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24, chemin de Borde Rouge -Auzeville - CS52627 31326 Castanet Tolosan cedex - France

Last update: May 2021

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MOSAIC - Olivier Monga IRD

The mode is based on a geometric approaches to simulate soil structure, (Ngom et al.,2012, Monga et al. 2014).


Author(s) Name(s) and Affiliation : Oliver Monga, IRD, Patricia Garnier INRA, Valérie Pot INRA


Mosaic model (Monga et al., 2008) simulates organic matter decomposition in the 3D pore space of soil.  The model explicitly describes the 3-D distribution of substrate and degraders and their spatial interactions within real CT images of soil. The 3D spatial model was used to test the impact of (i) spatial connectivity between substrate and degraders (Monga et al., 2008, 2009), (ii) the impact of water content on degradation (Monga et al., 2014) and (iii) the impact of soil structure on degradation (Ngom et al., 2011).

The geometry of the pore space was approximated by a network of volume primitives Ngom et al. (2012). We used a geometrical algorithm based on Delaunay triangulation to calculate the set of maximal spheres that describe the pore space geometry. Then we extracted a minimal set of the maximal spheres in order to obtain a compact representation of the pore space. A relational attributed valuated graph (‘graph based approach’) was attached to the spheres. Dissolved organic matter (DOM), coming from the hydrolysis of solid organic matter was one intermediate compartment that that can be submitted to mechanistic of diffusion in pores. DOM diffuses between spheres, where it is assimilated and mineralized using Monod kinetic. The microbial decomposition simulation was processed by graph updating using time discretization. The implementation of the diffusion process of DOM within water filled pore space by updating the valuated graph representing the pore network was performed according to classical diffusion scheme. The distribution of air and water in the sphere network was performed by applying an algorithm based on the Young-Laplace law in the sample border to determine spheres filled with water according to water potential. We assumed that only water filled sphere can mineralized organic matter.

Scientific articles

Monga O., P. Garnier, V. Pot, E. Coucheney, N. Nunan, W. Otten, C. Chenu. 2014. Simulating microbial degradation of organic matter in a simple porous system using the 3D diffusion based model MOSAIC. Biogeosciences, 11, 2201–2209.

Ngom N.F., Monga O., Ould Mohamed M.M., Garnier P. 2012. 3D shape extraction segmentation and representation of soil microstructures using generalized cylinders.. Computers & Geosciences. 39 : 50-63.

Ngom FN., Garnier P., Monga O., Peth S. 2011. Extraction of 3-D soil pore space from microtomography images using a geometrical approach. Geoderma. 163 : 127-134.

Monga O., Bousso M., Garnier P., Pot V. 2009. Using pore space 3D geometrical modeling to simulate biological activity: impact of soil structure. Computer & Geosciences. 35 : 1789-1801.

Monga O., Bousso M., Garnier P., Pot V. 2008. 3D geometrical structures and biological activity: application to soil organic matter microbial decomposition in pore space. Ecological Modelling. 216 : 291-302.