Statistical, Nonlinear, and Soft Matter Physics Commons^™

Investigation Of Domain Formation During Phase Separation In A Mixture Of Flexible And Rigid Biopolymers, Steven Huntley

All Theses

Complex fluids and heterogenous mixtures composed of multiple types of polymers are found throughout industrial and biological fluid systems. For example, extrusion based additive manufacturing systems pass dense mixtures of polymers through the extrusion heads to deposit composite polymeric materials. In cells, active and complex mixtures of biopolymers self-organize into assemblies that perform critical physiological functions.

Polymers in dense solutions undergo phase separation as a result of differences in physiochemical properties. A few examples of these properties include charge, structure, rigidity, and hydrophobicity. We observe the formation of polymer domains composed of rigid and a flexible biopolymer species that phase …

Aspects Of Stochastic Geometric Mechanics In Molecular Biophysics, David Frost

All Dissertations

In confocal single-molecule FRET experiments, the joint distribution of FRET efficiency and donor lifetime distribution can reveal underlying molecular conformational dynamics via deviation from their theoretical Forster relationship. This shift is referred to as a dynamic shift. In this study, we investigate the influence of the free energy landscape in protein conformational dynamics on the dynamic shift by simulation of the associated continuum reaction coordinate Langevin dynamics, yielding a deeper understanding of the dynamic and structural information in the joint FRET efficiency and donor lifetime distribution. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based …