We in the U.S. who are interested in nanotech tend to focus on NSF, but DoE deserves substantial attention as well. See their overview page, and then download the pdf brochure on their nanoscale science research centers (worth the effort for the illustrations alone): Center for Functional Nanomaterials, Center for Integrated Nanotechnologies, Center for Nanophase Materials Sciences, Center for Nanoscale Materials, and the catchily-named Molecular Foundry.
“Realizing the promise of nanoscale research, however, will require much more fundamental scientific knowledge and technological know-how. This includes a detailed understanding of the processes by which molecules organize and assemble themselves, the construction of quantum devices, and the operation of complex nanostructured systems. We also must find new ways to think about all aspects of materials and device fabrication. In the future, we will be building things from the bottom up as well as from the top down.” Emphasis added.