Date of Award

Spring 1-1-2016

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry & Biochemistry

First Advisor

Meredith D. Betterton

Second Advisor

Matthew A. Glaser

Third Advisor

Joel D. Eaves

Fourth Advisor

Tom Perkins

Fifth Advisor

Xuedong Liu

Abstract

In this thesis, we studied active systems in one or two dimensions in which particles are self-propelled and repel each other. In one-dimensional models, we considered driven particles on single lanes or in anti-parallel overlaps with both binding/unbinding and switching between the lanes. These models are inspired by experiments on kinesin proteins walking on microtubules or anti-parallel overlaps. In the single-lane case, we focused on length regulation controlled by end concentration or flux. In the anti-parallel overlap case, we used a phase space flow method to determine the density profiles and compared the analytic results with kinetic Monte Carlo simulations. In calculating the phase diagram, we also found a phase, the low density-high density-low density-high density phase, which was not found previously. In two dimensional systems, we studied high-aspect-ratio self-propelled rods with a repulsive potential over a wide range of packing fraction and driving to determine the nonequilibrium state diagram and dynamic behavior. Flocking and nematic-laning states occupy much of the parameter space. In the flocking state, the average internal pressure is high and structural and mechanical relaxation times are long, suggesting that rods in flocks are in a translating glassy state despite overall flock motion. In contrast, the nematic-laning state shows fluid-like behavior. The flocking state occupies regions of the state diagram at both low and high packing fraction separated by nematic-laning at low driving and a history-dependent region at higher driving; the nematic-laning state transitions to the flocking state for both compression and expansion. We propose that the laning-flocking transitions are a type of glass transition which, in contrast to other glass-forming systems, can show fluidization as density increases. The fluid internal dynamics and ballistic transport of the nematic-laning state may promote collective dynamics of rod-shaped microorganisms.

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