Nutrients are absorbed in the small intestines at a mucosal epithelium that covers multitudes of villi, fingerlike protrusions ~200-400 ?m in scale. The villi line the mucosal surface and have been observed to move in response to local stimulation. Luminal contractions (motility) create macroscale fluid motions that transport nutrient molecules to the epithelium surrounding these moving micro-scale villi. We combine multi-scale modeling with dynamic magnetic resonance imaging (MRI) of the motions of the gut lumen to investigate the hypothesis that gut function requires the coupling of macro-micro scale fluid motions generated by lumen-scale motility with micro-scale motions generated by moving villi. We have developed 2-D models within the lattice-Boltzmann framework with second-order moving boundary conditions for velocity and for passive "nutrient" scalar concentrations. The first model was used to study the relative contributions of macro-scale peristaltic and segmental contractions on transport, mixing and absorption in the intestines. The macro-scale gut motions were quantified from time-resolved MRI of the in vivo rat jejunum using three-dimensional segmentation. The simulations show that segmental and peristaltic motions have disparate roles in fluid motion and nutrient absorption. The gut wall motions were decomposed with principle component analysis and analyzed using topographic space-time representations of deformation. These results suggest that the neurophysiology can produce a wide range of complex contractile patterns by stimulating only a few basic modes with varying phase relationship (MRI) and that absorption is optimized with segmental contraction with peristalsis interfering in absorption (modeling). To analyze the role of the villi in absorption, we designed a second 2-D model that mimics intestinal macro-micro scale flow interactions. Along the lower surface of a lid-driven macro-scale cavity flow we modeled a series of micro-scale "villi" with controlled coordinated motions using a multi-grid lattice-Boltzmann method. We discover the existence of a villi-induced "micro-mixing" layer that couples with the macro-scale motions to enhance absorption and show that a common assumption is incorrect in 2-D. These models have recently been extended to 3-D and will be combined in the future.