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At least 991 records · Page 55

A computational thrombus formation model: application to an idealized two-dimensional aneurysm treated with bare metal coils

Cardiovascular implantable devices alter the biofluid dynamics and biochemistry of the blood in which they are placed. These perturbations can lead to thrombus formation which may or may not be desired, depending on the application. In this work, a computational model is developed that couples biofluid dynamics and biochemistry to predict the clotting response of blood to such devices. The model consists of 28 advection–diffusion–reaction partial differential equations to track proteins in the blood involved in clotting and utilizes boundary flux terms to model the initiation of the intrinsic clotting pathway at thrombogenic device surfaces. We use this model to simulate the transient clot growth within a 2D idealized bifurcation aneurysm filled with various distributions of bare metal coils with similar packing densities. The clot model predicts initial clot formation to occur in areas along coil surfaces where flow is minimal and where time-averaged shear rates are the smallest. Among the six coil-filled aneurysm cases simulated, maximum thrombus occlusion ranged between 80.8 and 92.2% of the post-treatment aneurysm volume and was achieved 325–450 s after treatment. Finally, with further refinement and validation, the computational clotting model will be a valuable engineering tool for evaluating and comparing the relative performance of cardiovascular implantable devices.

60 APPLIED LIFE SCIENCES↗

Hourly and daily rainfall intensification causes opposing effects on C and N emissions, storage, and leaching in dry and wet grasslands

Climate change is expected to alter hourly and daily rainfall regimes and, in turn, the dynamics of ecosystem processes controlling greenhouse gas emissions that affect climate. Here, we investigate the effects of expected twenty-first century changes in hourly and daily rainfall on soil carbon and nitrogen emissions, soil organic matter (SOM) stocks, and leaching using a coupled mechanistic carbon and nitrogen soil biogeochemical model (BAMS2). The model represents various abiotic and biotic processes involving 11 SOM pools. These processes include fungal depolymerization, heterotrophic bacterial mineralization, nitrification, denitrification, microbial mortality, necromass decomposition, microbial response to water stress, protection, aqueous advection and diffusion, aqueous complexation, and gaseous dissolution. Multi-decadal modeling with varying rainfall patterns was conducted on nine Australian grasslands in tropical, temperate, and semi-arid regions. Our results show that annual CO 2 emissions in the semi-arid grasslands increase by more than 20% with a 20% increase in annual rainfall (with no changes in the rainfall timing), but the tropical grasslands have opposite trends. A 20% increase in annual rainfall also increases annual N 2 O and NO emissions in the semi-arid grasslands by more than 10% but decreases emissions by at least 25% in the temperate grasslands. When subjected to low frequency and high magnitude daily rainfall events with unchanged annual totals, the semi-arid grasslands are the most sensitive, but changes in annual CO 2 emissions and SOM stocks are less than 5 %. Finally, intensification of hourly rainfall did not significantly alter CO 2 emissions and SOM stocks but changed annual NH 3 emissions in the tropical grasslands by more than 300%.

54 ENVIRONMENTAL SCIENCES↗

Development of energetic and enzymatic limitations on microbial carbon cycling in soils

Soil organic carbon (SOC) constitutes an important reservoir in the global carbon cycle that is vulnerable to transformation and loss from land use and climate change. Anoxic conditions protect SOC from microbial degradation through limiting the energetics of respiration and inhibiting extracellular oxidative enzymes. Given growing evidence of prevalent anaerobic microsites in upland soils, we designed an experiment testing the development of dissolved organic carbon (DOC) signatures of energetic and enzymatic limitations on microbial carbon utilization across simulated soil aggregates or peds. Reactors comprised a soil column “aggregate” underlying an advective “macropore” channel. Soils received downward diffusive inputs of aerated porewater media with added nitrate, sulfate, or no amendment—where native ferrihydrite served as dominant anaerobic terminal electron acceptor (TEA). After 40 days, added nitrate resulted in highest bulk respiration and DOC production while sulfate did not differ from the control. Nominal oxidation state of carbon (NOSC) was higher (more favorable) with added TEAs at soil surfaces and decreased with depth, while NOSC in the non-amended soil remained lower and constant with depth. DOC generally increased with depth, which along with decreasing NOSC values indicates joint electron-donor and acceptor control over respiration energetics. Of all organic compound classes, only the relative abundance of phenolics increased between 0 and 0.5 cm depth, which aligns with the oxic-anoxic transition and suggests oxidative enzyme inhibition. Furthermore, our results suggest that oxygen limitation within upland soil aggregates may preserve SOC via both energetic and enzymatic C protection mechanisms, which are vulnerable upon exposure to oxygen.

