Formulation and analysis of a diffusion-velocity particle model for transport-dispersion equations

The modelling of diffusive terms in particle methods is a delicate matter and several models were proposed in the literature to take such terms into account. The diffusion velocity method (DVM), originally designed for the diffusion of passive scalars, turns diffusive terms into convective ones by expressing them as a divergence involving a so-called diffusion velocity. In this paper, DVM is extended to the diffusion of vectorial quantities in the three-dimensional Navier–Stokes equations, in their incompressible, velocity–vorticity formulation. The integration of a large eddy simulation (LES) turbulence model is investigated and a DVM general formulation is proposed. Either with or without LES, a novel expression of the diffusion velocity is derived, which makes it easier to approximate and which highlights the analogy with the original formulation for scalar transport. From this statement, DVM is then analysed in one dimension, both analytically and numerically on test cases to point out its good behaviour.

Toward assessing the effects of aerosols on deep convection: a numerical study using the WRF-Chemistry model

As the formative agents of cloud droplets, aerosols play an undeniably important role in the development of clouds and precipitation. Few meteorological models have been developed or adapted to simulate aerosols and their contribution to cloud and precipitation processes. The Weather Research and Forecasting model (WRF) has recently been coupled with an atmospheric chemistry suite and is jointly referred to as WRF-Chem, allowing atmospheric chemistry and meteorology to influence each other’s evolution within a mesoscale modeling framework. Provided that the model physics are robust, this framework allows the feedbacks between aerosol chemistry, cloud physics, and dynamics to be investigated. This study focuses on the effects of aerosols on meteorology, specifically, the interaction of aerosol chemical species with microphysical processes represented within the framework of the WRF-Chem. Aerosols are represented by eight size bins using the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) sectional parameterization, which is linked to the Purdue Lin bulk microphysics scheme. The aim of this study is to examine the sensitivity of deep convective precipitation modeled by the 2D WRF-Chem to varying aerosol number concentration and aerosol type. A systematic study has been performed regarding the effects of aerosols on parameters such as total precipitation, updraft/downdraft speed, distribution of hydrometeor species, and organizational features, within idealized maritime and continental thermodynamic environments. Initial results were obtained using WRFv3.0.1, and a second series of tests were run using WRFv3.2 after several changes to the activation, autoconversion, and Lin et al. microphysics schemes added by the WRF community, as well as the implementation of prescribed vertical levels by the author. The results of WRFv3.2 runs contrasted starkly with WRFv3.0.1 runs. The WRFv3.0.1 runs produced a propagating system resembling a developing squall line, whereas the WRFv3.2 runs did not. The response of total precipitation, updraft/downdraft speeds, and system organization to increasing aerosol concentrations were opposite between runs with different versions of WRF. Results of the WRFv3.2 runs, however, were in better agreement in timing and magnitude of vertical velocity and hydrometeor content with a WRFv3.0.1 run using single-moment Lin et al. microphysics, than WRFv3.0.1 runs with chemistry. One result consistent throughout all simulations was an inhibition in warm-rain processes due to enhanced aerosol concentrations, which resulted in a delay of precipitation onset that ranged from 2-3 minutes in WRFv3.2 runs, and up to 15 minutes in WRFv.3.0.1 runs. This result was not observed in a previous study by Ntelekos et al. (2009) using the WRF-Chem, perhaps due to their use of coarser horizontal and vertical resolution within their experiment. The changes to microphysical processes such as activation and autoconversion from WRFv3.0.1 to WRFv3.2, along with changes in the packing of vertical levels, had more impact than the varying aerosol concentrations even though the range of aerosol tested was greater than that observed in field studies. In order to take full advantage of the input of aerosols now offered by the chemistry module in WRF, the author recommends that a fully double-moment microphysics scheme be linked, rather than the limited double-moment Lin et al. scheme that currently exists. With this modification, the WRF-Chem will be a powerful tool for studying aerosol-cloud interactions and allow comparison of results with other studies using more modern and complex microphysical parameterizations.

The Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS) - Part 1: Model description and evaluation

