Abstract
Partial Differential Equations (PDEs) have been already widely used to simulate various complex phenomena in porous media. This paper is one of the first attempts to apply PDEs for simulating in real 3D structures. We apply this scheme to the specific case study of the microbial decomposition of organic matter in soil pore space. We got a 3D geometrical representation of the pore space relating to a network of volume primitives. A mesh of the pore space is then created by using the network. PDEs system is solved by free finite elements solver Freefem3d in the particular mesh. We validate our PDEs model to experimental data with 3D Computed Tomography (CT) images of soil samples. Regarding the current state of art on soil organic matter decay models, our approach allows taking into account precise 3D spatialization of the decomposition process by a pore space geometry description.
Highlights
It is a fact that soil structure is a heterogeneous media and organic matter decomposition in soil is one of the most complex ecological processes
We focus on the Partial Differential Equations (PDEs) method because 1) PDEs have been widely used to simulate various complex phenomena, including transformation and diffusion processes in porous media but few studies have used this approach to biological soil systems; 2) the recently increasing performances of computer PDE solvers make it possible to simulate more and more complex systems
The soil columns were scanned by means of a high resolution micro-Computed Tomography (CT) machine (SIMCT Equipment: SIMBIOS, University of Abertay Dundee, Scotland) operating at 90 KeV and a current of 112 mA
Summary
It is a fact that soil structure is a heterogeneous media and organic matter decomposition in soil is one of the most complex ecological processes. The nature of organic matter, the dynamic of microorganisms, the environmental conditions etc. Despite that microbial dynamics plays an important role in soil organic matter decomposition, the majority of organic matter models make the assumption that carbon limitation is controlled only by the intrinsic degradability of organic matter [1]. Some attempts were made to simulate enzyme diffusion in artificial structured environments [6,7]. None of these models consider explicitly the real 3D soil structure. The improved performance of 3D X-ray computed tomography sensors makes it possible to obtain very high resolution images of soil sample volume
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