Computer Simulation of Self-Assembly of Complex System: Application to Globular Proteins and Grafted Nanoparticles.

Self-assembly is a process in which components spontaneously form ordered aggregates. It provides a fundamental mechanism to understand the diverse phenomena. Self-assembling of building blocks into desired structures always draws a great interest among researchers. Ever-improving synthesis techniques provide a range of building blocks with exotic shape and functionality. The rational control of self-assembly of these functionalized building blocks requires a fundamental understanding of underlying physics behind self-assembly. We use several minimal models which maintain the fundamental physics of the target system to explore the governing mechanism of self-assembly and related crystallization phenomenon. The minimal models covered in this dissertation include the square-well sphere system, the system of square-well spheres with sticky patches on the surface and the system of square-well spheres grafted with hard sphere chains, among which the first two systems model the globular proteins in aqueous solution, while the last one models the uniformly polystyrene grafted silica nanoparticles in the polystyrene matrix. Square-well fluids of three different attraction ranges have been investigated. The first direct estimate of the whole phase diagram was provided. The phase diagram of square well fluids with a potential range lambda = 1.15 which displays the fluid-solid coexistence with the metastable fluid-fluid separation qualitatively reproduces the protein phase diagram. Phase separation kinetics experiments show this system remains homogeneous until the binodal. Upon crossing the binodal, the system gets vapor-liquid separation. Only well below the binodal, crystallization takes place. Crystallization is clearly a two-step process where the vapor-liquid separation is followed by the crystallization. The patchy protein model remedies the underestimated width of vapor-liquid coexistence curve predicted by the isotropic protein model, and facilitates the protein crystallization by forming the transient clusters with the symmetry of resulting crystal through self-assembly due to the patchy interaction even in the region where the liquid phase is thermodynamically unstable. We emphasize the importance of a local high density fluctuation for crystallization, but we suggest that the origins of this effect might not only be the vicinity of a critical point, but more broadly due to the patchy nature of inter-protein interactions. Perhaps more pertinently, the presence of patches guides crystallization so that only those symmetries consistent with the patch symmetry are stabilized. This is in contrast to crystals formed from phase separation of protein solutions where polycrystallinity is prevalent. It appears that the presence of patchy interaction has several beneficial consequences on protein crystallization. Contrasted with the notion that the explicit introduction of anisotropy is necessary for formation of complex structures, our Monte Carlo results suggest the potential application of this "isotropic" class of nanoparticles as building blocks for assembling complex structures. The morphology of uniformly grafted nanoparticles with the increasing polymer chain length changes from spherical aggregates to flattened cylinder, branched cylinder, sheet, long chain, short chain to well-dispersed system. It has been suggested that grafted nanoparticles share features in common with surfactants and block copolymers. The underlying physics, by which nanoparticles try to minimize their free energy by aggregating with species of their own kind, subject to the topological constraints of grafted polymer chains governs the self assembly process....