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Project Description

Content

In graph theory, the Single Pair Shortest Path Problem (SPP) is one of the basic problems with many applications. Many computational methodssuch as Dijkstra algorithm, A-star search algorithm and Floyd-Warshal algorithm etc., can solve it in a tolerable computational complexity. However, as the technology of the traditional silicon computers is gradually meeting its physical limits, new methods of the high-volume computing has been looked for for years. As developing rapidly, synthetic biology makes bacterial computing possible and great potential. Programming Escherichia coli, the simplest model organism to implement these kinds of basic problems is very necessary. It will bring up with a brand new bio-computing method with better computational complexity.

Here, we will design a series of genetic circuits in Escherichia coli to solve the SPP in a directed graph. The nodes and arrows are programed as well-assigned promoters and transcription factors (TFs) respectively. For each arrow, the promoter of its source node initiates the expression of the TF which induces specifically the promoter of the target node. The paths in the graph are described by the transcriptional regulatory cascades. The promoter of destination node in SPP is followed by a green fluorescent protein (GFP) as a reporter. The temporal ordering of the fluorescent protein expression in E.coli reflects the distance difference among varied paths. According theoretical analysis, we can find the the shortest path consisted by all those arrows with linear computational complexity.

References

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