed a model to predict CEC from the DRS and used partial least squares (PLS) regression do to so. Leave-one-out cross-validation results suggested a reasonable predictive capability (R2 = 0.71 and RMSE = 0.048 molc kg− 1). However, the results from the independent validation were not as good, with R2 = 0.27, RMSE = 0.056 molc kg− 1 and an overall correlation of 0.52. This would indicate that DRS may not be useful for predictions of CEC. When we applied the analysis of covariance between predicted and observed we found significant scale-dependent correlations at scales of 50 and 500 m (0.82 and 0.73 respectively). DRS measurements can therefore be useful to predict CEC if predictions are required, for example, at the field scale (50 m). This study illustrates that the relationship between DRS and soil properties is scale-dependent and that this scale dependency has important consequences for prediction of soil properties from DRS data

Biodegradation of the herbicide mecoprop-p with soil depth and its relationship with class III tfdA genes

Mecoprop-p [(R)-2-(4-chloro-2-methylphenoxy) propanoic acid) is widely used in agriculture and poses an environmental concern because of its susceptibility to leach from soil to water. We investigated the effect of soil depth on mecoprop-p biodegradation and its relationship with the number and diversity of tfdA related genes, which are the most widely known genes involved in degradation of the phenoxyalkanoic acid group of herbicides by bacteria. Mecoprop-p half-life (DT50) was approximately 12 days in soil sampled from <30 cm depth, and increased progressively with soil depth, reaching over 84 days at 70–80 cm. In sub-soil there was a lag period of between 23 and 34 days prior to a phase of rapid degradation. No lag phase occurred in top-soil samples prior to the onset of degradation. The maximum degradation rate was the same in top-soil and sub-soil samples. Although diverse tfdAα and tfdA genes were present prior to mecoprop-p degradation, real time PCR revealed that degradation was associated with proliferation of tfdA genes. The number of tfdA genes and the most probable number of mecoprop-p degrading organisms in soil prior to mecoprop-p addition were below the limit of quantification and detection respectively. Melting curves from the real time PCR analysis showed that prior to mecoprop-p degradation both class I and class III tfdA genes were present in top- and sub-soil samples. However at all soil depths only tfdA class III genes proliferated during degradation. Denaturing gradient gel electrophoresis confirmed that class III tfdA genes were associated with mecoprop-p degradation. Degradation was not associated with the induction of novel tfdA genes in top- or sub-soil samples, and there were no apparent differences in tfdA gene diversity with soil depth prior to or following degradation.

A Bayesian approach to estimate sensible and latent heat over vegetated land surface

Sensible and latent heat fluxes are often calculated from bulk transfer equations combined with the energy balance. For spatial estimates of these fluxes, a combination of remotely sensed and standard meteorological data from weather stations is used. The success of this approach depends on the accuracy of the input data and on the accuracy of two variables in particular: aerodynamic and surface conductance. This paper presents a Bayesian approach to improve estimates of sensible and latent heat fluxes by using a priori estimates of aerodynamic and surface conductance alongside remote measurements of surface temperature. The method is validated for time series of half-hourly measurements in a fully grown maize field, a vineyard and a forest. It is shown that the Bayesian approach yields more accurate estimates of sensible and latent heat flux than traditional methods.

An integrated model of soil-canopy spectral radiances, photosynthesis, fluorescence, temperature and energy balance

This paper presents the model SCOPE (Soil Canopy Observation, Photochemistry and Energy fluxes), which is a vertical (1-D) integrated radiative transfer and energy balance model. The model links visible to thermal infrared radiance spectra (0.4 to 50 μm) as observed above the canopy to the fluxes of water, heat and carbon dioxide, as a function of vegetation structure, and the vertical profiles of temperature. Output of the model is the spectrum of outgoing radiation in the viewing direction and the turbulent heat fluxes, photosynthesis and chlorophyll fluorescence. A special routine is dedicated to the calculation of photosynthesis rate and chlorophyll fluorescence at the leaf level as a function of net radiation and leaf temperature. The fluorescence contributions from individual leaves are integrated over the canopy layer to calculate top-of-canopy fluorescence. The calculation of radiative transfer and the energy balance is fully integrated, allowing for feedback between leaf temperatures, leaf chlorophyll fluorescence and radiative fluxes. Leaf temperatures are calculated on the basis of energy balance closure. Model simulations were evaluated against observations reported in the literature and against data collected during field campaigns. These evaluations showed that SCOPE is able to reproduce realistic radiance spectra, directional radiance and energy balance fluxes. The model may be applied for the design of algorithms for the retrieval of evapotranspiration from optical and thermal earth observation data, for validation of existing methods to monitor vegetation functioning, to help interpret canopy fluorescence measurements, and to study the relationships between synoptic observations with diurnally integrated quantities. The model has been implemented in Matlab and has a modular design, thus allowing for great flexibility and scalability.

Molecular genetic differentiation in earthworms inhabiting a heterogeneous Pb-polluted landscape

A Pb-mine site situated on acidic soil, but comprising of Ca-enriched islands around derelict buildings was used to study the spatial pattern of genetic diversity in Lumbricus rubellus. Two distinct genetic lineages ('A' and 'B'), differentiated at both the mitochondrial (mtDNA COII) and nuclear level (AFLPs) were revealed with a mean inter-lineage mtDNA sequence divergence of approximately 13%, indicative of a cryptic species complex. AFLP analysis indicates that lineage A individuals within one central 'ecological island' site are uniquely clustered, with little genetic overlap with lineage A individuals at the two peripheral sites. FTIR microspectroscopy of Pb-sequestering chloragocytes revealed different phosphate profiles in residents of adjacent acidic and calcareous islands. Bioinformatics found over-representation of Ca pathway genes in ESTPb libraries. Subsequent sequencing of a Ca-transport gene, SERCA, revealed mutations in the protein's cytosolic domain. We recommend the mandatory genotyping of all individuals prior to field-based ecotoxicological assays, particularly those using discriminating genomic technologies.