Nanoparticles have garnered much attention in pharmaceutical and biomedical fields because their small size and high surface area facilitate drug absorption, improve access to cells and organs, and enhance optical imaging. However, delivery of nanoparticles to the body is not always feasible or effective. Here, nanoparticle assemblies (flocs or clusters) for pulmonary drug delivery and biomedical imaging in cells are shown to facilitate delivery, interactions with cells, and manipulation of optical properties of inorganic/organic nanocomposites. The formation of aggregates by physical techniques and their mechanisms are described in detail. For pulmonary delivery, particles with aerodynamic diameters between 1-5 [mu]m deposit efficiently in the deep lungs. However, crystalline, non-porous, poorly water soluble drugs of this size require long dissolution times, limiting absorption by the body. Therefore, drug dissolution must be “decoupled” from deposition to improve absorption. To address this challenge, drug nanoparticles were dispersed within 4-[mu]m water droplets when administered via nebulization or as micron-sized flocs using a pressurized metered dose inhaler (pMDI). Upon deposition in aqueous media, the aerosolized nanoparticle assemblies dissociated into constituent nanoparticles, raising the available surface area for dissolution and increasing dissolution rates, relative to solid particles. Poorly water soluble drug nanoparticles were prepared using a controlled precipitation (CP) or thin film freezing (TFF) process, in which stable nanoparticles (30-300 nm in diameter) with high potencies (>90 wt% drug) were produced by rapidly nucleating drug solutions in the presence of strongly adsorbing polymers or by freezing, respectively. Amorphous, nanoparticles prepared by CP produced stable aqueous dispersions with high fine particle fractions (FPF) of 77% and total emitted doses (TED) of 1.5 mg/min upon nebulization. CP and TFF also produced anisotropic particles (aspect ratios >5), which formed stable suspensions in a hydrofluoroalkane propellant. Inefficient packing of anisotropic particles formed loose, open flocs that stacked upon each other to prevent settling. Upon pMDI actuation, atomized propellant droplets shear apart and template portions of the floc to yield porous particles with high FPFs (49-64%) and TEDs (2.4 mg/actuation). The controlled assembly of gold nanoparticles into clusters is also of great interest for biomedical imaging and therapy because clusters exhibit improved near infrared absorbance (where blood and tissue are most transparent), relative to single spherical particles, and can biodegrade into clearable particles. Gold nanoparticles (5 nm) were assembled into clusters between 30 to 100 nm in diameter with high gold loadings, resulting in strong NIR absorbance. The assembly was kinetically controlled with weakly adsorbing polymers by manipulating electrostatic, van der Waals, steric, and depletion forces. Furthermore, clusters assembled with a biodegradable polymer deaggregated back into primary particles in physiological media and within cells. This kinetic assembly platform is applicable to a wide variety of fields that require high metal loadings and small particle sizes. / text