Title: Studies of Polymers, Active Colloids, and Proteins
Description: This thesis describes several molecular dynamics studies of polymers, proteins, and active colloids. These diverse systems fall under the purview of soft matter physics and in Part I, I explain what is soft matter and describe some of its essential features. In Part II, I introduce some basic polymer physics and show how confined polymers can be described using blob theory. I also discuss how phase separation of polymer mixtures can occur. These concepts are applied to systems of mixed polymer brushes on spheroids, objects that have surfaces with non-uniform curvature. I show how the interplay of phase separation and surface curvature give rise to striped patterns, and how an extension of blob theory can give analytical expressions for the free energy. Finally, I show how phase separation of miscible polymers can occur, driven solely by surface curvature. In Part III, I present an overview of self-assembly and describe how active, or self-propelled colloids can be used to assemble new materials.

I show how two large colloids immersed in a bath of smaller active colloids exhibit an effective short-ranged repulsion and long-ranged attraction, which stands in contrast to the standard short-ranged depletion attraction. I also explore how self-propulsion changes clustering by focusing on a system with short-ranged attractive and long-ranged repulsive particles, which under equilibrium, exhibit finite-sized clusters. I show that for certain parameters, spheres can form a fluid of living crystals, and dumbbells can form a crystal of rotors. In Part IV, I give a brief introduction to protein folding and describe how molecular chaperones combat misfolding in the human body. Then, taking inspiration from the chaperones, I show that a polymer-grafted “soft” nanopore can be used to unfold misfolded proteins and destroy undesired aggregates. I also show preliminary results for a hydrophobic “smart” nanopore that can selectively capture and unfold misfolded proteins.