Digital Commons Network^™

Filaments, Fibers, And Foliations In Frustrated Soft Materials, Daria Atkinson

Doctoral Dissertations

Assemblies of one-dimensional filaments appear in a wide range of physical systems: from biopolymer bundles, columnar liquid crystals, and superconductor vortex arrays; to familiar macroscopic materials, like ropes, cables, and textiles. Interactions between the constituent filaments in such systems are most sensitive to the distance of closest approach between the central curves which approximate their configuration, subjecting these distinct assemblies to common geometric constraints. Dual to strong dependence of inter-filament interactions on changes in the distance of closest approach is their relative insensitivity to reptations, translations along the filament backbone. In this dissertation, after briefly reviewing the mechanics and …

Dynamic Neuromechanical Sets For Locomotion, Aravind Sundararajan

Doctoral Dissertations

Most biological systems employ multiple redundant actuators, which is a complicated problem of controls and analysis. Unless assumptions about how the brain and body work together, and assumptions about how the body prioritizes tasks are applied, it is not possible to find the actuator controls. The purpose of this research is to develop computational tools for the analysis of arbitrary musculoskeletal models that employ redundant actuators. Instead of relying primarily on optimization frameworks and numerical methods or task prioritization schemes used typically in biomechanics to find a singular solution for actuator controls, tools for feasible sets analysis are instead developed …

Bayesian Topological Machine Learning, Christopher A. Oballe

Doctoral Dissertations

Topological data analysis encompasses a broad set of ideas and techniques that address 1) how to rigorously define and summarize the shape of data, and 2) use these constructs for inference. This dissertation addresses the second problem by developing new inferential tools for topological data analysis and applying them to solve real-world data problems. First, a Bayesian framework to approximate probability distributions of persistence diagrams is established. The key insight underpinning this framework is that persistence diagrams may be viewed as Poisson point processes with prior intensities. With this assumption in hand, one may compute posterior intensities by adopting techniques …

Compactifications Of Cluster Varieties Associated To Root Systems, Feifei Xie

Doctoral Dissertations

In this thesis we identify certain cluster varieties with the complement of a union of closures of hypertori in a toric variety. We prove the existence of a compactification $Z$ of the Fock--Goncharov $\mathcal{X}$-cluster variety for a root system $\Phi$ satisfying some conditions, and study the geometric properties of $Z$. We give a relation of the cluster variety to the toric variety for the fan of Weyl chambers and use a modular interpretation of $X(A_n)$ to give another compactification of the $\mathcal{X}$-cluster variety for the root system $A_n$.

Fuzzy Logistic Regression For Detecting Differential Dna Methylation Regions, Tarek M. Bubaker Bennaser

Doctoral Dissertations

“Epigenetics is the study of changes in gene activity or function that are not related to a change in the DNA sequence. DNA methylation is one of the main types of epigenetic modifications, that occur when a methyl chemical group attaches to a cytosine on the DNA sequence. Although the sequence does not change, the addition of a methyl group can change the way genes are expressed and produce different phenotypes. DNA methylation is involved in many biological processes and has important implications in the fields of biomedicine and agriculture.

Statistical methods have been developed to compare DNA methylation at …