Computational Studies of Packing and Jamming in Biological Systems / John D Treado.

9798841718635

[New Haven, Connecticut] : Yale University, 2022.

1 online resource (136 pages)

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 drasticcomplexity that can be found in the natural world. These models have been of particular use to thestudy of biological systems, as living things are typically highly complex and live far from thermodynamicequilibrium. In this thesis, I will present several coarse-grained computational models ofdifferent biological systems with the aim of identifying the role physical constraints, in particularthose of packing and jamming, play in different biological systems. In the first part of this thesis, Iwill describe a model of globular protein cores based on jammed granular materials. I will show thatthis model displays the same void structure as real globular protein cores, and that the inherentprotocol-dependence of packing generation yields insights into systematic differences between variousexperimental techniques used to resolve protein structures. In the second part of this thesis, Iwill describe a computational model of particles that can deform their shape in response to appliedstress. I will first analyze how the rigidity of single particles in this model affects the collectivebehavior of many co-interacting deformable particles, as well as indicate how this model may beadapted for the study of tissue fluidization. I end the thesis with an analysis of packing constraintsacross the development and phylogeny of the spongy mesophyll tissue of leaves and flowers.

Proquest dissertation Dissertations & Theses @ Yale University.

Books / Online

English

April 21, 2023

Ph.D. Yale University 2022.

Academic theses.