Today we’re talking with Damien Woods, a professor and molecular programmer at the Hamilton Institute, Maynooth University, Ireland. We first began by talking about how his early interests in dynamics and optical computers (the subject of his PhD thesis) led him to the field of molecular programming.
We then move on to talking about one of Damien’s well known papers, Diverse and robust molecular algorithms using reprogrammable DNA self-assembly. In this paper, Damien describes the implementation of 21 algorithms using a 6-bit boolean circuit built out of a DNA tile-set. Damien and his team built a set of DNA tiles which could implement any algorithm allowable by that 6-bit computer (the tiles are 6-bit universal). Damien describes how this allows anyone to wake up in the morning, design an algorithm, retrieve the appropriate tiles from the fridge, mix them and begin running the algorithm in a test tube on the very same day. This clearly has its advantages over other systems, which may require someone to wait for the DNA synthesis of their system before an implementation can be made. The readout of these circuits is by AFM to see a tape-recording of the computation, and so this paper generated a lot of pretty pictures!
We then moved on to talk about potential implementations of more complex computers, how Damien et al.’s 6-bit boolean circuit might be scaled up, and how the number of required tiles scales with the computational complexity (it’s linear!). This led us on to an extended discussion about universal tile-sets, their existence, and their ability to be implemented in DNA.
Finally we moved on to Damien’s experience in academia. He’s been to quite a few places, and has worked on many different things. He explains how his experience running a lab in two different countries differed, and how this shaped the way he runs his research group.
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly paper: https://www.nature.com/articles/s41586-019-1014-9
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