The permeability of rocks has a critical influence on their fluid transport response in critical geo-environmental applications, such as pollutant transport or underground storage of hazardous nuclear waste. In such processes, the materials microstructure may be altered as a result of various stimuli, thereby impacting the fluid transfer properties. Stress or strain state modifications are one of the main causes for such evolutions. To numerically address this concern, an integrated and automated numerical tool was developed and illustrated on subsets of microCT scans of a Vosges sandstone (i) to explore the links between the pore space properties and the corresponding macroscopic transfer properties, with (ii) an incorporation of the microstructural alterations associated with stress state variations by using a realistic image-based representation of the microstructural morphology. The ductile mechanical deformation behavior under high confining pressures at the scale of the microstructure, inducing pore closures by local plastifications, was modelled using finite elements simulations with a non-linear elastoplastic law, allowing to take into account the redistribution of local stresses. These simulations require robust discretization tools to capture the complex geometry of the porous network and the corresponding solid boundaries of the heterogeneous microstructural geometries. To achieve this, an integrated approach for the conformal discretization of complex implicit geometries based on signed distance fields was developed, producing high quality meshes from both imaging techniques and computational RVE generation methodologies. This conforming discretization approach was compared with an incompatible mode-based framework using a non conforming approach. This comparison highlighted the complementarity of both methods, the former capturing the effect of more detailed geometrical features, while the latter is more flexible as it allows using the same (non conforming) mesh for potentially variable geometries.The evolution of permeability was evaluated at different confining pressure levels using the Lattice-Bolzmann method. This uncoupled solid-fluid interaction made it possible to study the combined influence on the permeability, porosity and the pores size distribution of the pore space morphology and the solid skeleton constitutive law parameters during loading and unloading conditions. The results highlight the need to consider elastoplastic laws and heterogeneities in the rock model to simulate the ductile behavior of rocks at high confining pressures leading to significant permeability alterations under loading, and irreversible alterations under loading/unloading cycles induced by progressive pore closures.The proposed methodology is designed to be flexible thanks to the interfacing with 'classical' discretization approaches and can be easily readapted to other contexts given the block approach. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished