So this is another one of those articles where IBM got the headlines but HP is actually ahead on the technology?
What's interesting about his research and IBM's research (and the reason he's using an FPGA) is that both technologies will require highly defect tolerant architectures. The initial few years at least of self-assembling nanomolecular components will involve several percent defects. This would cripple one of today's conventional chips, but an FPGA could be programmed to route around defects (given a sophisticated enough algorithm?)