We introduce the Coupled Aerosol and Tracer Transport model to the Brazilian developments on the Regional Atmospheric Modeling System (CATT-BRAMS). CATT-BRAMS is an on-line transport model fully consistent with the simulated atmospheric dynamics. Emission sources from biomass burning and urban-industrial-vehicular activities for trace gases and from biomass burning aerosol particles are obtained from several published datasets and remote sensing information. The tracer and aerosol mass concentration prognostics include the effects of sub-grid scale turbulence in the planetary boundary layer, convective transport by shallow and deep moist convection, wet and dry deposition, and plume rise associated with vegetation fires in addition to the grid scale transport. The radiation parameterization takes into account the interaction between the simulated biomass burning aerosol particles and short and long wave radiation. The atmospheric model BRAMS is based on the Regional Atmospheric Modeling System (RAMS), with several improvements associated with cumulus convection representation, soil moisture initialization and surface scheme tuned for the tropics, among others. In this paper the CATT-BRAMS model is used to simulate carbon monoxide and particulate material (PM(2.5)) surface fluxes and atmospheric transport during the 2002 LBA field campaigns, conducted during the transition from the dry to wet season in the southwest Amazon Basin. Model evaluation is addressed with comparisons between model results and near surface, radiosondes and airborne measurements performed during the field campaign, as well as remote sensing derived products. We show the matching of emissions strengths to observed carbon monoxide in the LBA campaign. A relatively good comparison to the MOPITT data, in spite of the fact that MOPITT a priori assumptions imply several difficulties, is also obtained.

The role of the observed tropical convection in the generation of frost events in the southern cone of South America

Based on previous results obtained from observations and linear wave theory analysis, the hypothesis that large-scale patterns can generate extreme cold events in southeast South America through the propagation of remotely excited Rossby waves was already suggested. This work will confirm these findings and extend their analysis through a series of numerical experiments using a primitive equation model where waves are excited by a thermal forcing situated in positions chosen according to observed convection anomalies over the equatorial region. The basic state used for these experiments is a composite of austral winters with maximum and minimum frequency of occurrence of generalized frosts that can affect a large area known as the Wet Pampas located in the central and eastern part of Argentina. The results suggest that stationary Rossby waves may be one important mechanism linking anomalous tropical convection with the extreme cold events in the Wet Pampas. The combination of tropical convection and a specific basic state can generate the right environment to guide the Rossby waves trigged by the tropical forcing towards South America. Depending on the phase of the waves entering the South American continent, they can favour the advection of anomalous wind at low levels from the south carrying cold and dry air over the whole southern extreme of the continent, producing a generalized frost in the Wet Pampa region. On the other hand, when a basic state based on the composites of minimum frosts is used, an anomalous anticyclone over the southern part of the continent generates a circulation with a south-southeast wind which brings maritime air and therefore humidity over the Wet Pampas region, creating negative temperature anomalies only over the northeastern part of the region. Under these conditions even if frosts occur they would not be generalized, as observed for the other basic state with maximum frequency of occurrence of generalized frosts.

Turbulent magnetic pumping in a Babcock-Leighton solar dynamo model

Context. The turbulent pumping effect corresponds to the transport of magnetic flux due to the presence of density and turbulence gradients in convectively unstable layers. In the induction equation it appears as an advective term and for this reason it is expected to be important in the solar and stellar dynamo processes. Aims. We explore the effects of turbulent pumping in a flux-dominated Babcock-Leighton solar dynamo model with a solar-like rotation law. Methods. As a first step, only vertical pumping has been considered through the inclusion of a radial diamagnetic term in the induction equation. In the second step, a latitudinal pumping term was included and then, a near-surface shear was included. Results. The results reveal the importance of the pumping mechanism in solving current limitations in mean field dynamo modeling, such as the storage of the magnetic flux and the latitudinal distribution of the sunspots. If a meridional flow is assumed to be present only in the upper part of the convective zone, it is the full turbulent pumping that regulates both the period of the solar cycle and the latitudinal distribution of the sunspot activity. In models that consider shear near the surface, a second shell of toroidal field is generated above r = 0.95 R(circle dot) at all latitudes. If the full pumping is also included, the polar toroidal fields are efficiently advected inwards, and the toroidal magnetic activity survives only at the observed latitudes near the equator. With regard to the parity of the magnetic field, only models that combine turbulent pumping with near-surface shear always converge to the dipolar parity. Conclusions. This result suggests that, under the Babcock-Leighton approach, the equartorward motion of the observed magnetic activity is governed by the latitudinal pumping of the toroidal magnetic field rather than by a large scale coherent meridional flow. Our results support the idea that the parity problem is related to the quadrupolar imprint of the meridional flow on the poloidal component of the magnetic field and the turbulent pumping positively contributes to wash out this imprint.

