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Nanoscience offers the promise of producing revolutionary advances in many areas of science and technology, ranging from electronics and computing to biology and medicine, yet the realization of this promise will depend critically on the rational development of unique nanoscale structures whose properties and/or function are controlled during materials synthesis. This review will illustrate these concepts using nanowires as a platform material. First, a brief historical perspective on emergence of nanowires as a central material will be presented. Second, the `chemical' synthesis, atomic-level structural characterization and properties of complex modulated nanowires will be discussed with an emphasis on structures with radial and axial dopant modulation, and novel but controlled structural modulations. The implementation of these functional nanowires as a platform for investigating fundamental properties and performance limits of nanoscale quantum electronic and photovoltaic devices at the single nanowire level will be described. Second, the development of active interfaces between nanowire nanoelectronic devices and biological systems will be discussed, including label-free electronic detection at the single molecule level and multiplexed recording from individual cells through complex biological tissue, such as the brain. In addition, the development of novel nanowire probes that exploit unique synthetic capabilities for the nanowire platform and move beyond capabilities of conventional electrophysiological techniques will be discussed. Last, a critical look at progress made and scientific challenges that remain to realize true technologies in the future will be reviewed.