Computational studies of directed assembly and self assembly of building blocks and precise structures: From colloids to viruses

The directed-assembly and self-assembly of building blocks are promising techniques to make structures with three-dimensional precision, which are important in many practical applications and may serve as a new generation of starting materials for novel superstructures. Experimental techniques have improved significantly to create building blocks out of diverse materials with varying properties and shapes, and allow site specific, selective functionalization of certain building blocks. The rational design and successful control of materials requires an unprecedented understanding of how building blocks assemble on the small scale. It is thus imperative to develop a systematic way to identify assembly principles and predict final structures for a given building block.; The objective of this dissertation is to develop a general modeling and simulation approach to explore the governing principles underlying target directed-assembly and self-assembly. Exemplifying this approach, we use a "minimal model" approach, which contains a minimal set of parameters while still maintaining the key physics of the target problems to study selected assembly phenomena.; We first examine polymer and biomolecule directed-assembly of nanoparticles, and find that despite the recognitive capability of linkers, fractal-like structures, instead of precise structures, are formed under the conditions studied.; Further, we investigate the possibility of exploiting the anisotropic shapes and/or interactions of building blocks to assemble precise structures. We performed molecular simulations of the self-assembly of cone-shaped particles with specific attractions, and find that the cones self-assemble into a sequence of robust, precise clusters. We further show that this sequence is reproduced and is extended in simulations of two simple models of spheres self-assembling subject to convexity constraints. This sequence for small sizes is identical to those observed in evaporation-driven assembly of colloidal spheres, and contains multiple icosahedral virus capsid structures. Additionally, we study a phenomenological model where packings of spheres on a prolate spheroid surface are related to the precise structures observed in elongated virus capsids.; These findings may promote the application of the assembly strategy derived from studies of colloids to biological assemblies, or vice versa, which eventually will improve our understanding of both areas.