Beryllium abundances along the evolutionary sequence of the open cluster IC 4651-A new test for hydrodynamical stellar models

Context. Previous analyses of lithium abundances in main sequence and red giant stars have revealed the action of mixing mechanisms other than convection in stellar interiors. Beryllium abundances in stars with Li abundance determinations can offer valuable complementary information on the nature of these mechanisms. Aims. Our aim is to derive Be abundances along the whole evolutionary sequence of an open cluster. We focus on the well-studied open cluster IC 4651. These Be abundances are used with previously determined Li abundances, in the same sample stars, to investigate the mixing mechanisms in a range of stellar masses and evolutionary stages. Methods. Atmospheric parameters were adopted from a previous abundance analysis by the same authors. New Be abundances have been determined from high-resolution, high signal-to-noise UVES spectra using spectrum synthesis and model atmospheres. The careful synthetic modeling of the Be lines region is used to calculate reliable abundances in rapidly rotating stars. The observed behavior of Be and Li is compared to theoretical predictions from stellar models including rotation-induced mixing, internal gravity waves, atomic diffusion, and thermohaline mixing. Results. Beryllium is detected in all the main sequence and turn-off sample stars, both slow- and fast-rotating stars, including the Li-dip stars, but is not detected in the red giants. Confirming previous results, we find that the Li dip is also a Be dip, although the depletion of Be is more modest than for Li in the corresponding effective temperature range. For post-main-sequence stars, the Be dilution starts earlier within the Hertzsprung gap than expected from classical predictions, as does the Li dilution. A clear dispersion in the Be abundances is also observed. Theoretical stellar models including the hydrodynamical transport processes mentioned above are able to reproduce all the observed features well. These results show a good theoretical understanding of the Li and Be behavior along the color-magnitude diagram of this intermediate-age cluster for stars more massive than 1.2 M(circle dot).

Land planarians (Platyhelminthes) as a model organism for fine-scale phylogeographic studies: understanding patterns of biodiversity in the Brazilian Atlantic Forest hotspot

The Brazilian Atlantic Forest is one of the richest biodiversity hotspots of the world. Paleoclimatic models have predicted two large stability regions in its northern and central parts, whereas southern regions might have suffered strong instability during Pleistocene glaciations. Molecular phylogeographic and endemism studies show, nevertheless, contradictory results: although some results validate these predictions, other data suggest that paleoclimatic models fail to predict stable rainforest areas in the south. Most studies, however, have surveyed species with relatively high dispersal rates whereas taxa with lower dispersion capabilities should be better predictors of habitat stability. Here, we have used two land planarian species as model organisms to analyse the patterns and levels of nucleotide diversity on a locality within the Southern Atlantic Forest. We find that both species harbour high levels of genetic variability without exhibiting the molecular footprint of recent colonization or population expansions, suggesting a long-term stability scenario. The results reflect, therefore, that paleoclimatic models may fail to detect refugia in the Southern Atlantic Forest, and that model organisms with low dispersal capability can improve the resolution of these models.

Numerical solution of the two-phase expansion of a metastable flashing liquid jet using the dispersion-controlled dissipative scheme

This paper presents a study of the stationary phenomenon of superheated or metastable liquid jets, flashing into a two-dimensional axisymmetric domain, while in the two-phase region. In general, the phenomenon starts off when a high-pressure, high-temperature liquid jet emerges from a small nozzle or orifice expanding into a low-pressure chamber, below its saturation pressure taken at the injection temperature. As the process evolves, crossing the saturation curve, one observes that the fluid remains in the liquid phase reaching a superheated condition. Then, the liquid undergoes an abrupt phase change by means of an oblique evaporation wave. Across this phase change the superheated liquid becomes a two-phase high-speed mixture in various directions, expanding to supersonic velocities. In order to reach the downstream pressure, the supersonic fluid continues to expand, crossing a complex bow shock wave. The balance equations that govern the phenomenon are mass conservation, momentum conservation, and energy conservation, plus an equation-of-state for the substance. A false-transient model is implemented using the shock capturing scheme: dispersion-controlled dissipative (DCD), which was used to calculate the flow conditions as the steady-state condition is reached. Numerical results with computational code DCD-2D vI have been analyzed. Copyright (C) 2009 John Wiley & Sons, Ltd.

Coarse-grid higher order finite-difference time-domain algorithm with low dispersion errors

Higher order (2,4) FDTD schemes used for numerical solutions of Maxwell`s equations are focused on diminishing the truncation errors caused by the Taylor series expansion of the spatial derivatives. These schemes use a larger computational stencil, which generally makes use of the two constant coefficients, C-1 and C-2, for the four-point central-difference operators. In this paper we propose a novel way to diminish these truncation errors, in order to obtain more accurate numerical solutions of Maxwell`s equations. For such purpose, we present a method to individually optimize the pair of coefficients, C-1 and C-2, based on any desired grid size resolution and size of time step. Particularly, we are interested in using coarser grid discretizations to be able to simulate electrically large domains. The results of our optimization algorithm show a significant reduction in dispersion error and numerical anisotropy for all modeled grid size resolutions. Numerical simulations of free-space propagation verifies the very promising theoretical results. The model is also shown to perform well in more complex, realistic scenarios.

