This thesis focuses on the study of certain complex cooperative processes in soft condensed matter systems by computer simulation and theory. The systems studied include magnetic self-assembly on the centimeter scale, radial collapse of carbon nanotubes on a surface, water filling of hydrophobic pores, and the vitrification of screened Coulombic systems and the formation of a Wigner glass. After a brief introduction in Chapter 1, Chapter 2 describes the spontaneous folding of flat elastomeric sheets patterned with magnetic dipoles into free-standing, 3D objects that are the topological equivalents of spherical shells. Chapter 3 develops a variation of the well-established nudged elastic band method for the location of transition states in complicated physical systems. Chapter 4 presents a study of radial collapse in carbon nanotubes in contact with a surface. Relative stability of open and collapsed states are determined and a relatively simple method for producing a metal-semiconductor junction in carbon nanotubes is proposed. In Chapter 5 we show that increasing the flexibility of nanometer sized pores increases their hydrophobicity and slows down water transport across the pore. Finally, in Chapter 6, we report on a computer simulation of a successful approach to a Wigner glass---a glassy state in Coulombic purely repulsive systems, which is thought to form in low density charged colloids. The structural and dynamical properties of the system as the glassy region is approached show behavior characteristic of glass-forming liquids, and comparisons are made with Lennard-Jones systems and Mode Coupling Theory.
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