A general 3D flow-and-transport model in porous media is derived using an axiomatic continuum-mechanics approach and implemented with the finite element method to simulate microbial enhanced oil recovery (MEOR) at core scale under laboratory conditions. The development pipeline (conceptual -> mathematical -> numerical -> computational) is detailed. The model captures clogging/declogging from biomass, changes in interfacial tension due to biosurfactant, and the resulting impact on relative permeability, capillary pressure, and residual oil saturation via a trapping-number framework. The flow model is validated (Buckley-Leverett and coreflood benchmarks); transport (microbes/nutrients/surfactant) is validated against Hendry et al. 1997 breakthrough data. Finally, the model accurately predicts a Berea-core MEOR case study using field microbes and brine, matching recovery histories with small RMS error. Owing to its generality, the framework can be extended to other EOR scenarios and constitutive laws.

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