cell and microbial engineering laboratory solving tsp on lab-on-a-chip 1 jiyoun lee
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1Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Solving TSP on Lab-on-a-Chip
Jiyoun Lee
2Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
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
3Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
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0
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2 5
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0 1 2 3 4 5 6 0 (21)
start
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3end
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)
4Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
vertex weight(with low GC)
vertex weight(with low GC)
vertexedge edge
low melting temperature
weight
vertex weight vertex weight vertexweightweightlow melting temperature
more amplification by more denaturation
5Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
ds DNA
denaturation : more denaturation of DNA strands which have less weights
primer annealing
polymerization
6Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
ProcedureGenerating random paths
through the graph
Keep only those paths thatbegin with vin
Keep only those pathsthat enter exactly n vertices
Keep only those paths thatenter all of the vertices ofthe graph at least once
Separation of the solutions
Generating sequences& LIgation reaction
PCR with vin as primers
Gel electrophoresis separationby size
Affinity-purification with a biotin-avidin magnetic beads system
TGGE
Figure out the path Sequencing & readout
7Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
ProcedureGenerating random paths
through the graph
Keep only those paths thatbegin with vin
Keep only those pathsthat enter exactly n vertices
Keep only those paths thatenter all of the vertices ofthe graph at least once
Separation of the solutions
Generating sequences& LIgation reaction
PCR with vin as primers
Gel electrophoresis separationby size
Affinity-purification with a biotin-avidin magnetic beads system
TGGE
Figure out the path Sequencing & readout
8Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Affinity separation (7 nodes)
Ligation(Connecting each ssDNA)
PCR with Vin
Hybridization(Generating all possible paths )
Size separation by electrophoresis
Sequencing
Temperature gradient in reservoir
Isothermal reaction in reservoir
Expected problems : buffer compositionLigation bufferAffinity separation bufferCf) conventional method Purification of DNA by ethanol precipitation
Paramagnetic separationusing biotin-avidin interaction
Temperature cycling in reservoir
CE (or CGE)
9Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
Affinity unit
Reaction chamber for hybridizationand ligation
Reaction chamber for PCR
Electrophoresisseparation
Buffer change
Buffer changeVolume reduction?
I wish to..Eliminate the affinity stepChange the buffers in flow
10Cell and Microbial Engineering Laboratory
Solving TSP on Lab-on-a-Chip
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 …