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Solving minimum -vertex separator problems in the
AdlemanLipton model
Ardashir Dolati1, M.S Haghighat2, Saeed Safaei2,*, Hajar Mozaffar3
1) Department of Mathematics, Shahed University, Tehran, Tehran, Iran
2) Department of Mathematics, Arak University, Arak, Markazi, Iran
3) Computer Engineering, Isfahan University, Isfahan, Isfahan, Iran
(9) Discard (T): for a given test tube T it discards the tube T;
(10) Append (T, Z): for a given test tube T and a given short
DNA singled strand Z it appends Z onto the end of every
strand in the tube T;
After above six steps of manipulation, singled strands in tube (2 - 2) Separation (T1 ,{B i 2A i }, T2 )
P will encode all 3n partitions of V in the form of n-digit (2 - 3) Append (T2 , y k,i )
ternary numbers. For example, for the graph in Fig. 1 with n8
we have, e.g. the singled (2 - 4) Merge (T1 , T2 )
strand
# B8 0 A8 B7 0 A7 B6 2 A6 B5 2 A5 B4 2 A4 B31A3 B2 1A2 B1 0 A1 # , End For
which denotes the partition R = { A4 , A5 , A6 } , S = { A2 , A3 } , (2 - 5) Merge (P, T1 )
T = { A1 , A7 , A8 } corresponding to the ternary number
End For
00222110 .
(2 - 6) Separation (P,{y11}, T1 )
Existence of Bi kAi in a singled strand, where k is equal to 0, 1
(2 - 7) Discard (T1 )
or 2 means vertex i is in T, S or R respectively.
In the above operation we use two For clauses. Thus this
This operation can be finished in O( 1) steps since each operation can be finished in O(n 2 ) steps since each single
manipulation above works in O(1 ) steps. manipulation above works in O(1) steps.
3.3 Counting number of vertices of each subset 3.4 Finding the minimum size of subset T
and select invalid partition Now, among all (valid) partitions, we separate the
partitions in which the size of T is minimum.
For each element in the data pool that represents some
partition {R, S , T } of V , we count the vertices number of For i = 1 to i = n
R , S and T . Let the partition {R, S , T } correspond the n- (4 - 1) Separation (P, {33...33
123}, T1 )
digit ternary number an K ai K a j K a1 . For each element ai i times
with ai = 2 we append the singled strand 5 to the end of (4 - 2) Separation (T1 , {33...33
123 }, T2 )
the singled strand which encode the n-digit ternary i +1 times
number a n K ai K a j K a1 .and also For each element ai with If Detect (T2 ) is yes , then End For and i is the number of
ai = 1 we append the singled strand 4 and For each element vertex corresponding to minimum - vertex separator
ai with ai = 0 we append the singled strand 3 to the end of , else continue the circulation.
(3 - 1) Separation (P, {B i 2A i }, T1 )
5 References
[1] Adleman, L.M., Molecular computation of solution to
combinatorial problems. Science 266, 1021 1024, 1994.
[5] Guo, M.Y., Chang, W.L., Ho, M., Lu, J., Cao, J.N. Is
optimal solution of every NP-complete or NP-hard problem
determined from its characteristic for DNA-Based computing.
BioSystem 80, 7182, 2005.
[9] Li, D., Huang, H., Li, X., Li, X. Hairpin formation in
DNA computation presents limits for large NP-complete
problems. BioSystem 72, 203207, 2003.