5 research outputs found
Delay Line as a Chemical Reaction Network
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 in
a chemistry that can reliably capture information over an extended period of
time. The delay line is capable of parallel operations in a single instruction,
multiple data (SIMD) fashion.
Using Michaelis-Menten kinetics, we describe the chemical delay line
implementation featuring an enzyme acting as a means to reduce copy errors. We
also discuss how information is randomly accessible from any element on the
delay line. Our work shows how the chemical delay line retains and provides a
value from a previous cycle. The system's modularity allows for integration
with existing chemical systems. We exemplify the delay line capabilities by
integration with a threshold asymmetric signal perceptron to demonstrate how it
learns all 14 linearly separable binary functions over a size two sliding
window. The delay line has applications in biomedical diagnosis and treatment,
such as smart drug delivery.Comment: 9 pages, 11 figures, 6 table
COEL: A Web-based Chemistry Simulation Framework
The chemical reaction network (CRN) is a widely used formalism to describe
macroscopic behavior of chemical systems. Available tools for CRN modelling and
simulation require local access, installation, and often involve local file
storage, which is susceptible to loss, lacks searchable structure, and does not
support concurrency. Furthermore, simulations are often single-threaded, and
user interfaces are non-trivial to use. Therefore there are significant hurdles
to conducting efficient and collaborative chemical research. In this paper, we
introduce a new enterprise chemistry simulation framework, COEL, which
addresses these issues. COEL is the first web-based framework of its kind. A
visually pleasing and intuitive user interface, simulations that run on a large
computational grid, reliable database storage, and transactional services make
COEL ideal for collaborative research and education. COEL's most prominent
features include ODE-based simulations of chemical reaction networks and
multicompartment reaction networks, with rich options for user interactions
with those networks. COEL provides DNA-strand displacement transformations and
visualization (and is to our knowledge the first CRN framework to do so), GA
optimization of rate constants, expression validation, an application-wide
plotting engine, and SBML/Octave/Matlab export. We also present an overview of
the underlying software and technologies employed and describe the main
architectural decisions driving our development. COEL is available at
http://coel-sim.org for selected research teams only. We plan to provide a part
of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl
COEL: A Cloud-Based Reaction Network Simulator
Chemical Reaction Networks (CRNs) are a formalism to describe the macroscopic behavior of chemical systems. We introduce COEL, a web- and cloud-based CRN simulation framework, which 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. We present an overview of the underlying software, the technologies, and the main architectural approaches employed. Some of COEL’s key features include ODE-based simulations of CRNs and multicompartment reaction networks with rich interaction options, a built-in plotting engine, automatic DNA-strand displacement transformation and visualization, SBML/Octave/Matlab export, and a built-in genetic-algorithm- based optimization toolbox for rate constants. COEL is an open-source project hosted on GitHub (doi:10.5281/zenodo.46544), which allows interested research groups to deploy it on their own sever. Regular users can simply use the web instance at no cost at coel-sim.org. The framework is ideally suited for a collaborative use in both research and education
Learning Two-input Linear and Nonlinear Analog Functions with a Simple Chemical System
The current biochemical information processing systems behave in a predetermined manner because all features are defined during the design phase. To make such unconventional computing systems reusable and programmable for biomedical applications, adaptation, learning, and self-modification baaed on external stimuli would be highly desirable. However, so far, it haa been too challenging to implement these in real or simulated chemistries. In this paper we extend the chemical perceptron, a model previously proposed by the authors, to function as an analog instead of a binary system. The new analog asymmetric signal perceptron learns through feedback and supports MichaelisMenten kinetics. The results show that our perceptron is able to learn linear and nonlinear (quadratic) functions of two inputs. To the best of our knowledge, it is the first simulated chemical system capable of doing so. The small number of species and reactions allows for a mapping to an actual wet implementation using DNA-strand displacement or deoxyribozymes. Our results are an important step toward actual biochemical systems that can learn and adapt