We examine the opportunities brought about by recent progress in electronic nanotechnology and describe the methods needed to harness them for building a new computer architecture. In this process we decompose some traditional abstractions, such as the transistor, into fine-grain pieces, such as signal restoration and input-output isolation. We also show how we can forgo the extreme reliability of CMOS circuits for low-cost chemical self-assembly at the expense of large manufacturing defect densities. We discuss advanced testing methods that can be used to recover perfect functionality from unreliable parts. We proceed to show how the molecular switch, the regularity of the circuits created by self-assembly and the high defect densities logically require the use of reconfigurable hardware as a basic building block for hardware design. We then capitalize on the convergence of compilation and hardware synthesis (which takes place when programming reconfigurable hardware) to propose the complete elimination of the instruction-set architecture from the system architecture, and the synthesis of asynchronous dataflow machines directly from high-level programming languages, such as C. We discuss in some detail a scalable compilation system that performs this task.