54 ENVIRONMENTAL SCIENCES↗

A simple method for simulating wind profiles in the boundary layer of tropical cyclones

A method to simulate characteristics of wind speed in the boundary layer of tropical cyclones in an idealized manner is developed and evaluated. The method can be used in a single-column modelling set-up with a planetary boundary-layer parametrization, or within large-eddy simulations (LES). The key step is to include terms in the horizontal velocity equations representing advection and centrifugal acceleration in tropical cyclones that occurs on scales larger than the domain size. Compared to other recently developed methods, which require two input parameters (a reference wind speed, and radius from the centre of a tropical cyclone) this new method also requires a third input parameter: the radial gradient of reference wind speed. With the new method, simulated wind profiles are similar to composite profiles from dropsonde observations; in contrast, a classic Ekman-type method tends to overpredict inflow-layer depth and magnitude, and two recently developed methods for tropical cyclone environments tend to overpredict near-surface wind speed. When used in LES, the new technique produces vertical profiles of total turbulent stress and estimated eddy viscosity that are similar to values determined from low-level aircraft flights in tropical cyclones. Lastly, temporal spectra from LES produce an inertial subrange for frequencies ≳0.1 Hz, but only when the horizontal grid spacing ≲20 m.

17 WIND ENERGY↗

Large-Scale Synoptic Systems and Fog During the C-FOG Field Experiment

Abstract The goal of this work is to summarize synoptic meteorological conditions during the Coastal Fog (C-FOG) field project that took place onshore and offshore of the Avalon Peninsula, Newfoundland, from 25 August until 8 October 2018. Visibility was measured at three locations at the Ferryland supersite that are about 1 km from each other, and at two additional sites 66 and 76 km to the north. Supporting meteorological measurements included surface winds, air temperature, humidity, pressure, radiation, cloud-base height, and atmospheric thermodynamic profiles from radiosonde soundings. Statistics are presented for surface measurements during fog events including turbulence kinetic energy, net longwave radiation, visibility, and precipitation. Eleven fog events are observed at Ferryland. Each significant fog event is related to a large-scale cyclonic system. The longest fog event is due to interaction of a northern deep low and a tropical cyclone. Fog occurrence is also examined across Atlantic Canada by including Sable Island, Yarmouth, Halifax, and Sydney. It is concluded that at Ferryland, all significant fog events occur under a cyclonic system while at Sable Island all significant fog events occur under both cyclonic and anticyclonic systems. The fog-formation mechanism involves cloud lowering and stratus broadening or only stratus broadening for the cyclonic systems while for the anticyclonic systems it is stratus broadening or radiation. Although widely cited as the main cause of fog in Atlantic Canada, advection fog is not found to be the primary or sole fog type in the events examined.

