Thesis (Ph.D.) - Indiana University, Luddy School of Informatics, Computing, and Engineering, 2021Soft matter underlies many facets of modern life, including nanotechnology, biological life itself, and the repurposing of biomimetic entities for these nanotechnologies. Soft matter-based bulk materials used in everyday life include cosmetics (creams, powders, gels, foams), adhesives, the soft polymeric rubber of tires, and colloidal processes involved in a variety of culinary applications. Key characteristics of soft matter that provide as-needed utility include the relatively weak bond structure, correlated susceptibility to thermal fluctuations, and resulting propensity to transiently and reversibly undergo transitions such as self-assembly, deformation, and disassembly, dictating their functionality. These transitions can occur by design under given circumstances, allowing man and nature to meet targeted needs expeditiously, with soft matter literally underlying the phrase “well-oiled machine,” e.g. viscosity-variable rheological lubricants in internal combustion engines. Here, we categorically investigate the processes of self-assembly, deformation, and disassembly employed by both man and nature. We investigate both in silico and in vitro the predominantly electrostatic mechanisms underlying hierarchical self-assembly of biomimetic nanoparticle super lattices, wherein repurposed (spherical) viruses serve as aggregated nanoreactors. These variably well-ordered nanoreactor lattices demonstrably enhance catalytic activity due to virus porosity. We also investigate the again predominantly electrostatic mechanisms underlying the deformation of soft nanoparticles in silico, with an eye towards expanding the phase space of hierarchically self-assembled materials made of aspherical building blocks and targeted drug delivery vesicles given the shape dependence of endocytosis. Finally, we present an experimentally validated percolation theory of viral nanoparticle disassembly with an eye towards understanding resilience of different virus species and, technologically, the extent to which subunit removal and replacement strategies may be used tune their properties relevant to hierarchical self-assembly and deformation processes (e.g. porosity, net charge, and elasticity).