Welcome to Scribd, the world's digital library. Read, publish, and share books and documents. See more
Download
Standard view
Full view
of .
Save to My Library
Look up keyword
Like this
2Activity
0 of .
Results for:
No results containing your search query
P. 1
Solving traveling salesman problem in the Adleman–Lipton model

Solving traveling salesman problem in the Adleman–Lipton model

Ratings: (0)|Views: 310 |Likes:
Published by slartibartfastibast
The traveling salesman problem is to find a minimum cost (weight) path for a given set of cities (vertices) and roads (edges). The path must start at a specified city and end there after going through all the other given cites only once. It is a classical NP-complete problem in graph theory. In this paper, we consider a DNA procedure for solving the traveling salesman problem in the Adleman–Lipton model. The procedure works in O(n) steps for the traveling salesman of an edge-weighted graph with n vertices.
The traveling salesman problem is to find a minimum cost (weight) path for a given set of cities (vertices) and roads (edges). The path must start at a specified city and end there after going through all the other given cites only once. It is a classical NP-complete problem in graph theory. In this paper, we consider a DNA procedure for solving the traveling salesman problem in the Adleman–Lipton model. The procedure works in O(n) steps for the traveling salesman of an edge-weighted graph with n vertices.

More info:

Published by: slartibartfastibast on Jan 11, 2013
Copyright:Attribution Non-commercial

Availability:

Read on Scribd mobile: iPhone, iPad and Android.
download as PDF, TXT or read online from Scribd
See more
See less

05/14/2014

pdf

text

original

 
Solving traveling salesman problem in the Adleman–Lipton model
Zhaocai Wang
a,
, Yiming Zhang
b
, Weihua Zhou
c
, Haifeng Liu
a
a
College of Information, Shanghai Ocean University, Shanghai 201306, PR China
b
School of Economics and Management, Yancheng Institute of Technology, Yancheng 224051, PR China
c
The Central Laboratory, Shandong Vocational College of Science and Technology, Weifang 261053, PR China
a r t i c l e i n f o
Keywords:
DNA computingThe traveling salesman problemAdleman–Lipton modelNP-complete problem
a b s t r a c t
The traveling salesman problem is to find a minimum cost (weight) path for a given set of cities (vertices) and roads (edges). The path must start at a specified city and end thereaftergoingthroughalltheothergivencitesonlyonce.ItisaclassicalNP-completeproblemingraphtheory. Inthis paper, we consider a DNAprocedure for solving the traveling sales-man problem in the Adleman–Lipton model. The procedure works in
O
ð
n
Þ
steps for thetraveling salesman of an edge-weighted graph with
n
vertices.Crown Copyright
Ó
2012 Published by Elsevier Inc. All rights reserved.
1. Introduction
DNAcomputingisanewlyemerginginterdisciplinarysciencethatusesDNAmolecularbiotechnologiestosolveproblemsincomputerscienceormathematics.DNAcomputingcanexecutebillionsofoperationssimultaneously. DNAalsoprovidesahuge storage capacity since they encode information on the molecular scale. As the first work for DNA computing, Adleman[1]presented an idea of solving the Hamiltonian path problemof size
n
in
O
ð
n
Þ
steps using DNA molecules. Lipton[2]dem-onstratedthatAdleman’sexperimentcouldbeusedtodeterminetheNP-completesatisfiabilityproblem.Inrecentyears,lotsof papers have occurred for designing DNA procedures and algorithms to solve various NP-complete problems[3–9].In this paper, a DNA procedure is introduced for figuring out solutions of the traveling salesman problem: for an edge-weightedgraph
G
¼ ð
;
Þ
findaminimumcost(weight)path.Thepathmustbeginataspecifiedcity(vertice)andendthereafter going through all the other given cites (vertices) only once. For instance, the edge-weighted graph
G
inFig. 1definessuch a problem. We assume that the starting and ending vertice is
1
. It is not difficult to find that the path
1
!
7
!
6
!
5
!
4
!
3
!
2
!
1
with total weight 21 is a solution to the traveling salesman problem forgraph
G
inFig. 1.The rest of this paper is organized as follows. In Section2, the Adleman–Lipton model is introduced in detail. Section3 introducesa DNAalgorithmfor solving the travelingsalesman problemandthe complexityof the proposedalgorithmis de-scribed. We give conclusions in Section4.
2. The Adleman–Lipton model
The DNA operations proposed by Aldeman[1]and Lipton[2]are described below. These operations will be used for fig- uringoutsolutionsofthetravelingsalesmanprobleminthispaper.TheAdleman–Liptonmodel:A(test)tubeisasetofmol-ecules of DNA (i.e., a multi-set of finite strings over the alphabet {A,C,G,T}). Given a tube, one can perform the followingoperations[9]: Merge, Copy, Detect, Separation, Selection, Cleavage, Annealing, Denaturation, Discard and Read. Since these
0096-3003/$ - see front matter Crown Copyright
Ó
2012 Published by Elsevier Inc. All rights reserved.http://dx.doi.org/10.1016/j.amc.2012.08.073
Corresponding author.
E-mail address:
Contents lists available atSciVerse ScienceDirect
Applied Mathematics and Computation
journal homepage:www.elsevier.com/locate/amc
 
