Modeling flow, transport, and microbial dynamics in realistic intestinal geometries

The intestinal surface comprises a complex architecture of villi (finger-like projections) and crypts (cavities between the villi). In this work, we aim to understand the role of the intestinal surface in nutrient absorption and microbial dynamics in the presence of an unsteady flow field. To model the flow, we solve the Navier-Stokes equation with an axisymmetric formulation in a cylindrical domain consisting of radially protruding villi. We prescribe a Womersley solution for the inlet condition of the flow to model the effect of peristalsis due to gut motility. Nutrient and bacterial dynamics are solved by coupled nonlinear reaction-advection-diffusion equations with Monod kinetics. The research provides fundamental insights into the fluid dynamics and transport in the gut in healthy and diseased conditions and has implications for developing therapeutic strategies against gastrointestinal disorders. Our numerical approach is flexible and can be adapted to model a range of intestinal flow conditions and reaction kinetics for nutrients and the gut microbiome.