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Unformatted text preview: the directed Hamiltonian Path Problem (HPP). Recall that the HPP involves ﬁnding a path through a graph that visits each
vertex exactly once. The instance of the HPP that Adleman solved is depicted
in Fig. 5.2, with the unique Hamiltonian Path (HP) highlighted by a dashed
232 line.
CHAPTER IV. MOLECULAR COMPUTATION
1 2 3 7 6 4
5 Fig. 5.2. Instance of the HPP solved by Adleman Figure IV.6: HPP solved by Adleman. The HP is indicated by the dotted
edges. [source: Amos, Fig. 5.2]
Adleman’s approach was simple:
1. Generate strands encoding random paths such that the Hamiltonian Path
(HP) is represented with high probability. The quantities of in his seminal
They did it in a manner similar to the one Adleman usedDNA used
far exceeded
1994 paper.”4 those necessary for the small graph under consideration, so
it is likely that many strands encoding the HP were present.
2. Remove all strands that do not encode the HP.
3. Check that the remaining strands encode a solution to the HPP. B.1.b Problem Representation The individual steps were implemented as follows:
Stage 1: of Adleman’s algorithm is a a distinct 20mer sequence of
¶1. The heartEach vertex and edge was assignedclever way to encode candidate
DNA (Fig. DNA.This implies that strands encoding a HP were of length 140
paths in 5.3a).
b.p. Sequences representing edges act as ‘splints’ between strands representing
¶2. their endpoints (Fig. 5.3b). represented by singlestranded 20mers, that
Vertices: Vertices were
In formal terms, the sequence associated with an edge i → j is the 3’ 10is, of the sequence representing vi followed
mer sequences of 20nt (...
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 Fall '13
 BruceMacLennan

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