Date of Award

Spring 1-1-2018

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

First Advisor

Meredith D. Betterton

Second Advisor

Matthew A. Glaser

Third Advisor

Loren E. Hough

Fourth Advisor

Franck J. Vernerey

Fifth Advisor

Joseph E. MacLennan

Abstract

Interactions between particles and their environment can alter the dynamics of biological systems. In crowded media like the cell, interactions with obstacles can introduce anomalous subdiffusion. Active matter systems, e.g., bacterial swarms, are nonequilibrium fluids where interparticle interactions and activity cause collective motion and dynamical phases. In this thesis, I discuss my advances in the fields of crowded media and active matter. For crowded media, I studied the effects of soft obstacles and bound mobility on tracer diffusion using a lattice Monte Carlo model. I characterized how bound motion can minimize the effects of hindered anomalous diffusion and obstacle percolation, which has implications for protein movement and interactions in cells. I extended the analysis of binding and bound motion to study the effects of transport across biofilters like the nuclear pore complex (NPC). Using a minimal model, I made predictions on the selectivity of the NPC in terms of physical parameters. Finally, I looked at active matter systems. Using dynamical density functional theory, I studied the temporal evolution of a self-propelled needle system. I mapped out a dynamical phase diagram and discuss the connection between a banding instability and microscopic interactions.

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