PhD Comprehensive Exam | Julien Smith-Roberge, A Modelling Framework for Bacterial Colonies Exhibiting Contact-Based Interactions

MC 6460

Candidate

Julien Smith-Roberge | Applied Math, University of Waterloo

Title

A Modelling Framework for Bacterial Colonies Exhibiting Contact-Based Interactions

 Abstract

Advances in cell tracking algorithms and experimental techniques have made it possible for researchers to observe thousands of cells over the course of a single experiment, collecting quantitative data on cell states and tracking their lineages. Agent-based modelling techniques can mirror this single-cell resolution and realistically replicate the complex dynamics of microbial communities. However, this level of detail comes at the cost of analytical tractability. Using appropriate coarse-graining techniques, we can approximate these agent-based models with partial differential equations (PDEs). We propose a three step pipeline, starting with cell-tracking experiments, progressing through agent-based simulations, and finally ending in a PDE model, which would allow researchers to obtain robust mathematical descriptions of microbial system grounded in real-world data. Applications to systems involving contact based cell-cell interaction are discussed.