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Title: Petri-net-based 2D Design of DNA Walker Circuits
Authors: Gilbert, D
Heiner, M
Rohr, C
Keywords: Stochastic petri nets;Coloured petri nets;DNA walker systems;Design assessment;Leakage transitions;Structural analysis
Issue Date: 2018
Citation: Natural Computing, 2018
Abstract: We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative assessment of circuit designs, design comparison, and design optimisation. The ability to identify leakage transitions is an important step in the process of optimising DNA circuit layouts where the aim is to minimise the computational error inherent in a circuit while minimising the area of the circuit. Our 2D modelling approach of DNA walker circuits relies on coloured stochastic Petri nets which enable functionality, topology and dimensionality all to be integrated in one two-dimensional model. Our modelling and analysis approach can be easily extended to 3-dimensional walker systems.
ISSN: 1567-7818
Appears in Collections:Dept of Computer Science Research Papers

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