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Soil desiccation cracking typically exhibits a hierarchical structure in homogeneous materials but is often disrupted by inherent heterogeneities. The processes governing the degradation and potential recovery of this hierarchy remain poorly understood. This study investigates these mechanisms using an advanced three-dimensional discrete-element method (DEM) model that explicitly simulates surface evaporation and internal moisture transfer to simulate sequential crack propagation. By introducing non-shrinkable inclusions at varying contents (0–30%) to represent heterogeneity, it is revealed that increased inclusion content degrades the hierarchical pattern, shifting crack initiation to multiple points and favouring Y-shaped junctions (∼120°) over perpendicular intersections. A critical inclusion content of 10% is identified, marking the threshold where stress influence zones of inclusions significantly overlap. Below this threshold, initial hierarchy loss can recover during subsequent drying. Once exceeded, the hierarchical breakdown is permanent. The degradation and recovery of hierarchy are fundamentally governed by the evolution of the internal tensile stress field, which transitions between a progressive state (promoting hierarchy) and a concentrated state (disrupting it). These findings provide novel micromechanical insights into cracking patterns and advance the predictive modelling of desiccation cracking in natural, heterogeneous soils.

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