Statistical Effective Diffusivity Estimation in Porous Media Using an Integrated On-site Imaging Workflow for Synchrotron Users.

Transport in porous media plays an essential role for many physical, engineering, biological and environmental processes. Novel synchrotron imaging techniques and image-based models have enabled more robust quantification of geometric structures that influence transport through the pore space. However, image-based modelling is computationally expensive, and end users often require, while conducting imaging campaign, fast and agile bulk-scale effective parameter estimates that account for the pore-scale details. In this manuscript we enhance a pre-existing image-based model solver known as OpenImpala to estimate bulk-scale effective transport parameters. In particular, the boundary conditions and equations in OpenImpala were modified in order to estimate the effective diffusivity in an imaged system/geometry via a formal multi-scale homogenisation expansion. Estimates of effective pore space diffusivity were generated for a range of elementary volume sizes to estimate when the effective diffusivity values begin to converge to a single value. Results from OpenImpala were validated against a commercial finite element method package COMSOL Multiphysics (abbreviated as COMSOL). Results showed that the effective diffusivity values determined with OpenImpala were similar to those estimated by COMSOL. Tests on larger domains comparing a full image-based model to a homogenised (geometrically uniform) domain that used the effective diffusivity parameters showed differences below 2 % error, thus verifying the accuracy of the effective diffusivity estimates. Finally, we compared OpenImpala's parallel computing speeds to COMSOL. OpenImpala consistently ran simulations within fractions of minutes, which was two orders of magnitude faster than COMSOL providing identical supercomputing specifications. In conclusion, we demonstrated OpenImpala's utility as part of an on-site tomography processing pipeline allowing for fast and agile assessment of porous media processes and to guide imaging campaigns while they are happening at synchrotron beamlines. Supplementary Information: The online version contains supplementary material available at 10.1007/s11242-023-01993-7.

Space and time-resolved monitoring of phosphorus release from a fertilizer pellet and its mobility in soil using microdialysis and X-ray computed tomography.

Phosphorus is an essential nutrient for crops. Precise spatiotemporal application of P fertilizer can improve plant P acquisition and reduce run-off losses of P. Optimizing application would benefit from understanding the dynamics of P release from a fertilizer pellet into bulk soil, which requires space- and time-resolved measurements of P concentration in soil solutions. In this study, we combined microdialysis and X-ray computed tomography to investigate P transport in soil. Microdialysis probes enabled repeated solute sampling from one location with minimal physical disturbance, and their small dimensions permitted spatially resolved monitoring. We observed a rapid initial release of P from the source, producing high dissolved P concentrations within the first 24 h, followed by a decrease in dissolved P over time compatible with adsorption onto soil particles. Soils with greater bulk density (i.e., reduced soil porosity) impeded the P pulse movement, which resulted in a less homogeneous distribution of total P in the soil column at the end of the experiment. The model fit to the data showed that the observed phenomena can be explained by diffusion and adsorption. The results showed that compared with conventional measurement techniques (e.g., suction cups), microdialysis measurements present a less invasive alternative. The time-resolved measurements ultimately highlighted rapid P dynamics that require more attention for improving P use efficiency.

Linking root structure to functionality: the impact of root system architecture on citrate-enhanced phosphate uptake.

Root citrate exudation is thought to be important for phosphate solubilization. Previous research has concluded that cluster-like roots benefit most from this exudation in terms of increased phosphate uptake, suggesting that root structure plays an important role in citrate-enhanced uptake (additional phosphate uptake due to citrate exudation). Time-resolved computed tomography images of wheat root systems were used as the geometry for 3D citrate-phosphate solubilization models. Citrate-enhanced uptake was correlated with morphological measures of the root systems to determine which had the most benefit. A large variation of citrate-enhanced uptake over 11 root structures was observed. Root surface area dominated absolute phosphate uptake, but did not explain citrate-enhanced uptake. Number of exuding root tips correlated well with citrate-enhanced uptake. Root tips in close proximity could collectively exude high amounts of citrate, resulting in a delayed spike in citrate-enhanced uptake. Root system architecture plays an important role in citrate-enhanced uptake. Singular morphological measurements of the root systems cannot entirely explain variations in citrate-enhanced uptake. Root systems with many tips would benefit greatly from citrate exudation. Quantifying citrate-enhanced uptake experimentally is difficult as variations in root surface area would overwhelm citrate benefits.

Root-induced soil deformation influences Fe, S and P: rhizosphere chemistry investigated using synchrotron XRF and XANES.

Rhizosphere soil has distinct physical and chemical properties from bulk soil. However, besides root-induced physical changes, chemical changes have not been extensively measured in situ on the pore scale. In this study, we couple structural information, previously obtained using synchrotron X-ray computed tomography (XCT), with synchrotron X-ray fluorescence microscopy (XRF) and X-ray absorption near-edge structure (XANES) to unravel chemical changes induced by plant roots. Our results suggest that iron (Fe) and sulfur (S) increase notably in the direct vicinity of the root via solubilization and microbial activity. XANES further shows that Fe is slightly reduced, S is increasingly transformed into sulfate (SO42- ) and phosphorus (P) is increasingly adsorbed to humic substances in this enrichment zone. In addition, the ferrihydrite fraction decreases drastically, suggesting the preferential dissolution and the formation of more stable Fe oxides. Additionally, the increased transformation of organic S to sulfate indicates that the microbial activity in this zone is increased. These changes in soil chemistry correspond to the soil compaction zone as previously measured via XCT. The fact that these changes are colocated near the root and the compaction zone suggests that decreased permeability as a result of soil structural changes acts as a barrier creating a zone with increased rhizosphere chemical interactions via surface-mediated processes, microbial activity and acidification.

Multiple Scale Homogenisation of Nutrient Movement and Crop Growth in Partially Saturated Soil.

In this paper, we use multiple scale homogenisation to derive a set of averaged macroscale equations that describe the movement of nutrients in partially saturated soil that contains growing potato tubers. The soil is modelled as a poroelastic material, which is deformed by the growth of the tubers, where the growth of each tuber is dependent on the uptake of nutrients via a sink term within the soil representing root nutrient uptake. Special attention is paid to the reduction in void space, resulting change in local water content and the impact on nutrient diffusion within the soil as the tubers increase in size. To validate the multiple scale homogenisation procedure, we compare the system of homogenised equations to the original set of equations and find that the solutions between the two models differ by [Formula: see text]. However, we find that the computation time between the two sets of equations differs by several orders of magnitude. This is due to the combined effects of the complex three-dimensional geometry and the implementation of a moving boundary condition to capture tuber growth.