25 research outputs found
Biomodelkit - a framework for modular biomodel-engineering
Otto-von-Guericke-Universität Magdeburg, Fakultät für Naturwissenschaften, Dissertation, 2017von Dipl.-Ing. Mary-Ann BlätkeLiteraturverzeichnis: Seite [177]-18
Petri-net-based 2D Design of DNA Walker Circuits
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