Double generalized linear model for tissue culture proportion data: a Bayesian perspective

Joint generalized linear models and double generalized linear models (DGLMs) were designed to model outcomes for which the variability can be explained using factors and/or covariates. When such factors operate, the usual normal regression models, which inherently exhibit constant variance, will under-represent variation in the data and hence may lead to erroneous inferences. For count and proportion data, such noise factors can generate a so-called overdispersion effect, and the use of binomial and Poisson models underestimates the variability and, consequently, incorrectly indicate significant effects. In this manuscript, we propose a DGLM from a Bayesian perspective, focusing on the case of proportion data, where the overdispersion can be modeled using a random effect that depends on some noise factors. The posterior joint density function was sampled using Monte Carlo Markov Chain algorithms, allowing inferences over the model parameters. An application to a data set on apple tissue culture is presented, for which it is shown that the Bayesian approach is quite feasible, even when limited prior information is available, thereby generating valuable insight for the researcher about its experimental results.

Heat transfer and entropy generation optimization of forced convection in a porous-saturated duct of rectangular cross-section

We investigate analytically the first and the second law characteristics of fully developed forced convection inside a porous-saturated duct of rectangular cross-section. The Darcy-Brinkman flow model is employed. Three different types of thermal boundary conditions are examined. Expressions for the Nusselt number, the Bejan number, and the dimensionless entropy generation rate are presented in terms of the system parameters. The conclusions of this analytical study will make it possible to compare, evaluate, and optimize alternative rectangular duct design options in terms of heat transfer, pressure drop, and entropy generation. (c) 2006 Elsevier Ltd. All rights reserved.

Analytical solution of forced convection in a duct of rectangular cross-section saturated by a porous medium

A theoretical analysis is presented to investigate fully developed (both thermally and hydrodynamically) forced convection in a duct of rectangular cross-section filled with a hyper-porous medium. The Darcy-Brinkman model for flow through porous media was adopted in the present analysis. A Fourier series type solution is applied to obtain the exact velocity and temperature distribution within the duct. The case of uniform heat flux on the walls, i.e. the H boundary condition in the terminology of Kays and Crawford [1], is treated. Values of the Nusselt number and the friction factor as a function of the aspect ratio, the Darcy number, and the viscosity ratio are reported.

Entropy generation for forced convection in a porous saturated circular tube with uniform wall temperature

A numerical study is reported to investigate both the First and the Second Law of Thermodynamics for thermally developing forced convection in a circular tube filled by a saturated porous medium, with uniform wall temperature, and with the effects of viscous dissipation included. A theoretical analysis is also presented to study the problem for the asymptotic region applying the perturbation solution of the Brinkman momentum equation reported by Hooman and Kani [1]. Expressions are reported for the temperature profile, the Nusselt number, the Bejan number, and the dimensionless entropy generation rate in the asymptotic region. Numerical results are found to be in good agreement with theoretical counterparts.

Thermally developing Brinkman–Brinkman forced convection in rectangular ducts with isothermal walls

The Extended Weighted Residuals Method (EWRM) is applied to investigate the effects of viscous dissipation on the thermal development of forced convection in a porous-saturated duct of rectangular cross-section with isothermal boundary condition. The Brinkman flow model is employed for determination of the velocity field. The temperature in the flow field was computed by utilizing the Green’s function solution based on the EWRM. Following the computation of the temperature field, expressions are presented for the local Nusselt number and the bulk temperature as a function of the dimensionless longitudinal coordinate. In addition to the aspect ratio, the other parameters included in this computation are the Darcy number, viscosity ratio, and the Brinkman number.

Analysis of heat transfer and entropy generation for a thermally developing Brinkman–Brinkman forced convection problem in a rectangular duct with isoflux walls

Heat transfer and entropy generation analysis of the thermally developing forced convection in a porous-saturated duct of rectangular cross-section, with walls maintained at a constant and uniform heat flux, is investigated based on the Brinkman flow model. The classical Galerkin method is used to obtain the fully developed velocity distribution. To solve the thermal energy equation, with the effects of viscous dissipation being included, the Extended Weighted Residuals Method (EWRM) is applied. The local (three dimensional) temperature field is solved by utilizing the Green’s function solution based on the EWRM where symbolic algebra is being used for convenience in presentation. Following the computation of the temperature field, expressions are presented for the local Nusselt number and the bulk temperature as a function of the dimensionless longitudinal coordinate, the aspect ratio, the Darcy number, the viscosity ratio, and the Brinkman number. With the velocity and temperature field being determined, the Second Law (of Thermodynamics) aspect of the problem is also investigated. Approximate closed form solutions are also presented for two limiting cases of MDa values. It is observed that decreasing the aspect ratio and MDa values increases the entropy generation rate.