Neural network computation with DNA strand displacement cascades

@article{Qian2011NeuralNC,
  title={Neural network computation with DNA strand displacement cascades},
  author={Lulu Qian and Erik Winfree and Jehoshua Bruck},
  journal={Nature},
  year={2011},
  volume={475},
  pages={368-372}
}
The impressive capabilities of the mammalian brain—ranging from perception, pattern recognition and memory formation to decision making and motor activity control—have inspired their re-creation in a wide range of artificial intelligence systems for applications such as face recognition, anomaly detection, medical diagnosis and robotic vehicle control. Yet before neuron-based brains evolved, complex biomolecular circuits provided individual cells with the ‘intelligent’ behaviour required for… Expand
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References

SHOWING 1-10 OF 70 REFERENCES
Experimental aspects of DNA neural network computation
TLDR
The model for a DNA analog neural network in which the usual axons and neurons are replaced by the diffusion and molecular recognition of DNA is reviewed, the ultimate speed of DNA computations is estimated, an enzymatic representation of DNA matrix algebra is presented and some exploratory experimental results are shown. Expand
Neural Network Computation by In Vitro Transcriptional Circuits
TLDR
A simple biochemical system whose architecture mimics that of genetic regulation and whose components allow for in vitro implementation of arbitrary circuits, allowing a simple network without explicit mutual inhibition to perform the winner-take-all computation. Expand
DNA computing circuits using libraries of DNAzyme subunits.
TLDR
The construction of a DNA-based computational platform that uses a library of catalytic nucleic acids, and their substrates, for the input-guided dynamic assembly of a universal set of logic gates and a half-adder/half-subtractor system is reported. Expand
A programming language for composable DNA circuits
TLDR
A programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism and includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure is presented. Expand
Neural networks and physical systems with emergent collective computational abilities
TLDR
A model of a system having a large number of simple equivalent components, based on aspects of neurobiology but readily adapted to integrated circuits, produces a content-addressable memory which correctly yields an entire memory from any subpart of sufficient size. Expand
DNA computing and molecular programming : 18th International Conference, DNA 18, Aarhus, Denmark, August 2012 : proceedings
TLDR
A DNA Based Molecular Logic Gate Capable of a Variety of Logical Operations and a Geometric Approach to Gibbs Energy Landscapes and Optimal DNA Codeword Design are presented. Expand
Chemical implementation of neural networks and Turing machines.
TLDR
A mechanism of interneuronal connections in which the stationary state of a chemical neuron is determined by the state of other neurons in a homogeneous chemical system and is thus a "hardware" chemical implementation of neural networks. Expand
Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades
TLDR
This work experimentally demonstrated several digital logic circuits, culminating in a four-bit square-root circuit that comprises 130 DNA strands, which enables fast and reliable function in large circuits with roughly constant switching time and linear signal propagation delays. Expand
Training a molecular automaton to play a game.
TLDR
A multipurpose reprogrammable molecular automaton that goes beyond single-purpose 'hard-wired' molecular automata and is a model system for more general molecular field programmable gate array (FPGA)-like devices that can be programmed by example, which means that the operator need not have any knowledge of molecular computing methods. Expand
Construction of an in vitro bistable circuit from synthetic transcriptional switches
TLDR
Construction of larger synthetic circuits provides a unique opportunity for evaluating model inference, prediction, and design of complex biochemical systems and could be used to control nanoscale devices and artificial cells. Expand
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