Delay Line as a Chemical Reaction Network

  title={Delay Line as a Chemical Reaction Network},
  author={Joshua Stephen Moles and Peter Banda and Christof Teuscher},
  journal={Parallel Process. Lett.},
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
An Analog Chemical Circuit with Parallel-Accessible Delay Line for Learning Temporal Tasks
A new parallel model of a chemical delay line, which stores past concentrations over time with minimal latency is introduced, which is based on chemical reaction networks and follows mass-action and Michaelis-Menten kinetics. Expand
Chemical Reaction Network Control Systems for Agent-Based Foraging Tasks
This work demonstrates the functionality of a chemical control system by evaluating classic genetic algorithm problems: Koza's Santa Fe trail, Je↵erson’s John Muir trail, and threeSanta Fe trail segments and presents the first implementation of a simulated chemical memory in two di↵erent models that can reliably capture and store information over time. Expand
Towards Temporal Logic Computation Using DNA Strand Displacement Reactions
It is shown that DNA strand displacement reaction networks can be used to implement computations that check certain temporal relationships within time-varying input signals, and opens up the possibility of developing DNA circuits capable of long-term monitoring of processes such as cellular function. Expand
COEL: A Web-based Chemistry Simulation Framework
A new enterprise chemistry simulation framework, COEL, which provides DNA-strand displacement transformations and visualization, GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export and is the rst web-based framework of its kind. Expand
Learning Two-Input Linear and Nonlinear Analog Functions with a Simple Chemical System
This paper extends the chemical perceptron, a model previously proposed by the authors, to function as an analog instead of a binary system, and shows that the perceptron is able to learn linear and nonlinear (quadratic) functions of two inputs. Expand
Novel Methods for Learning and Adaptation in Chemical Reaction Networks
Several approaches to learning and adaptation in Chemical Reaction Networks (CRNs), a type of simulated chemistry, where species are unstructured, i.e., they are identified by symbols rather than molecular structure, and their dynamics or concentration evolution are driven by reactions and reaction rates that follow mass-action and Michaelis-Menten kinetics are proposed. Expand
COEL: A Cloud-Based Reaction Network Simulator
COEL is introduced, a web- and cloud-based CRN simulation framework that does not require a local installation, runs simulations on a large computational grid, provides reliable database storage, and offers a visually pleasing and intuitive user interface. Expand
Feedforward Chemical Neural Network: An In Silico Chemical System That Learns xor
This work design and simulate a chemically implemented feedforward neural network, which learns by a novel chemical-reaction-based analogue of backpropagation, which allows a variety of network topologies to be constructed from the same building blocks. Expand
Complex Systems Modelling and Simulation Cosmos 2014 Programme Committee Using Cosmos to Reverse Engineer a Domain Model for Aevol . . 61 Using the Cosmos Approach to Study Schelling's Bounded Neighbourhood Model
The basic CoSMoS process concerns the design, implementation, and use of a simulation built from scratch. However, the CoSMoS approach may be tailored and adapted for other styles of use. Here weExpand


Computational functions in biochemical reaction networks.
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
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.
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
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
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
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
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
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
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