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High-energy X-ray and spallation neutron total scattering data provide information about each pair of atoms in a nanoparticle sample, allowing for quantitative whole-particle structural modeling based on pair distribution function analysis. The realization of this capability has been hindered by a lack of versatile tools for describing complex finite structures. Here, the implementation of whole-particle refinement for complete nanoparticle systems is described within two programs, DISCUS and DIFFEV, and the diverse capabilities they present are demonstrated. The build-up of internal atomic structure (including defects, chemical ordering and other types of disorder), and nanoparticle size, shape and architecture (including core-shell structures, surface relaxation and ligand capping), are demonstrated using the program DISCUS. The structure refinement of a complete nanoparticle system (4 nm Au particles with organic capping ligands at the surface), based on neutron pair distribution function data, is demonstrated using DIFFEV, a program using a differential evolutionary algorithm to generate parameter values. These methods are a valuable addition to other probes appropriate for nanomaterials, adaptable to a diverse and complex set of materials systems, and extendable to additional data-set types.

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