DARPA is quietly leading the way in nanotechnology as well as other advanced research sectors(DARPA: Defense Advanced Research Projects Agency). One excellent, readable inside view on DARPA was provided in the recent book, The Department of Mad Scientists, How DARPA is Remaking our World, from the Internet to Artificial Limbs (by Michael Belfiore, 2009). This provided inspiration to look briefly at the impact of DARPA on nanotechnology patenting, as the book mentions the role of nanotechnology in, for example, high efficiency solar cells.
A crude search of 977 nanotechnology patents finds 100 granted patents which apparently derived from DARPA funding based on the government funding clauses. These cover a twenty-one year span, starting with Stanford University's patent 4,908,519 issued March 13, 1990 (Professor Quate et al., "Loading Mechanism and Support Structure having Improved Vibration Damping Useful in Scanning Tunneling Microscopy"). The most recent issued just last week to Caltech (Professor Heath et al., 7,906,775, "Superlattice Nanopatterning of Wires and Complex Patterns")
The 100 patents cover a balance of both university and corporate research, focusing on areas such as nanopatterning, microfabrication, sensors, assorted nanomaterials, AFM, and transistors. The subjects even include nanobio subjects such as nanofluidic chips, protein printing, and virus arrays. For example, Princeton's Professor Chou et al. have patented use of nanochannels for evaluating, isolating, and imaging biopolymers (see US Patent No. 7,670,770). Sequencing DNA continues to be one of the cutting edge issues in nanobio. Indeed, pulling DNA strands through nanopores is featured in the last Technology Quarterly in the Economist magazine (March 12-18 issue, page 13, "Nanopore Sequencing").
The "mad scientist" label for DARPA projects can create fear of the future. However, Belfiore's book says DARPA is not so much frightening as it is inspiring for our future. For example, DARPA is also contributing to novel alternative energy technology such as high efficiency solar cells. Based on the review of their nanotechnology patenting results - agreed (at least for civilian applications).