Flux Balance Analysis & Reductive Stress in Biofilms
Coupling flux balance analysis with reaction–diffusion PDEs to model oxygen-driven reductive stress in microbial biofilms.
How does oxygen availability drive reductive stress in a Pseudomonas aeruginosa biofilm? This project couples genome-scale metabolic modeling (flux balance analysis) with reaction–diffusion PDEs to capture how metabolism plays out across space and time. A key contribution is measuring reductive stress as a flux — the NADH a cell is forced to dump without oxygen — and showing that the biofilm core naturally becomes oxygen-limited and high-stress.
This is the basis of my first-author preprint (Senya et al., bioRxiv 2026).
Tools: Python, COBRApy, SBML (iSD1509 genome-scale model), reaction–diffusion PDEs.