A New Approach to Advance the DNA

ComputingZ. F. Qiu and M. Lu

Applied Soft Computing, v.3, pp.177-189, 2003

Summarized by In-Hee Lee

Introduction

• Provide new model.• Provide new algorithm to solve 3-

Coloring problem.

New(?) Model

• Synthesis• Ligation L(P3, P1, P2)– Each strand in P1 is ligated to to every other strand in

P2.• Separation S(P, Pt, Pf, c)– Partition P under criteria c.– Pt : strands that meet the criteria c– Pf : strands that do not meet c

• Detection– Check if there is any strand left in the pool.

3-Coloring Problem

• Paint all nodes with one of 3 colors.• Do not paint nodes which are directly

connected by edge with the same color.

• Input: graph• Answer: 3-colorable or not.

The New(?) Algorithm

• Divide and conquer• Divide the graph until one node is left in ea

ch partition.• Edge 를 붙여가면서 edge 의 양끝 node 가

같은 색인 것은 제거 .• 마지막에 남은 것이 있으면 그 그래프는 3-

colorable.

Performance

• Up to 256 vertices in 2 days.– Assumes average DNA operation takes

20 min.

• With 1 % false negative error rate,– The overall false negative rate can be

reduced to 0.0001%.

Conclusion

• A new model for DNA computing is introduced.

• Parallelization of the separation operation on multiple edges and other process.