49,615 research outputs found

    Emergent behavior of soil fungal dynamics:influence of soil architecture and water distribution

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    Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a "looped" configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass

    On pore-scale modeling and simulation of reactive transport in 3D geometries

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    Pore-scale modeling and simulation of reactive flow in porous media has a range of diverse applications, and poses a number of research challenges. It is known that the morphology of a porous medium has significant influence on the local flow rate, which can have a substantial impact on the rate of chemical reactions. While there are a large number of papers and software tools dedicated to simulating either fluid flow in 3D computerized tomography (CT) images or reactive flow using pore-network models, little attention to date has been focused on the pore-scale simulation of sorptive transport in 3D CT images, which is the specific focus of this paper. Here we first present an algorithm for the simulation of such reactive flows directly on images, which is implemented in a sophisticated software package. We then use this software to present numerical results in two resolved geometries, illustrating the importance of pore-scale simulation and the flexibility of our software package.Comment: 15 pages, 6 figure

    A new ghost cell/level set method for moving boundary problems:application to tumor growth

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    In this paper, we present a ghost cell/level set method for the evolution of interfaces whose normal velocity depend upon the solutions of linear and nonlinear quasi-steady reaction-diffusion equations with curvature-dependent boundary conditions. Our technique includes a ghost cell method that accurately discretizes normal derivative jump boundary conditions without smearing jumps in the tangential derivative; a new iterative method for solving linear and nonlinear quasi-steady reaction-diffusion equations; an adaptive discretization to compute the curvature and normal vectors; and a new discrete approximation to the Heaviside function. We present numerical examples that demonstrate better than 1.5-order convergence for problems where traditional ghost cell methods either fail to converge or attain at best sub-linear accuracy. We apply our techniques to a model of tumor growth in complex, heterogeneous tissues that consists of a nonlinear nutrient equation and a pressure equation with geometry-dependent jump boundary conditions. We simulate the growth of glioblastoma (an aggressive brain tumor) into a large, 1 cm square of brain tissue that includes heterogeneous nutrient delivery and varied biomechanical characteristics (white matter, gray matter, cerebrospinal fluid, and bone), and we observe growth morphologies that are highly dependent upon the variations of the tissue characteristics—an effect observed in real tumor growth

    Numerical simulation of combined mixing and separating flow in channel filled with porous media

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    Various flow bifurcations are investigated for two dimensional combined mixing and separating geometry. These consist of two reversed channel flows interacting through a gap in the common separating wall filled with porous media of Newtonian fluids and other with unidirectional fluid flows. The Steady solutions are obtained through an unsteady finite element approach that employs a Taylor-Galerkin/pressure-correction scheme. The influence of increasing inertia on flow rates are all studied. Close agreement is attained with numerical data in the porous channels for Newtonian fluids.Peer reviewedSubmitted Versio

    Wall Orientation and Shear Stress in the Lattice Boltzmann Model

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    The wall shear stress is a quantity of profound importance for clinical diagnosis of artery diseases. The lattice Boltzmann is an easily parallelizable numerical method of solving the flow problems, but it suffers from errors of the velocity field near the boundaries which leads to errors in the wall shear stress and normal vectors computed from the velocity. In this work we present a simple formula to calculate the wall shear stress in the lattice Boltzmann model and propose to compute wall normals, which are necessary to compute the wall shear stress, by taking the weighted mean over boundary facets lying in a vicinity of a wall element. We carry out several tests and observe an increase of accuracy of computed normal vectors over other methods in two and three dimensions. Using the scheme we compute the wall shear stress in an inclined and bent channel fluid flow and show a minor influence of the normal on the numerical error, implying that that the main error arises due to a corrupted velocity field near the staircase boundary. Finally, we calculate the wall shear stress in the human abdominal aorta in steady conditions using our method and compare the results with a standard finite volume solver and experimental data available in the literature. Applications of our ideas in a simplified protocol for data preprocessing in medical applications are discussed.Comment: 9 pages, 11 figure

    Diffusion in pores and its dependence on boundary conditions

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    We study the influence of the boundary conditions at the solid liquid interface on diffusion in a confined fluid. Using an hydrodynamic approach, we compute numerical estimates for the diffusion of a particle confined between two planes. Partial slip is shown to significantly influence the diffusion coefficient near a wall. Analytical expressions are derived in the low and high confinement limits, and are in good agreement with numerical results. These calculations indicate that diffusion of tagged particles could be used as a sensitive probe of the solid-liquid boundary conditions.Comment: soumis \`a J.Phys. Cond. Matt. special issue on "Diffusion in Liquids, Polymers, Biophysics and Chemical Dynamics
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