Mechanical Constraint and Cell Shape Interaction Modeling of Bacterial Growth in Microfluidic Traps

Modeling mechanical interactions of bacteria is integral to capturing their dynamics in close-knit populations, because mechanical signals can be a primary means of inter-cellular communication in these environments. Agent-based models are used to study such mechanical interactions; however, conventional frameworks usually neglect the role of mechanical constraint and its coupling to other cellular dynamics. Continuum models often neglect sufficient description of cellular ordering dynamics, which depend on the complex interactions of cell shape anisotropy and shear flow that can originate from cellular growth expansion.

In this thesis, we present models for the study of mechanical interactions of bacterial consortia in microfluidic traps. We include in our study an agent-based model that directly incorporates mechanical growth inhibition into the dynamics of the model and we show how emergent dynamics can be shaped by differences in model parameters. We also study a continuum model that considers growth through the evolution of the cell pressure and the resulting spatially-mapped velocity gradients. Our continuum model borrows ordering dynamics equations from liquid crystal theory in a two-dimensional setting and we use our model to predict how both persistent order and disorder can exist among close-packed bacterial cells in a microfluidic trap .

Further, we explore the impact of dynamic aspect ratio control on bacterial consortia and show how it can be used as a population control modality. We conclude with a conjecture and model for the modulation of a protein production rate by mechanical constraint that helps explain anomalous experiments.