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Solving TSP on Lab-on-a-Chip

This paper discusses the application of the Traveling Salesman Problem (TSP) on a Lab-on-a-Chip platform. It explores the use of graphs, edges, and costs to find Hamiltonian paths with the smallest sum of costs.

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Solving TSP on Lab-on-a-Chip

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  1. Solving TSP on Lab-on-a-Chip Jiyoun Lee

  2. Introduction • TSP (Traveling Salesman Problem) • Graph with given vertexes, edges, and costs (weights) •  Hamiltonian paths containing the smallest sum of costs • Airlines, transportation • Graph dimension • 7 vertexes, 24 edges, 5 costs

  3. 3 4 3 7 1 3 0 11 11 start 3 3 6 5 3 end 3 9 3 2 5 0  1  2  3  4  5  6  0 (21) 0  1  6  5  4  3  2 0 (31) 0  2  1  3  4  5  6  0 (27) 0  2  3  4  5  6  1  0 (31) 0  6  5  4 3  1  2  0 (27) 0  6  5  4  3  2  1  0 (21)

  4. (with low GC) (with low GC) vertex weight weight vertex weight vertex edge edge low melting temperature vertex weight weight vertex weight vertex weight low melting temperature more amplification by more denaturation

  5. ds DNA denaturation : more denaturation of DNA strands which have less weights primer annealing polymerization

  6. Procedure Generating random paths through the graph Generating sequences & LIgation reaction Keep only those paths that begin with vin PCR with vin as primers Keep only those paths that enter exactly n vertices Gel electrophoresis separation by size Keep only those paths that enter all of the vertices of the graph at least once Affinity-purification with a biotin -avidin magnetic beads system Separation of the solutions TGGE Figure out the path Sequencing & readout

  7. Procedure Generating random paths through the graph Generating sequences & LIgation reaction Keep only those paths that begin with vin PCR with vin as primers Keep only those paths that enter exactly n vertices Gel electrophoresis separation by size Keep only those paths that enter all of the vertices of the graph at least once Affinity-purification with a biotin -avidin magnetic beads system Separation of the solutions TGGE Figure out the path Sequencing & readout

  8. Hybridization (Generating all possible paths ) Temperature gradient in reservoir Ligation (Connecting each ssDNA) Isothermal reaction in reservoir • Expected problems : buffer composition • Ligation buffer • Affinity separation buffer • Cf) conventional method • Purification of DNA by ethanol precipitation Affinity separation (7 nodes) PCR with Vin Paramagnetic separation using biotin-avidin interaction Size separation by electrophoresis Temperature cycling in reservoir Sequencing CE (or CGE)

  9. Reaction chamber for hybridization and ligation Buffer change Affinity unit I wish to.. Eliminate the affinity step Change the buffers in flow Buffer change Volume reduction? Reaction chamber for PCR Electrophoresis separation

  10. Questions and Discussions… • Danny’s idea: addition of salts.. • Not reservoir type, but channel type • In English, please… • Questions to Danny: • Method for inserting beads to channel. • Channeling effect or something… • TRIS, .. Some buffer names.. • Many beads – Yield of …

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