Hello everyone,

I will defend my PhD on Thursday September 11th at 2pm in the amphi Charpak, you are all welcome to join! The defense will be in english. 

Here is the title and abstract :

Multi-scale modeling of transport in the gastrointestinal tract

Transport in the digestive tract is important for nutrient absorption, as well as for the dynamics of the gut microbiota. However, transport in the digestive tract is poorly characterized. This is due in particular to the complexity of interactions between wall movements, intestinal structures and microbial dynamics. This thesis models several aspects of this transport.

In the first chapter, the density of structures such as villi (in the small intestine) and crypts (in the colon) that maximize absorption is calculated analytically, assuming that these structures are static, and that transport is diffusive in their vicinity. While it is often thought that more surface area necessarily increases absorption, structures too close together limit diffusion. There is therefore a finite optimum distance between these structures. Physiological data from various animal species align with the optimal range predicted by the model. This suggests that evolution may have optimized these structures to promote absorption.

In the second chapter, we focus on the opposite effect: as the walls of the digestive tract on which the villi are located move, the space between villi can vary, resulting in flow. Computational fluid dynamics simulations allow us to systematically explore the impact of the spatial period of the contraction wave on the thickness of the layer where villi movement leads to mixing, and on the resulting net flow in the intestinal lumen. The latter corresponds to what an analytical approximation predicts.

In the third part, I focus on the flow and transport of molecules generated by longitudinal contractions in the digestive tract. Idealized contractions are implemented in computational fluid dynamics simulations. In these simulations, particle trajectories are tracked, and an effective diffusion coefficient is calculated.

In the final chapter, we look at the impact of transport on competition between bacterial strains, taking the simplest description of transport, which focuses solely on the longitudinal position along the digestive tract, and considers the mean flow velocity and an effective diffusion coefficient representing mixing. We consider a flow of one nutrient at the inlet, and two bacterial strains, one that replicates faster when nutrient is abundant, and the other that acquires it better when it becomes limiting. If there is no spatial structure and the strains are limited by the same nutrient, there is no possible coexistence between them. Through a combination of simulations and analytical approximations, we determine in which parameter space the flow-induced spatial structure allows such strains to coexist.

This work contributes to a better understanding of the interplay between transport in the intestines and the function of the digestive tract, such as absorption and the promotion of a diverse microbiota.