Qian MPP 2011

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Nano-scale dynamic LEGOs: digital logic computation and neural network computation with DNA strand displacement cascades

  • Lulu Qian, Erik Winfree, and Jehoshua Bruck.
  • Californian Insitute of Technology

Abstract

To construct sophisticated biochemical circuits from scratch, one needs to understand how simple the building blocks can be and how robustly circuits can scale up. Using a simple DNA reaction mechanism based on a reversible strand displacement process, we experimentally demonstrated several digital logic circuits, culminating in a four-bit square root circuit that comprises over a hundred DNA strands. These multilayer circuits include thresholding and catalysis within every logical operation to perform digital signal restoration, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler. Using the same DNA gate architecture, we also developed a systematic procedure for transforming arbitrary linear threshold circuits (an artificial neural network model) into DNA strand displacement cascades. We demonstrated our approach by successfully implementing several small neural networks, including a Hopfield associative memory that has four fully connected artificial neurons. This tiny DNA "brain" can play a game called "read your mind" (a variation of "20 questions") with a human. Our results suggest that DNA strand displacement cascades could be used to embed "intelligence within autonomous chemical systems, capable of recognizing patterns of molecular events, making decisions and responding to the environment.

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