Delay Line as a Chemical Reaction Network

@article{Moles2015DelayLA,
  title={Delay Line as a Chemical Reaction Network},
  author={Joshua Stephen Moles and Peter Banda and Christof Teuscher},
  journal={Parallel Process. Lett.},
  year={2015},
  volume={25},
  pages={1540002:1-1540002:18}
}
Chemistry as an unconventional computing medium presently lacks a systematic approach to gather, store, and sort data over time. To build more complicated systems in chemistries, the ability to look at data in the past would be a valuable tool to perform complex calculations. In this paper we present the first implementation of a chemical delay line providing information storage that can reliably capture information over an extended period of time. The delay line is capable of parallel… Expand
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References

SHOWING 1-10 OF 58 REFERENCES
Computational functions in biochemical reaction networks.
TLDR
The computational properties of several enzymatic (single and multiple) reaction mechanisms are investigated: it is shown their steady states are analogous to either Boolean or fuzzy logic gates. Expand
On Multitasking in Parallel Chemical Processors: Experimental Findings
TLDR
This work designs a multitasking chemical processor that independently and simultaneously computes Voronoi diagrams of two different data planar sets and finds that when a single reactant is on a gel layer containing either one or two substrates the same single Voronoa diagram corresponding to the original location of the reactant drops is constructed. Expand
Discrete-time signal processing with DNA.
TLDR
This work presents a methodology for implementing discrete-time signal processing operations, such as filtering, with molecular reactions, and describes two approaches: one entails synchronization with a clock signal, implemented through sustained chemical oscillations; the other is "self-timed" or asynchronous. Expand
Chemical Organization Theory as a Theoretical Base for Chemical Computing
TLDR
It is demonstrated how the chemical organization theory can help in designing and understanding chemical computing systems, and how the theoretical analysis provides insight into the potential behavior of chemical reaction systems. Expand
Online Learning in a Chemical Perceptron
TLDR
It is suggested that DNA strand displacement could, in principle, provide an implementation substrate for the first full-featured implementation of a perceptron in an artificial (simulated) chemistry, allowing the chemical perceptron to perform reusable, programmable, and adaptable wet biochemical computing. Expand
Training an asymmetric signal perceptron through reinforcement in an artificial chemistry
TLDR
A novel chemical perceptron that can solve all 14 linearly separable logic functions and introduces thresholds that amplify the outputs makes an actual wet implementation, in particular by DNA-strand displacement, possible. Expand
Some Computer Organizations and Their Effectiveness
  • M. J. Flynn
  • Computer Science
  • IEEE Transactions on Computers
  • 1972
TLDR
A hierarchical model of computer organizations is developed, based on a tree model using request/service type resources as nodes, which indicates that saturation develops when the fraction of task time spent locked out approaches 1/n, where n is the number of processors. Expand
Flow Management in Packet Networks Through Interacting Queues and Law-of-Mass-Action Scheduling
TLDR
This report introduces the LoMA-scheduling approach and provides a solid mathematical framework adopted from chemistry that simplifies the analysis of the corresponding queueing networks, including the prediction of the underlying protocols’ dynamics. Expand
Molecular computation: RNA solutions to chess problems
TLDR
This work considers a variant of the "Knight problem," which asks generally what configurations of knights can one place on an n x n chess board such that no knight is attacking any other knight on the board, and developed a molecular algorithm that applied it to a 3 x 3 chessboard as a 9-bit instance of this problem. Expand
An Introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos
Part I: Overview 1. Introduction - A Bit of History 2. Fundamentals 3. Apparatus 4. Chemical Oscillations: Synthesis 5. Chemical Oscillations: Analysis 6. Waves and Patterns 7. Computational ToolsExpand
...
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2
3
4
5
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