54 ENVIRONMENTAL SCIENCES↗

Analysis of Coastal Fog from a Ship During the C-FOG Campaign

This work presents ship-based measurements of fog off St John’s Newfoundland on 13 September 2018 during the Coastal Fog (C-FOG) field campaign. The measurements included cloud-particle spectra, cloud-base height and aerosol backscatter, radiation, turbulence, visibility, and sea surface temperature. Radiosonde soundings were made at intervals less than 2 hours. Fog occurred in two episodes under the center of eastward-moving synoptic low-pressure system. The boundary layer structure during the first fog episode consisted of 3 layers, separated by 2 saturated air temperature inversions and capped by a subsidence inversion. The lowest layer was fog and the upper layers were cloud. The second fog episode consisted of one well-mixed fog layer capped by a subsidence inversion. Low wind speeds and stable stratification maintained low surface-layer turbulence during fog. Droplet size distributions had typical bimodal distributions. The visibility correlated with the droplet number concentration and liquid water content. The air temperature was higher than the sea surface temperature for the first 30 minutes of the first fog episode but was colder than the sea for the remainder of all fog. The sensible heat flux was upward, from sea to air, for the first 62 % of the first fog episode and then reversed to downward, from air to sea, for the remainder of the first fog episode and the second fog episode. Here, the counter-gradient heat fluxes observed (i.e., opposite to what is expected from the instantaneous air-sea temperature difference) appear to be related to turbulence, entrainment and stratification in the fog layer that overwhelmed the influence of air-sea temperature difference. While the synoptic-scale dynamics preconditioned the area for fog formation, the final step of fog appearance in this case was nuanced by stratification-turbulence interactions, local advective processes and microphysical environment.

54 ENVIRONMENTAL SCIENCES↗

Study of Stratus-Lowering Marine-Fog Events Observed During C-FOG

Two stratus lowering marine fog events observed on 28 September and 04 October 2018 during the Coastal Fog (C-Fog) field campaign that took place offshore of Eastern Canada during 1 September to 6 October 2018 are described. In-situ, profiling and remote sensing observations were made at selected land sites in eastern Newfoundland (NL) and Nova Scotia (NS) as well as aboard the research vessel (R/V) Hugh R. Sharp that cruised in adjoining coastal waters. Synoptic scale analysis showed that both fog episodes were an outcome of the interaction between synoptic-scale surface level low-pressure systems and a contiguous high-pressure system. At the same time, back trajectories revealed that the bulk of the fog layer is formed due to differential advection. Here, the diameter of the fog droplets at the surface gradually decreased from the centre of the fog layer to its leading/trailing edges. The bimodal fog droplet diameter distribution with peaks at 5-10 µm and 20-25 µm provided clues on droplet collision and coalescence processes. The observed difference between microphysical variables and droplet distribution between the two fog events and within same fog layer may have been governed by atmospheric boundary layer conditions (e.g., humidity conditions and turbulence) prevailed in the fog layer. Overall, it is concluded that the life cycle of observed stratus-lowering coastal-fog episodes is dependent on synoptic conditions as well as atmospheric boundary layer characteristics such as stability, cloud top cooling and entrainment.

54 ENVIRONMENTAL SCIENCES↗

Topography-Induced TKE Budget Behavior Over an Amazon Forest

Data from three different heights (35, 50 and 81 m) of one of the ATTO Project towers in the Amazon forest were used to calculate the TKE (turbulence kinetic energy) budget and some other statistics within the RSL (roughness sublayer). The statistical analyses were carried out for unstable and stable cases. The vertical transport and the vertical advection terms do not explain the imbalances found in the TKE budget, highlighting the impor- tance of horizontal terms in complex terrain. Indeed, patterns independent of the time of day were found for vertical transport, horizontal and vertical velocity skewness, the mean vertical component velocity, and momentum and vertical TKE flux. Here, the highest values of mean vertical velocity were observed from the direction where there is a valley near the tower, which may indicate a topographical effect. Monin-Obukhov Similarity Theory (MOST) predictions for the mean velocity gradient, strictly applicable only in the inertial sublayer (ISL), gave reasonable predictions at 35 and 50 m, but dimensionless dissipation rates displayed large scatter. At 81 m, there were clear deviations from MOST for the two functions, disclosing the effect of topography. In addition, a neutral LES (large-eddy simu- lation) study showed good agreement with tower data for the same general wind direction.

