2018 Foundations of Nanoscience invited talk

Abstract

The promise of molecular programming lies in its ability to not only process information autonomously, but to do so in a biochemical context in order to sense and actuate matter. The most sophisticated molecular computing systems have been built upon the DNA strand displacement (DSD) primitive, where a soup of rationally designed nucleotide sequences interact, react, and recombine over time in order to carry out sophisticated computation. Existing systems are often slow, error-prone, require bespoke design and weeks of effort to realize experimentally. Building upon the leakless DSD architecture we have developed a reconfigurable molecular breadboard. Its purpose is to ‘scale-up’ what is possible with this technology and to ‘scale-out’ its adoption to new contexts. The power of this approach is found in its simplicity and the high quality of the rationally designed components. In order to facilitate the rapid design of new circuits from a common molecular broth, we have developed a compiler that takes as input a logic description and provides as output the optimized set of breadboard components necessary to activate the desired logic behavior. By mixing these pre-existing components as prescribed, it is possible to achieve fast, leakless and robust molecular circuits, from conception to implementation, within the time frame of an afternoon as confirmed by undergraduate students at Caltech. We expect our molecular breadboard approach will enable the implementation of circuits 10 times larger than have been previously demonstrated. Due to the large separation of time scales between designed and spurious computation, we expect the breadboard architecture will open new research directions in molecular sensing, actuation and interfacing with self-assembly systems.

Chris Thachuk

Assistant Professor

My research focuses on applying principles from computer science and engineering to create programmable matter.