10manipulationsareimplementedwithaconstantnumberofbiologicalstepsforDNAstrands[3],weassumethatthecom-plexity of each manipulation is
O
ð
1
Þ
steps.
3. DNA algorithm for the traveling salesman problem
Let
G
¼ ð
;
Þ
be a edge-weighted graph with the set of vertices
¼ f
k
j
k
¼
1
;
2
;
. . .
;
n
g
and the set of edges
¼ f
e
i
;
 j
j
1
6
i
;
 j
6
n
;
i
 j
g
. Note that both
e
i
;
 j
and
e
 j
;
i
are in
if the vertices
i
and
 j
are connected by an edge. Without lossof generality, we assume that
1
is the starting and ending vertex. Let
j
j ¼
s
, Then,
s
6
12
n
ð
n
þ
1
Þ
.In the following, we use the symbols
#
;
 A
k
;
B
k
ð
k
¼
1
;
2
. . .
;
n
Þ
and
w
i
;
 j
to denote distinct DNA singled strands for which
jj
#
jj ¼ jj
 A
k
jj ¼ jj
B
k
jj
, where
jj Á jj
denotes the length of the DNA singled strand. The symbols
A
k
B
k
ð
k
¼
2
;
3
;
. . .
;
n
Þ
denote thevertex
k
. Meanwhile the symbols
#
 A
1
B
1
;
 A
1
B
1
#
denote the starting and ending vertex
1
which the symbol
#
is the signalofstartingandending.Supposethatallweightsinthegivengrapharecommensurable.TheDNAsingledstrands
w
i
;
 j
areusedto denote the weights
k
i
;
 j
on the edges
e
i
;
 j
2
with
jj
w
i
;
 j
jj ¼
k
i
;
 j
w
where
w
is a constant, e.g., take
w
¼
5 mer in the followingdiscussion, Then, the
jj
w
i
;
 j
jj ¼
5
k
i
;
 j
. Let
m
¼
max
e
i
;
 j
2
5
k
i
;
 j
and
jj
#
jj ¼ jj
 A
k
jj ¼ jj
B
k
jj ¼
n
Ã
m
¼
. For example, for the graph inFig. 1. We can let
m
¼
max
f
5
Ã
3
;
5
Ã
5
;
5
Ã
7
;
5
Ã
9
;
5
Ã
10
g ¼
50 mer, Then
jj
#
jj ¼ jj
 A
k
jj ¼ jj
B
k
jj ¼
n
Ã
m
¼
¼
7
Ã
50
¼
350mer. Let
¼ f
w
i
;
 j
;
#
 A
1
B
1
;
 A
1
B
1
#
;
 A
k
B
k
j
e
i
;
 j
2
;
k
¼
2
;
3
;
. . .
;
n
g
;
¼ f
#
;
 A
1
;
B
1
;
B
i
w
i
;
 j
 A
 j
j
e
i
;
 j
2
;
1
6
i
;
 j
6
n
;
i
 j
g
:
We design the following algorithm to solve the traveling salesman problem and give the corresponding DNA operationsas follows:(1) We choose all possible paths, which start at
1
and end at
1
.(1-1)
Merge
ð
;
Þ
;(1-2)
Annealing 
ð
Þ
;(1-3)
Denaturation
ð
Þ
;(1-4)
Separation
ð
;
f
#
 A
1
B
1
g
;
tmp
Þ
;(1-5)
Discard
ð
Þ
;(1-6)
Separation
ð
tmp
;
f
 A
1
B
1
#
g
;
Þ
;Aftertheabovesixstepsofmanipulations,thesingledstrandsintube
willencodeallpathswhichstartandendat
1
.For example, for the graph inFig. 1, we have singled strands:
#
 A
1
B
1
w
1
;
2
 A
2
B
2
w
2
;
7
 A
7
B
7
w
7
;
6
A
6
B
6
w
6
;
4
 A
4
B
4
w
4
;
3
 A
3
B
3
w
3
;
1
 A
1
B
1
#
2
which correspond to the path
1
!
2
!
7
!
6
!
4
!
3
!
1
respectively. This operation can be fin-ished in
O
ð
1
Þ
steps since each manipulation above works in
O
ð
1
Þ
steps.(2) We choose all possible paths which pass all the other vertices (cities) at least once.For
k
¼
2 to
k
¼
n
.(2-1)
Separation
ð
;
f
 A
k
B
k
g
;
Þ
;(2-2)
Discard
ð
Þ
;(2-3)
Merge
ð
;
Þ
;End forIn the above operations, we get the strands that denote starting and ending specified vertex
1
, synchronously goingthrough all the other vertices at least once. For example, for the graph inFig. 1, we have singled strands:
Fig. 1.
An edge-weighted graph
G
with 7 vertices.2268
Z. Wang et al./Applied Mathematics and Computation 219 (2012) 2267–2270
 