ATTO project↗

Implementation and evaluation of permeability-porosity and tortuosity-porosity relationships linked to mineral dissolution-precipitation

Changes of porosity, permeability, and tortuosity due to physical and geochemical processes are of vital importance for a variety of hydrogeological systems, including passive treatment facilities for contaminated groundwater, engineered barrier systems (EBS), and host rocks for high-level nuclear waste (HLW) repositories. Due to the nonlinear nature and chemical complexity of the problem, in most cases, it is impossible to verify reactive transport codes analytically, and code intercomparisons are the most suitable method to assess code capabilities and model performance. This paper summarizes model intercomparisons for six hypothetical scenarios with generally increasing geochemical or physical complexity using the reactive transport codes CrunchFlow, HP1, MIN 3 P, PFlotran, and TOUGHREACT. Benchmark problems include the enhancement of porosity and permeability through mineral dissolution, as well as near complete clogging due to localized mineral precipitation, leading to reduction of permeability and tortuosity. Processes considered in the benchmark simulations are advective-dispersive transport in saturated media, kinetically controlled mineral dissolution-precipitation, and aqueous complexation. Porosity changes are induced by mineral dissolution-precipitation reactions, and the Carman-Kozeny relationship is used to describe changes in permeability as a function of porosity. Archie’s law is used to update the tortuosity and the pore diffusion coefficient as a function of porosity. Results demonstrate that, generally, good agreement is reached amongst the computer models despite significant differences in model formulations. As a result, some differences are observed, in particular for the more complex scenarios involving clogging; however, these differences do not affect the interpretation of system behavior and evolution.

58 GEOSCIENCES↗

Smoothed Particle Hydrodynamics and its applications for multiphase flow and reactive transport in porous media

Smoothed Particle Hydrodynamics (SPH) is a Lagrangian method based on a meshless discretization of partial differential equations. In this review, we present SPH discretization of the Navier-Stokes and Advection-Diffusion-Reaction equations, implementation of various boundary conditions, and time integration of the SPH equations, and we discuss applications of the SPH method for modeling pore-scale multiphase flows and reactive transport in porous and fractured media.

Tartakovsky, Alexandre M.↗

A model for discrete fracture-clay rock interaction incorporating electrostatic effects on transport

Abstract A model based on the code CrunchClay is presented for a fracture-clay matrix system that takes electrostatic effects on transport into account. The electrostatic effects on transport include those associated with the development of a diffusion potential as captured by the Nernst-Planck equation, and the formation of a diffuse layer bordering negatively charged clay particles within which partial anion exclusion occurs. The model is based on a dual continuum formulation that accounts for diffuse layer and bulk water pore space, providing a more flexible framework than is found in the classical mean electrostatic potential models. The diffuse layer model is obtained by volume averaging ion concentrations in the Poisson-Boltzmann equation, but also includes the treatment of longitudinal transport within this continuum. The calculation of transport within the bulk and diffuse layer porosity is based on a new formulation for the Nernst-Planck equation that considers averaging of diffusion coefficients and accumulation factors at grid cell interfaces. Equations for function residuals and the associated Jacobian matrix are presented such that the system of nonlinear differential-algebraic equations can be solved with Newton’s method. As an example, we consider a 2D system with a single discrete fracture within which flow and advective transport occurs that is coupled to diffusion in the clay-rich matrix. The simulation results demonstrate the lack of retardation for anions (e.g., 36 Cl − ) of the contaminant plume within the fracture flow system because they are largely excluded from the charged clay rock, while the migration of cations (e.g., 90 Sr ++ ) is more strongly attenuated. The diffusive loss of divalent cations in particular from the fracture is accentuated by their accumulation in the diffuse layer within the clay-rich matrix.

58 GEOSCIENCES↗

A mineral precipitation model based on the volume of fluid method

A novel volume of fluid method is presented for mineral precipitation coupled with fluid flow and reactive transport. The approach describes the fluid-solid interface as a smooth transitional region, which is designed to provide the same precipitation rate and viscous drag force as a sharp interface. Specifically, the governing equation of mineral precipitation is discretized by an upwind scheme, and a rigorous effective viscosity model is derived around the interface. The model is validated against analytical solutions for mineral precipitation in channel and ring-shaped structures. It also compares well with interface tracking simulations of advection-diffusion-reaction problems. Here, the methodology is finally employed to model mineral precipitation in fracture networks, which is challenging due to the low porosity and complex geometry. Compared to other approaches, the proposed model has a concise algorithm and contains no free parameters. In the modeling, only the pore space requires meshing, which improves the computational effciency especially for low-porosity media.

