Date of Award
Doctor of Philosophy (PhD)
Mechanical Engineering & Materials Science (ENAS)
The application of coarse-grained computational models to the study of physical systems has explodedin recent years, in part due to the relative simplicity of such models compared to the drastic complexity that can be found in the natural world. These models have been of particular use to the study of biological systems, as living things are typically highly complex and live far from thermodynamic equilibrium. In this thesis, I will present several coarse-grained computational models of different biological systems with the aim of identifying the role physical constraints, in particular those of packing and jamming, play in different biological systems. In the first part of this thesis, I will describe a model of globular protein cores based on jammed granular materials. I will show that this model displays the same void structure as real globular protein cores, and that the inherent protocol-dependence of packing generation yields insights into systematic differences between various experimental techniques used to resolve protein structures. In the second part of this thesis, I will describe a computational model of particles that can deform their shape in response to applied stress. I will first analyze how the rigidity of single particles in this model affects the collective behavior of many co-interacting deformable particles, as well as indicate how this model may be adapted for the study of tissue fluidization. I end the thesis with an analysis of packing constraints across the development and phylogeny of the spongy mesophyll tissue of leaves and flowers.
Treado, John Durkin, "Computational Studies of Packing and Jamming in Biological Systems" (2022). Yale Graduate School of Arts and Sciences Dissertations. 669.