An urban parameterization for a global climate model. Part I: Formulation and evaluation for two cities

Urbanization, the expansion of built-up areas, is an important yet less-studied aspect of land use/land cover change in climate science. To date, most global climate models used to evaluate effects of land use/land cover change on climate do not include an urban parameterization. Here, the authors describe the formulation and evaluation of a parameterization of urban areas that is incorporated into the Community Land Model, the land surface component of the Community Climate System Model. The model is designed to be simple enough to be compatible with structural and computational constraints of a land surface model coupled to a global climate model yet complex enough to explore physically based processes known to be important in determining urban climatology. The city representation is based upon the “urban canyon” concept, which consists of roofs, sunlit and shaded walls, and canyon floor. The canyon floor is divided into pervious (e.g., residential lawns, parks) and impervious (e.g., roads, parking lots, sidewalks) fractions. Trapping of longwave radiation by canyon surfaces and solar radiation absorption and reflection is determined by accounting for multiple reflections. Separate energy balances and surface temperatures are determined for each canyon facet. A one-dimensional heat conduction equation is solved numerically for a 10-layer column to determine conduction fluxes into and out of canyon surfaces. Model performance is evaluated against measured fluxes and temperatures from two urban sites. Results indicate the model does a reasonable job of simulating the energy balance of cities.

Up-gradient eddy fluxes of potential vorticity near the subtropical jet

The role of eddy fluxes in the general circulation is often approached by treating eddies as (macro)turbulence. In this approach, the eddies act to diffuse certain quasiconservative quantities, such as potential vorticity (PV), along isentropic surfaces in the free atmosphere. The eddy fluxes are determined primarily by the eddy diffusivities and are necessarily down-gradient of the basic state PV field. Support for the (macro)turbulence approach stems from the fact that the eddy fluxes of PV in the free atmosphere are generally down-gradient in the long-term mean. Here we call attention to a pronounced and significant region of upgradient eddy PV fluxes on the poleward flank of the jet core in both hemispheres. The region of up-gradient (i.e., notionally “antidiffusive”) eddy PV fluxes is most pronounced during the winter and spring seasons and partially contradicts the turbulence approach described above. Analyses of the PV variance (potential enstrophy) budget suggest that the up-gradient PV fluxes represent local wave decay and are maintained by poleward fluxes of PV variance. Finite-amplitude effects thus represent leading order contributions to the PV variance budget, whereas dissipation is only of secondary importance locally. The appearance of up-gradient PV fluxes in the long-term mean is associated with the poleward shift of the jet—and thus the region of wave decay relative to wave growth—following wave-breaking events.

Implementation of an interior point source in the ultra weak variational formulation through source extraction

The Ultra Weak Variational Formulation (UWVF) is a powerful numerical method for the approximation of acoustic, elastic and electromagnetic waves in the time-harmonic regime. The use of Trefftz-type basis functions incorporates the known wave-like behaviour of the solution in the discrete space, allowing large reductions in the required number of degrees of freedom for a given accuracy, when compared to standard finite element methods. However, the UWVF is not well disposed to the accurate approximation of singular sources in the interior of the computational domain. We propose an adjustment to the UWVF for seismic imaging applications, which we call the Source Extraction UWVF. Differing fields are solved for in subdomains around the source, and matched on the inter-domain boundaries. Numerical results are presented for a domain of constant wavenumber and for a domain of varying sound speed in a model used for seismic imaging.

A laminated polymer film formulation for enteric delivery of live vaccine and probiotic bacteria

Live bacterial cells (LBC) are administered orally as attenuated vaccines, to deliver biopharmaceutical agents, and as probiotics to improve gastrointestinal health. However, LBC present unique formulation challenges and must survive gastrointestinal antimicrobial defenses including gastric acid after administration. We present a simple new formulation concept, termed Polymer Film Laminate (PFL). LBC are ambient dried onto cast acid-resistant enteric polymer films that are then laminated together to produce a solid oral dosage form. LBC of a model live bacterial vaccine and a probiotic were dried directly onto a cast film of enteric polymer. The effectiveness at protecting dried cells in a simulated gastric fluid (pH 2.0) depended on the composition of enteric polymer film used, with a blend of ethylcellulose plus Eudragit L100 55 providing greater protection from acid than Eudragit alone. However, although PFL made from blended polymers films completely released low molecular weight dye into intestinal conditions (pH 7.0), they failed to release LBC. In contrast, PFL made from Eudragit alone successfully protected dried probiotic or vaccine LBC from simulated gastric fluid for 2h, and subsequently released all viable cells within 60min of transfer into simulated intestinal fluid. Release kinetics could be controlled by modifying the lamination method.

