Molecular Programming

Nucleic acids (DNA/RNA) encode information digitally, and are currently the only truly ‘user-programmable’ entities at the molecular scale. They can be used to manufacture nano-scale structures, to produce physical forces, to act as sensors and actuators, and to do computation in between. Eventually we will be able to use them to produce nanomaterials at the bottom end of Moore’s Law, and to interface them with biological machinery to detect and cure diseases at the cellular level under program control. Recently, computational schemes have been developed that are autonomous (run on their own power) and involve only short, easily producible, DNA strands with no other complex molecules. While simple in mechanism, these schemes are highly combinatorial and concurrent. Understanding and programming systems of this new kind requires new software technologies. Computer science has developed a large body of techniques for analyzing (modeling) and developing (engineering) complex programmable systems. Many of those techniques have a degree of mathematical generality that makes them suitable for applications to new domains. This is where we can make critical contributions: in developing and applying programming techniques (in a broad sense) that are unique to computing to other areas of science and engineering, and in particular at the interface between biology and nanotechnology.