Development and testing of numerical methods for two-way nested air pollution modelling

A new 3-D model REGINA (REGIonal high resolutioN Air pollution model) is under development at the National Environmental Research Institute (NERI). The model is based on pieces from several models developed over the last decades at NERI. The aim of the work is to develop a nested model which can operate with very high resolution in both space and time. To fulfill this aim the choice and implementation of accurate numerical methods is crucial. The model will be applied for studying air pollution phenomena (both monitoring, forecasting and scenarios) over Denmark. The present paper is focussed on the modification, implementation and testing of a numerical method for treating the horizontal advection in the model as well as the implementation of two-way nesting techniques. The horizontal transport in the model is solved using an accurate space derivative algorithm. This method is traditionally implemented with periodic boundary conditions, however, this is not an option for nested modelling. A new method for calculating non-periodic boundary conditions has been developed in order to overcome this problem. Extensive testing of the numerical solution of the advection and the coupling of the solution of advection and chemistry in the model using Molenkamp–Crowley rotation tests have been carried out. The results show that the model with the current implementation of numerical methods is suitable for calculating air pollution levels with high resolution.     

Comparison of isotope pairing and N2:Ar methods for measuring sediment denitrification—Assumption, modifications, and implications

Denitrification has been measured during the last few years using two different methods in particular: isotope pairing measured on a triple-collector isotopic ratio mass spectrometer and N₂:Ar ratios measured on a membrane inlet mass spectrometer (MIMS). This study compares these two techniques in short-term batch experiments. Rates obtained using the original N₂∶Ar method were up to 3 to 4 times higher than rates obtained using the isotope pairing technique due to O₂ reacting with the N₂ during MIMS analysis. Oxygen combines with N₂ within the mass spectrometer ion source forming NO⁺ which reduces the N₂ concentration. The decrease in N₂ is least at lower O₂ concentrations and since oxygen is typically consumed during incubations of sediment cores, the result is often a pseudo-increase in N₂ concentration being interpreted as denitrification activity. The magnitude of this ocygen effect may be instrument specific. The reaction of O₂ with N₂ and the subsequent decrease in N₂ was only partly correctly using an O₂ correction curve for the relationship between N₂ and O₂ concentrations. The O₂ corrected N₂∶Ar denitrification rates were lower, but still did not match the isotope pairing rates and the variability between replicates was much higher. Using a copper reduction column heated to 600°C to remove all of the O₂ from the sample before MIMS analysis resulted in comparable rates (slightly lower), and comparable variability between replicates, to the isotope pairing technique. The N₂:Ar technique determines the net N₂ production as the difference between N₂ production by denitrification and N₂ consumption by N-fixation, while N-fixation has little effect on the isotope pairing technique which determines a rate very close to the gross N₂ production. When the two different techniques were applied on the same sediment, the small difference in rates obtained by the two methods seemed to reflect N-fixation as also supported from measurements of ethylene production in acetylene enriched sediment cores. The N₂:Ar and isotope pairing techniques may be combined to provide simultaneous measurements of denitrification and N-fixation. Both techniques have several assumptions that must be met to achieve accurate rates; a number of tests are outlined that can be applied to demonstrate that these assumptions are being meet.     

Multi-species chemical data assimilation with the Danish Eulerian hemispheric model: system description and verification

Satellite retrievals of atmospheric composition provide a wealth of data on a global scale. These complement results from atmospheric chemistry-transport models (CTMs), and can be combined using data assimilation. We present two assimilation schemes coupled to the Danish Eulerian Hemispheric Model (DEHM), a three-dimensional, off-line CTM with full photochemistry: a variant on the ensemble Kalman filter and the three-dimensional variational scheme. The aim of this paper is to describe the two schemes and present an initial assessment of their impacts on model skill. Retrievals of multiple atmospheric trace gases are assimilated, namely: NO₂ tropospheric column densities, CH₄ total column densities, and partial column concentrations of O₃, CO and CH₄; these data are retrieved from four satellite sensors. Data for each species are assimilated independently of one another, and other species are only adjusted indirectly via the model’s chemistry and dynamics. Assimilation results are compared with measurements from surface monitoring stations and other satellite retrievals, and preliminary validation results are presented.Reference simulations (without assimilation) grossly underestimate surface CO concentrations, and both assimilation schemes eliminate this large and systematic model bias. The assimilation improves the spatial correlation of modelled CO with surface observations, and improves the spatial correlation between forecasts and retrievals for CO, NO₂ and O₃. Results for CH₄ show a loss of skill due to a mismatch in model bias between two assimilated CH₄ data-sets. Finally, we discuss differences in methodology and results between this paper and a recent study on multi-species chemical data assimilation. Joint optimisation of initial conditions and emission rates offers a promising direction for improving modelled boundary-layer concentrations.     

Oxygen and nutrient dynamics within mats of the filamentous macroalga Chaetomorpha linum

Concentration profiles of O₂, NH₄ ⁺, NO₃ ⁻, and PO₄ ³⁻ were measured at high spatial resolution in a 12-cm thick benthic mat of the filamentous macroalga Chaetomorpha linum. Oxygen and nutrient concentration profiles varied depending on algal activity and water turbulence. High surface irradiance stimulated O₂ production in the surface layers and introduced O₂ to deeper parts of the mat while the bottom layers of the mat and the underlying sediment were anoxic. Nutrient concentrations were highest in the bottom layers of the mat directly above the sediment nutrient source and decreased towards the surface layers due to algal assimilation and enhanced mixing with the overlying water column. Increased turbulence during windy periods resulted in more homogeneous oxygen and nutrient concentration profiles and shifted the oxic-anoxic interface downward. Denitrification within the mat, as measured by the isotope pairing technique on addition of ¹⁵NO₃ ⁻, was found to take place directly below the oxic-anoxic interface. Denitrification activity was always due to coupled nitrification-denitrification, whereby nitrifiers in the mat utilize NH₄ ⁺ diffusing from below and O₂ diffusing from above. The denitrification rate in the mat ranged from 22 μmol m⁻² h⁻¹ to 28 μmol m⁻² h⁻¹, approximately equivalent to that measured in the surrounding nonvegetated sediment. Although sediment denitrification is suppressed when the sediment surface is covered by a dense macroalgal mat, the denitrification zone may migrate up into the mat. In eutrophic estuaries with a large area of macroalgal cover, the physical structure and growth stage of algal mats may thus play an important role in the regulation of nitrogen removal by denitrification.     

High levels of site fidelity in movement patterns of Southern Rock Lobster (Jasus edwardsii) in Victoria,Australia

ABSTRACT

Movement patterns of the Southern Rock Lobster Jasus edwardsii in Victoria, Australia were investigated from 8,533 tag-recapture events across a 20-year period (1992–2012). In total, 83% of lobsters were recaptured within 1?km of their tagging site and 93% within 5?km. While largely resident, elevated movements were observed within specific regions, with the overall direction of movement being from inshore to offshore areas. Movement was not impacted by lobster sex, size, or reproductive stage. The fishery for Southern Rock Lobster within Victoria is currently managed into two zones with separate total allowable commercial catches in each area. Given the high levels of site fidelity, our findings suggest that management of the resource at this spatial scale is appropriate and that consideration of significant movement between zones is not warranted in fishery stock assessment models.