Curl free pressure gradients over orography in a solution of the fully compressible Euler equations with implicit treatment of acoustic and gravity waves

Steep orography can cause noisy solutions and instability in models of the atmosphere. A new technique for modelling flow over orography is introduced which guarantees curl free gradients on arbitrary grids, implying that the pressure gradient term is not a spurious source of vorticity. This mimetic property leads to better hydrostatic balance and better energy conservation on test cases using terrain following grids. Curl-free gradients are achieved by using the co-variant components of velocity over orography rather than the usual horizontal and vertical components. In addition, gravity and acoustic waves are treated implicitly without the need for mean and perturbation variables or a hydrostatic reference profile. This enables a straightforward description of the implicit treatment of gravity waves. Results are presented of a resting atmosphere over orography and the curl-free pressure gradient formulation is advantageous. Results of gravity waves over orography are insensitive to the placement of terrain-following layers. The model with implicit gravity waves is stable in strongly stratified conditions, with N∆t up to at least 10 (where N is the Brunt-V ̈ais ̈al ̈a frequency). A warm bubble rising over orography is simulated and the curl free pressure gradient formulation gives much more accurate results for this test case than a model without this mimetic property.

Formulation and implementation of a residual-mean ocean circulation model

A parameterization of mesoscale eddies in coarse-resolution ocean general circulation models (GCM) is formulated and implemented using a residual-mean formalism. In that framework, mean buoyancy is advected by the residual velocity (the sum of the Eulerian and eddy-induced velocities) and modified by a residual flux which accounts for the diabatic effects of mesoscale eddies. The residual velocity is obtained by stepping forward a residual-mean momentum equation in which eddy stresses appear as forcing terms. Study of the spatial distribution of eddy stresses, derived by using them as control parameters to ‘‘fit’’ the residual-mean model to observations, supports the idea that eddy stresses can be likened to a vertical down-gradient flux of momentum with a coefficient which is constant in the vertical. The residual eddy flux is set to zero in the ocean interior, where mesoscale eddies are assumed to be quasi-adiabatic, but is parameterized by a horizontal down-gradient diffusivity near the surface where eddies develop a diabatic component as they stir properties horizontally across steep isopycnals. The residual-mean model is implemented and tested in the MIT general circulation model. It is shown that the resulting model (1) has a climatology that is superior to that obtained using the Gent and McWilliams parameterization scheme with a spatially uniform diffusivity and (2) allows one to significantly reduce the (spurious) horizontal viscosity used in coarse resolution GCMs.

A diabatically-generated potential vorticity structure near the extratropical tropopause in three simulated extratropical cyclones

The structure of near-tropopause potential vorticity (PV) acts as a primary control on the evolution of extratropical cyclones. Diabatic processes such as the latent heating found in ascending moist warm conveyor belts modify PV. A dipole in diabatically-generated PV (hereafter diabatic PV) straddling the extratropical tropopause, with the positive pole above the negative pole, was diagnosed in a recently published analysis of a simulated extratropical cyclone. This PV dipole has the potential to significantly modify the propagation of Rossby waves and the growth of baroclinically-unstable waves. This previous analysis was based on a single case study simulated with 12-km horizontal grid spacing and parameterized convection. Here, the dipole is investigated in three additional cold-season extratropical cyclones simulated in both convection-parameterizing and convection-permitting model configurations. A diabatic PV dipole across the extratropical tropopause is diagnosed in all three cases. The amplitude of the dipole saturates approximately 36 hours from the time diabatic PV is accumulated. The node elevation of the dipole varies between 2-4 PVU in the three cases, and the amplitude of the system-averaged dipole varies between 0.2-0.4 PVU. The amplitude of the negative pole is similar in the convection-parameterizing and convection-permitting simulations. The positive pole, which is generated by long-wave radiative cooling, is weak in the convection-permitting simulations due to the small domain size which limits the accumulation of diabatic tendencies within the interior of the domain. The possible correspondence between the diabatic PV dipole and the extratropical tropopause inversion layer is discussed.

Potential vorticity in warm conveyor belt outflow

Warm conveyor belts (WCBs) are the main ascending air masses within extratropical cyclones. They often exhibit strong condensation and precipitation, associated with ascent on large scales or embedded convection. Most of the air outflows into the upper troposphere as part of a ridge. Such ridges are an integral part of Rossby waves propagating along the tropopause and are identified with a negative potential vorticity (PV) anomaly and associated anticyclonic circulation. It has been argued that diabatic modification of PV in WCBs has an important influence on the extent of the ridge, propagation of Rossby waves and weather impacts downstream. Following the coherent ensemble of trajectories defining a WCB, PV is expected to increase with time while below the level of maximum latent heating and then decrease as trajectories ascend above the heating maximum. In models, it is found that the net change is approximately zero, so that the average PV of the WCB outflow is almost equal to the PV of its inflow. Here, the conditions necessary for this evolution are explored analytically using constraints arising from the conservation of circulation. It is argued that the net PV change is insensitive to the details of diabatic processes and the PV maximum midway along a WCB depends primarily on the net diabatic transport of mass from the inflow to the outflow layer. The main effect of diabatic processes within a WCB is to raise the isentropic level of the outflow, rather than to modify PV.

