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.
|Advisor:||Betterton, Meredith D., Glaser, Matthew A.|
|Commitee:||Hough, Loren E., MacLennan, Joseph E., Vernerey, Franck J.|
|School:||University of Colorado at Boulder|
|School Location:||United States -- Colorado|
|Source:||DAI-B 80/02(E), Dissertation Abstracts International|
|Subjects:||Computational physics, Condensed matter physics, Biophysics|
|Keywords:||Active matter, Anomalous diffusion, Brownian dynamics, Crowded media, Dynamical density functional theory, Nuclear pore complex|
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