RTL2DNA: An automatic flow of large-scale DNA-based logic circuit design

Document Type : Article


1 Faculty of Computer Engineering, University of Isfahan, Isfahan, Iran

2 Faculty of Computer Science and Engineering, Shahid Beheshti University, G.C., Velenjak, Tehran 19839-63113, Iran


DNA computing is a new kind of computation for solving the complex problems with the huge degree of parallelism. Recently it is found that DNA-based logic systems can be useful in many of biomedical applications such as early cancer detection. As an example, DNA logic systems have been utilized successfully to detect the risky patterns of nucleotide-based cancer biomarkers (microRNAs).
In this paper, an automatic design flow is proposed to facilitate the design, verification and physical implementation of multi-stage and large-scale DNA logic circuits. Digital Microfluidic Biochips (DMFB) have been used recently as a promising platform for efficient implementation of DNA-based computing systems and circuits. We used this technology as the physical platform for implementation of DNA-based circuits.
Our experiments and implementations show the feasibility, accuracy, efficiency and simplicity of the proposed design flow. Final DNA reactions that are synthesized by the proposed design flow are verified and simulated with stochastic DNA-reaction simulators to prove the correctness of the proposed design flow. This design flow can open a new horizon for researchers and scientists to design, implement and evaluate the DNA-based logic systems.


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