A parallel formulation for the simulation of a generic branch predictor

A parallel formulation for the simulation of a branch prediction algorithm is presented. This parallel formulation identifies independent tasks in the algorithm which can be executed concurrently. The parallel implementation is based on the multithreading model and two parallel programming platforms: pthreads and Cilk++. Improvement in execution performance by up to 7 times is observed for a generic 2-bit predictor in a 12-core multiprocessor system.

Effects of orange juice formulation on prebiotic functionality using an in vitro colonic model sytem

A three-stage continuous fermentative colonic model system was used to monitor in vitro the effect of different orange juice formulations on prebiotic activity. Three different juices with and without Bimuno, a GOS mixture containing galactooligosaccharides (B-GOS) were assessed in terms of their ability to induce a bifidogenic microbiota. The recipe development was based on incorporating 2.75g B-GOS into a 250 ml serving of juice (65°Brix of concentrate juice). Alongside the production of B-GOS juice, a control juice - orange juice without any additional Bimuno and a positive control juice, containing all the components of Bimuno (glucose, galactose and lactose) in the same relative proportions with the exception of B-GOS were developed. Ion Exchange Chromotography analysis was used to test the maintenance of bimuno components after the production process. Data showed that sterilisation had no significant effect on concentration of B-GOS and simple sugars. The three juice formulations were digested under conditions resembling the gastric and small intestinal environments. Main bacterial groups of the faecal microbiota were evaluated throughout the colonic model study using 16S rRNA-based fluorescence in situ hybridization (FISH). Potential effects of supplementation of the juices on microbial metabolism were studied measuring short chain fatty acids (SCFAs) using gas chromatography. Furthermore, B-GOS juices showed positive modulations of the microbiota composition and metabolic activity. In particular, numbers of faecal bifidobacteria and lactobacilli were significantly higher when B-GOS juice was fermented compared to controls. Furthermore, fermentation of B-GOS juice resulted in an increase in Roseburia subcluster and concomitantly increased butyrate production, which is of potential benefit to the host. In conclusion, this study has shown B-GOS within orange juice can have a beneficial effect on the fecal microbiota.

Optimization of a sponge cake formulation with inulin as fat replacer: structure, physicochemical, and sensory properties

The effects of several fat replacement levels (0%, 35%, 50%, 70%, and 100%) by inulin in sponge cake microstructure and physicochemical properties were studied. Oil substitution for inulin decreased significantly (P < 0.05) batter viscosity, giving heterogeneous bubbles size distributions as it was observed by light microscopy. Using confocal laser scanning microscopy the fat was observed to be located at the bubbles’ interface, enabling an optimum crumb cake structure development during baking. Cryo-SEM micrographs of cake crumbs showed a continuous matrix with embedded starch granules and coated with oil; when fat replacement levels increased, starch granules appeared as detached structures. Cakes with fat replacement up to 70% had a high crumb air cell values; they were softer and rated as acceptable by an untrained sensory panel (n = 51). So, the reformulation of a standard sponge cake recipe to obtain a new product with additional health benefits and accepted by consumers is achieved.

Optimisation of oat milk formulation to obtain fermented derivatives by using probiotic Lactobacillus reuteri microorganisms

Functional advantages of probiotics combined with interesting composition of oat were considered as an alternative to dairy products. In this study, fermentation of oat milk with Lactobacillus reuteri and Streptococcus thermophilus was analysed to develop a new probiotic product. Central composite design with response surface methodology was used to analyse the effect of different factors (glucose, fructose, inulin and starters) on the probiotic population in the product. Optimised formulation was characterised throughout storage time at 4 ℃ in terms of pH, acidity, β-glucan and oligosaccharides contents, colour and rheological behaviour. All formulations studied were adequate to produce fermented foods and minimum dose of each factor was considered as optimum. The selected formulation allowed starters survival above 107/cfu ml to be considered as a functional food and was maintained during the 28 days controlled. β-glucans remained in the final product with a positive effect on viscosity. Therefore, a new probiotic non-dairy milk was successfully developed in which high probiotic survivals were assured throughout the typical yoghurt-like shelf life.