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.

中文翻译：

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DNA步行器电路基于Petri网的2D设计。

我们考虑局部DNA计算，其中DNA链沿着二进制决策图行走以计算二进制函数。设计可靠的助步器电路的挑战之一在于泄漏过渡，当助步器跳入决策图的另一个分支时会发生泄漏。我们会自动识别泄漏过渡，从而可以对电路设计，设计比较和设计优化进行详细的定性和定量评估。识别泄漏跃迁的能力是优化DNA电路布局过程中的重要步骤，其目的是在最小化电路面积的同时最大程度地减小电路固有的计算误差。我们的DNA Walker电路的2D建模方法依赖于有色随机Petri网，可实现功能，拓扑和维度都集成在一个二维模型中。我们的建模和分析方法可以轻松扩展到3维步行者系统。