Building Programmable Matter Through DNA-based Chemical Computing

Abstract

Biology offers compelling proof that macroscopic “living materials” can emerge from reactions between diffusing biomolecules. This work presents how molecular self-organization could be a similarly powerful approach for engineering functional synthetic materials. We focus on programmable DNA-hydrogels that produces tunable patterns at the centimeter length scale. We generate these patterns by implementing chemical reaction networks through synthetic DNA complexes, embedding the complexes in hydrogel, and triggering with locally applied input DNA strands. Chapter 1 provides an overview of the state of the art in programmable matter research. It also examines where current approaches, such as modular robotics and nanoscale engineering, may fall short. Chapter 2 presents chemical reaction-diffusion as an alternative approach to synthesizing programmable materials. Chapter 3 describes DNA computing and why it is ideal for realizing programmable reaction-diffusion systems. Chapters 4 and 5 introduce the DNA-based reaction-diffusion systems we have implemented for making programmable spatial patterns. In Chapter 4, we demonstrate a DNA-based multi-layered cascade circuit where each layer consists of signal generation, signal suppression, and signal restoration modules. In Chapter 5, we couple in vitro experiments with computer simulation to demonstrate programmable spatial patterns that can be designed and simulated in advance.