Bacterial microcompartments are protein-based organelles that organize and enhance chemical reactions inside cells. They are remarkable examples of how biological systems achieve efficiency through spatial organization. Our research seeks to understand how these structures assemble, how their geometry and permeability emerge from molecular interactions, and how environmental conditions influence their stability and function. We combine physical modeling and simulation to uncover the principles that govern their formation and dynamic behavior. By identifying what makes certain microcompartments robust or adaptable, we aim to reveal general design rules for protein-based compartments. This work has implications for both fundamental biology and the development of engineered microreactors for biotechnology.