58 GEOSCIENCES↗

Log-Correlated Large-Deviation Statistics Governing Huygens Fronts in Turbulence

Analyses have disagreed on whether the velocity u T of bulk advancement of a Huygens front in turbulence vanishes or remains finite in the limit of vanishing local front propagation speed u 0 . Here, a connection to the large-deviation statistics of log-correlated random processes enables a definitive determination of the correct small- u 0 asymptotics. This result reconciles several theoretical and phenomenological perspectives with the conclusion that u T remains finite for vanishing u 0 , which implies a propagation anomaly akin to the energy-dissipation anomaly in the limit of vanishing viscosity. Various leading-order structural properties such as a novel u 0 dependence of a bulk length scale associated with front geometry are predicted in this limit. As a result, the analysis involves a formal analogy to random advection of diffusive scalars.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

An efficient three-dimensional rhizosphere modeling capability to study the effect of root system architecture on soil water and reactive transport

This research was to develop a rhizosphere modeling capability for plant-soil interactions by integrating water and ion uptake and release from three dimensional (3D) root systems and 3D variably saturated flow and multicomponent reactive transport in soil. We combined open source software for simulating plant and soil interactions with parallel processing computational technologies to address highly-resolved root system architecture and soil hydrobiogeochemical processes. Simulation capability was demonstrated on Brachypodium distachyon . Our demonstration problem showed that availability of water and plant nutrients is controlled by the interplay between 1) transpiration-driven cycles of water uptake, root zone saturation and desaturation; 2) sorption and desorption via competitive ion exchange; 3) buildup of ions not taken up during kinetic uptake of nutrients/ions from pore water; and 4) advection, dispersion, and diffusion of ions in the soil. The uptake of water and ions by individual roots leads to dynamic, local gradients in ion concentrations. The resulting higher solution ionic strength can lead to increasing sorption of K+ and NH4+ on the soil exchange sites, despite their preferential absorption by roots. The modeling framework makes it possible to explore alternative conceptual models and improve the understanding of the biogeochemical and physical environment within the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗

Colloid Transport in Porous Media: A Review of Classical Mechanisms and Emerging Topics

To celebrate the tenth anniversary of InterPore, here we present an interdisciplinary review of colloid transport through porous media. This review aims to explore both classical colloid transport and topics that fall outside that purview and thus offer transformative insights into the physics governing transport behavior. First, we discuss the unique colloid characteristics relative to molecules and larger particles. Then, the classical advection–dispersion–filtration models (both conceptual and mathematical) of colloid transport are introduced as well as anomalous transport behaviors. Next, the forces of interaction between colloids and porous media surfaces are discussed. Fourth, applications that are interested in maximizing the transport of colloids through porous media are considered. Then the concept of motile, active biocolloids is introduced, and finally, colloid swarming as a newly recognized mode of transport is summarized.

42 ENGINEERING↗

Seasonal variation of the surface cross-shelf exchange in the northern South China Sea: a Lagrangian perspective

Previous studies on cross-shelf exchange, predominantly adopted an Eulerian perspective, struggled to identify water sources and pathways. Using a high-resolution regional ocean modeling system (ROMS) and Lagrangian particle tracking, this study systematically investigates the seasonal variation and dynamics of surface cross-shelf exchange in the northern South China Sea (NSCS) from a Lagrangian perspective. Based on daily released 30-day drifter trajectories we identify the key pathways, source regions for surface cross-shelf exchange, revealing pronounced seasonal variability. Results show the surface cross-shelf exchange generally following monsoon-driven Ekman transport. However, local dynamics, especially topographic modulation, can outweigh the expected Ekman-driven transport, producing surface exchange patterns opposite to that predicted from the prevailing winds. Topographic effects vary across different scales. In the coastal waters of western Guangdong during winter, despite downwelling-favorable winds, the modulation of alongshore currents by island topography induces an eastward pressure gradient. This gradient, through geostrophic balance, drives offshore flows opposite to wind-driven Ekman onshore transport. Furthermore, the eastern widened shelf exhibits a distinct seasonal variation of cross-shelf exchange, with strong offshore transport (opposite to the direction of Ekman transport) in winter and exceedingly weak exchange in summer. Analysis of the underlying mechanisms reveals that this winter offshore transport is primarily attributed to geostrophic flows driven by surface pressure gradient that is jointly modulated by the Kuroshio intrusion and local widened shelf topography, and enhanced by cumulative submesoscale processes. In summer, a persistent and strong along-isobath jet acts as a dynamic barrier, effectively suppressing the exchange. These findings highlight the important role of topography in regulating surface material transport, and have important implications for predicting the advection and dispersion of plankton or oil spills over the continental shelf influenced by monsoon.

