Silica chemistry provides a uniquely tunable platform for nanoparticle synthesis, where particle size, nanoscale morphology, and surface properties can be precisely controlled. Recent advances demonstrate that conveniently accessible parameters, including silica precursor chemistry, solvent, and reaction pH, can be used to tune particle size down to below 10 nm. By cooperative assembly of inorganic silica species and organic molecular structure directing agents, a diverse range of mesoporous silica nanoparticles with hexagonal, cubic, and multicompartment structures can be produced. This versatile chemistry provides pathways for answering fundamental questions about structure formation and developing novel functional nanomaterials for applications including separation, catalysis, and drug delivery. In this dissertation, two examples of such silica nanoparticle systems are discussed. As a first example, the development of an intensity-based fluorescent silica nanoparticle barcode is discussed. This work is motivated by a need for fluorescent tags that increase the number of molecular species that can be simultaneously labeled and reliably distinguished using commercially available fluorescence microscopes. In this study, the synthetic parameters that govern the incorporation of precisely controlled numbers of fluorescent dyes into silica nanoparticles in batch reactions are identified. Heterogeneities within particle batches are mapped using single particle fluorescence microscopy. Proof-of-concept experiments demonstrate that fluorescent silica nanoparticles with well-separated high and low fluorescence intensity distribution levels can be synthesized in batch reactions and used as an intensity barcode in fluorescence microscopy. In the second example, a mesoporous silica nanoparticle system, structure directed by surfactant-micelle self-assembly, is investigated. As a function of an added pore expander molecule or reaction stirring rate, a series of four distinct mesoporous silica nanoparticle structures is observed: hexagonal, cubic/hexagonal multicompartment, cubic, and dodecagonal quasicrystalline. The mechanism driving the structural transition between cubic crystalline and dodecagonal quasicrystalline mesoporous silica nanoparticles is investigated. Control of nanoparticle size down to a single tiling unit (< 30 nm), allows direct comparison between experimental results and a simple theoretical growth model, providing insights into the early growth trajectories of quasicrystalline mesoporous silica. This work identifies simple synthetic control parameters for quasicrystal growth that may be translated to other self-assembled systems.