Imaging microstructure of the barley rhizosphere:particle packing and root hair influences

Soil adjacent to roots has distinct structural and physical properties from bulk soil, affecting water and solute acquisition by plants. Detailed knowledge on how root activity and traits such as root hairs affect the three-dimensional pore structure at a fine scale is scarce and often contradictory. Roots of hairless barley (Hordeum vulgare L. cv Optic) mutant (NRH) and its wildtype (WT) parent were grown in tubes of sieved (&lt;250 μm) sandy loam soil under two different water regimes. The tubes were scanned by synchrotron-based X-ray computed tomography to visualise pore structure at the soil–root interface. Pore volume fraction and pore size distribution were analysed vs distance within 1 mm of the root surface. Less dense packing of particles at the root surface was hypothesised to cause the observed increased pore volume fraction immediately next to the epidermis. The pore size distribution was narrower due to a decreased fraction of larger pores. There were no statistically significant differences in pore structure between genotypes or moisture conditions. A model is proposed that describes the variation in porosity near roots taking into account soil compaction and the surface effect at the root surface.</p

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high resolution (~5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare L.), with and without root hairs, were grown for 8 days in microcosms packed with sandy loam soil at 1.2 g cm-3 36 dry bulk density. Root hairs were visualised within air filled pore spaces, but not in the fine-textured soil regions. - We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (&gt; 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore-space between 0.8 mm and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. - Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image based modelling

LEGO® bricks as building blocks for centimeter-scale biological environments

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil

A lattice BGK model for advection and anisotropic dispersion equation

This paper presents a lattice Boltzmann model (LBM) for 2-D advection and anisotropic dispersion equation (AADE) based on the Bhatnagar, Gross and Krook (BGK) model. In the proposed model, the particle speed space is discretized using a rectangular lattice that has four speeds in nine directions, and the single relaxation time is assumed to be directionally dependent. To ensure that the collision is mass-invariant when the relaxation time is directionally dependent, the concentration is calculated from a weighted summation of the particle distribution functions. The proposed model was verified against benchmark problems and the finite difference solution of solute transport with spatially variable dispersion coefficients and non-uniform velocity field. The significant results are that it conserves mass perfectly and offers accurate and efficient solutions for both dispersion-dominated and advection-dominated problems

Performance evaluation of the cell-based algorithms for domain decomposition in flow simulation

Purpose The cell‐based method of domain decomposition was first introduced for complex 3D geometries. To further assess the method, the aim is to carry out flow simulation in rectangular ducts to compare the known analytical solutions. Design/methodology/approach The method is not based on equal subvolumes but on equal numbers of active cells. The variables of the simulation are stored in ordered 1D arrays to replace the conventional 3D arrays, and the domain decomposition of the complex 3D problems therefore becomes 1D. Finally, the 3D results can be recovered using a coordinate matrix. Through the flow simulation in the rectangular ducts how the algorithm of the domain decompositions works was illustrated clearly, and the numerical solution was compared with the exact solutions. Findings The cell‐based method can find the subdomain interfaces successfully. The parallelization based on the algorithm does not cause additional errors. The numerical results agree well with the exact solutions. Furthermore, the results of the parallelization show again that domains of 3D geometries can be decomposed automatically without inducing load imbalances. Practical implications Although, the approach is illustrated with lattice Boltzmann method, it is also applicable to other numerical methods in fluid dynamics and molecular dynamics. Originality/value Unlike the existing methods, the cell‐based method performs the load balance first based on the total number of fluid cells and then decomposes the domain into a number of groups (or subdomains). Thus, the task of the cell‐based method is to recover the interface rather than to balance the load as in the traditional methods. This work has examined the celled‐based method for the flow in rectangular ducts. The benchmark test confirms that the cell‐based domain decomposition is reliable and convenient in comparison with the well‐known exact solutions

Domain-decomposition method for parallel lattice Boltzmann simulation of incompressible flow in porous media

The lattice Boltzmann method has proven to be a promising method to simulate flow in porous media. Its practical application often relies on parallel computation because of the demand for a large domain and fine grid resolution to adequately resolve pore heterogeneity. The existing domain-decomposition methods for parallel computation usually decompose a domain into a number of subdomains first and then recover the interfaces and perform the load balance. Normally, the interface recovery and the load balance have to be performed iteratively until an acceptable load balance is achieved; this costs time. In this paper we propose a cell-based domain-decomposition method for parallel lattice Boltzmann simulation of flow in porous media. Unlike the existing methods, the cell-based method performs the load balance first to divide the total number of fluid cells into a number of groups (or subdomains), in which the difference of fluid cells in each group is either 0 or 1, depending on if the total number of fluid cells is a multiple of the processor numbers; the interfaces between the subdomains are recovered at last. The cell-based method is to recover the interfaces rather than the load balance; it does not need iteration and gives an exact load balance. The performance of the proposed method is analyzed and compared using different computer systems; the results indicate that it reaches the theoretical parallel efficiency. The method is then applied to simulate flow in a three-dimensional porous medium obtained with microfocus x-ray computed tomography to calculate the permeability, and the result shows good agreement with the experimental data

A lattice BGK model for advection and anisotropic dispersion equation

This paper presents a lattice Boltzmann model (LBM) for 2-D advection and anisotropic dispersion equation (AADE) based on the Bhatnagar, Gross and Krook (BGK) model. In the proposed model, the particle speed space is discretized using a rectangular lattice that has four speeds in nine directions, and the single relaxation time is assumed to be directionally dependent. To ensure that the collision is mass-invariant when the relaxation time is directionally dependent, the concentration is calculated from a weighted summation of the particle distribution functions. The proposed model was verified against benchmark problems and the finite difference solution of solute transport with spatially variable dispersion coefficients and non-uniform velocity field. The significant results are that it conserves mass perfectly and offers accurate and efficient solutions for both dispersion-dominated and advection-dominated problems