@article{fdi:010095567,
  title = {{G}eometric modelling of 3{D} pore space using curve skeleton : application to computational microbiology of soil organic matter mineralization},
  author = {{B}elghali, {Z}. and {M}onga, {O}livier and {K}lai, {M}. and {A}bdelwahed, {E}. and {D}ruoton, {L}. and {P}ot, {V}. and {B}aveye, {P}. {C}.},
  editor = {},
  language = {{ENG}},
  abstract = {{R}ecent advances in 3{D} {X}-ray {C}omputed {T}omography ({CT}) sensors have stimulated research efforts to unveil the extremely complex micro-scale processes that control the activity of soil microorganisms. {C}lassical methods for the numerical simulation of biological dynamics using meshes of voxels, such as the {L}attice {B}oltzmann {M}ethod ({LBM}), tend to require long computation times. {T}he use of more compact geometrical representations of the pore space can drastically decrease the computational cost of simulations. {R}ecent research has introduced basic analytic volume primitives to define piece-wise approximations of the pore space to simulate drainage, diffusion, and microbial mineralization of organic matter in soils. {S}uch approaches work well but a drawback is that they give rise to significant approximation errors caused by imposing a priori shapes to represent the pores. {I}n the present article, another alternative is proposed, where pore space is described by means of geometrically relevant connected subsets of voxels (regions) regrouped on the basis of the curve skeleton (3{D} medial axis). {T}he curve skeleton has been adopted to characterize 3{D} shapes in various fields (e.g., medical imaging, material sciences, etc.). {T}he few publications that have used it in the context of soils have dealt exclusively with the determination of pore throats. {T}his technique is used mostly to describe shape and not to partition it into connected subsets like in the present work. {H}ere, the pore space is partitioned by using the branches of the curve skeleton, then an {A}ttributed {R}elational {G}raph ({ARG}) is created in order to simulate numerically the microbial mineralization of organic matter, including the diffusion of by-products. {E}ach node of the {ARG} is attached to an element of the partition (pore) and each arc to an adjacency relationship between pores (connectivity). {T}he graph is valuated in the sense that the attributes related both to geometry and dynamic are linked to nodes and arcs. {T}his new representation can be used for graph-based simulations, which are different from voxel-based simulations.},
  keywords = {},
  booktitle = {},
  journal = {{PL}o{S} {O}ne},
  volume = {20},
  numero = {11},
  pages = {e0331031 [24 p.]},
  year = {2025},
  DOI = {10.1371/journal.pone.0331031},
  URL = {https://www.documentation.ird.fr/hor/fdi:010095567},
}