Hao, Dongliang↗

Insights of Boundary Layer Turbulence Over the Complex Terrain of Central Himalaya from GVAX Field Campaign

Limited observations hinder understanding of turbulent characteristics in mountainous terrain resulting from heating or cooling of slopes, wind, vertical motions, and heat or moisture advection, which disperse aerosols and other pollutants over the region. In this study, the 1290 MHz radar wind profiler data are utilized to compute the boundary layer height (BLH), the refractive index structure constant (C n 2 ), and the energy dissipation rate (ε) over the central Himalayan site for the period of November 2011 to March 2012, from the intense Ganges Valley Aerosol Experiment (GVAX) field measurements. The radar wind profiler (RWP) based estimation of BLH and ε is validated against the radiosonde, representing the effectiveness of the datasets for further investigation. The strong seasonal variation of log C n 2 and log ε, with average values of ≈ -12 m -2/3 and -2 m 2 s -3 , respectively, is associated with the mountain-induced local circulations and stability in the atmospheric boundary layer. The weak stratification during weak flow is found to be responsible for deep mixing, particularly in the nocturnal boundary layer in spring. Furthermore, the level of cloud cover significantly impacts the strength of turbulence, with the highest cloud cover resulting in a substantial increase in log C n 2 (approximately -11 m -2/3 ) due to intense updraft and downdraft motions compared to clear skies. Additionally, the distribution of aerosol loading across the site, coupled with the behavior of BLH, atmospheric stability, and orographic-induced circulations, implies distinctive seasonal mechanisms for transporting aerosols toward the mountains. This study offers valuable insights into the diurnal and seasonal patterns of turbulent mixing and the mechanisms behind the transport of pollutants through boundary layer processes over the region.

54 ENVIRONMENTAL SCIENCES↗

Variational multiscale element-free Galerkin method combined with the moving Kriging interpolation for solving some partial differential equations with discontinuous solutions

Solving partial differential equations with discontinuous solutions is an important challenging problem in numerical analysis. To this end, there are some methods such as finite volume method, discontinuous Galerkin approach and particle technique that are able to solve these problems. In the current paper, the moving Kriging element-free Galerkin method has been combined with the variational multiscale algorithm to obtain acceptable and high-resolution solutions. For testing this technique, we select some PDEs with discontinuous solution such as Burgers’, Sod’s shock tube, advection–reaction–diffusion, Kuramoto–Sivashinsky, Boussinesq and shallow water equations. First, we obtain a time-discrete scheme by approximating time derivative via finite difference technique. Then we introduce the moving Kriging interpolation and also obtain their shape functions. We use the element-free Galerkin method for approximating the spatial derivatives. This method uses a weak form of the considered equation that is similar to the finite element method with the difference that in the classical element-free Galerkin method test and trial functions are moving least squares approximation (MLS) shape functions. Since the shape functions of moving least squares (MLS) approximation do not have Kronecker delta property, we cannot implement the essential boundary condition, directly. Thus, we employ the shape functions of moving Kriging interpolation and radial point interpolation technique which have the mentioned property. Also, in the element-free Galekin method, we do not use any triangular, quadrangular or other type of meshes. The element-free Galerkin method is a global method while finite element method is a local one. This technique employs a background mesh for integration which makes it different from the truly mesh procedures. Several test problems are solved and numerical simulations are reported which confirm the efficiency of the proposed schemes.

97 MATHEMATICS AND COMPUTING↗