49,615 research outputs found
Emergent behavior of soil fungal dynamics:influence of soil architecture and water distribution
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
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
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
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
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
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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