UC Berkeley

Living systems offer a richness of behaviors that are of broad interest to many fields of science. For instance, cells that are dwelling in their natural environment are mostly subject not only to the scarcity of energy resources, but also the space in which they can grow and live. This space limitation eventually leads to the emergence of contact forces (mechanical stress) between neighboring cells or the cells and their confining environment. These emergent forces may further have a crucial impact on the cells' biology, the dynamics of the whole population, or even the integrity of confinement (resulting in the remodeling of the environment). Even though the general importance of these forces has been widely recognized, technical difficulties and the complexity of the emergent phenomena prevented much progress in this direction. In this thesis, using mostly computer simulations, I make steps towards overcoming these barriers. In the first part of this thesis, I describe, on the coarse level, how the geometric properties of micro-confinement entails clogging of the microbial populations of Saccharomyces cerevisiae. These clogged populations are found to be quite disordered, with intermittent growth dynamics and heterogeneous mechanical stresses - properties much more like those of granular materials than a continuum. Thus, granular materials are an appealing framework to describe dense microbial populations. However, using a simple 2D model, I numerically show that the coupling between cellular growth rate and mechanical stress gives rise to deviation from the expected behavior of inanimate granular materials, and it increases the complexity of the emergent phenomena. The simple and coarse model used in the first part of the thesis is sufficient for relatively low density systems, but it is not adequate for strongly compacted systems. Thus, in the second part of this thesis, I employ the Finite Element Method to study in detail the structure and mechanics of the disordered packings of elastic shells - our proxy model for dense cellular packings. Therein, I discuss how deformations resulting from large compressive forces couple the structural and mechanical properties of the compact packings. Finally, using Lattice-Boltzmann simulations, I investigate the fluid transport in such compacted packings of deformable shells. I show that a relatively simple model proposed by Kozeny & Carman, combined with a percolation theory, can capture the fluid transport in porous materials. This result is of interest not only in dense biological systems, but also in a broader class of granular porous materials.