A fast, robust and reconfigurable molecular circuit breadboard

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 labor to realize experimentally. I will detail our efforts to fix these issues by introducing a molecular breadboard, capable of computing billions of functions including all $2^{32}$ Boolean predicates with $5$ distinct inputs. Its purpose is to “scale-up” what is possible with this technology and to “scale-out” its adoption to new contexts. 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, autonomous and robust molecular circuits, from conception to implementation, within a single afternoon. 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.

Date
Dec 5, 2019 3:00 PM
Event
UC Davis, Computer Science Colloquium
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Chris Thachuk
Senior Postdoctoral Fellow

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