#
 A
1
B
1
w
1
;
2
 A
2
B
2
w
2
;
7
 A
7
B
7
w
7
;
6
 A
6
B
6
w
6
;
5
 A
5
B
5
w
5
;
4
 A
4
B
4
w
4
;
3
A
3
B
3
w
3
;
2
 A
2
B
2
w
2
;
1
 A
1
B
1
#
2
which denote the path
1
!
2
!
7
!
6
!
5
!
4
!
3
!
2
!
1
. Of course, it cannot be the optimum solution because thepath passes the vertex
2
twice. In the above operation we use a ‘‘For’’ clause. Thus this operation can be finishedin
O
ð
n
Þ
steps since each single manipulation above works in
O
ð
1
Þ
steps.(3) Each singled strand in tube
denotes the path starting and ending at
1
, synchronously passing the other
n
À
1 ver-ticesatleastonce.Whilethetravelingsalesmanproblemrequiresgoingthroughalltheothergivenverticesonlyonce.So first of all, we set the length of DNA stands as following:
m
¼
max
e
i
;
 j
2
5
k
i
;
 j
and
jj
#
jj ¼ jj
 A
k
jj ¼ jj
B
k
jj ¼
nm
¼
. ThelengthofStrands
 A
k
B
k
denotingthevertex
k
is 2
. Thelengthofthestrands
#
denotingthestartingandendingsignalis
. Consequently the length of DNA strands which denote starting and ending vertex
1
then passing the other
n
À
1vertices one time in tube
must be between
ð
2
n
þ
4
Þ
and
ð
2
n
þ
5
Þ
. We can get the strands denoting the optimumsolution in this length range. This is done by the following manipulations.For
k
¼
1 to
k
¼
.(3-1)
Selection
ð
;
ð
2
n
þ
4
Þ
þ
k
;
Þ
;(3-2) If 
Detect 
ð
Þ
is ‘‘yes’’, thenEndFor andthe minimumcost (weight) pathis obtained, else continuethecirculation.In the above operation we use a ‘‘For’’ clause. Thus If 
k
is independent of 
n
, then this operation can be finished in
O
ð
n
Þ
steps since each single manipulation above works in
O
ð
1
Þ
steps.End for(4) Finally the
Read
operationis applied to givingthe exact edges in the travelingsalesman problem. For example, for thegraph inFig. 1, the minimum cost (weight) paths are
1
!
2
!
3
!
4
!
5
!
6
!
7
!
1
and
1
!
7
!
6
!
5
!
4
!
3
!
2
!
1
with total weights 21.(4-1)
read
ð
Þ
;Thefollowingtheoremtellsthatthealgorithmproposedabovereallycangetsolutionsofthetravelingsalesmanprob-lem in
O
ð
n
Þ
steps using DNA molecules.
 Theorem 1.
Suppose m is a limit quantity having nothing to do with n, So m
¼
O
ð
1
Þ
. We can get the solution of traveling salesman problem with n vertices in O
ð
n
Þ
steps.
Proof.
After the operations of second step, all the singled strands in tube
denote starting and ending vertex
1
, synchro-nously passing the other vertices at least one time. We reasonably design the length of 
#
;
 A
k
;
B
k
and
w
i
;
 j
, For
jj
w
i
;
 j
jj ¼
5
Ã
k
i
;
 j
ð
k
i
;
 j
is the weights of edge
e
i
;
 j
2
Þ
;
m
¼
max
f
5
Ã
k
i
;
 j
g ¼
max
fjj
w
i
;
 j
jjg
;
jj
#
jj ¼ jj
 A
k
jj ¼ jj
B
k
jj ¼
n
Ã
m
¼
:
So we define
as the strands which denote starting and ending vertex
1
, then going through the other
n
À
1 vertices onlyonce. Then,
can be described:
#
 A
1
B
1
w
1
;
d
2
 A
d
2
B
d
2
ÁÁÁ
 A
d
n
B
d
n
w
d
n
;
1
 A
1
B
1
#
:
So
jj
jj ¼ jj
#
jj þ jj
 A
1
jj þ jj
B
1
jj þ jj
w
1
;
d
2
jj þ ÁÁÁ þ jj
w
d
n
;
1
jj þ jj
 A
1
jj þ jj
B
1
jj þ jj
#
jj¼ jj
#
jj þ jj
 A
1
jj þ jj
B
1
jj þ
X
e
di
;
d j
2
jj
w
d
i
;
d
 j
jj þ
X
nd
k
¼
2
jj
 A
d
k
B
d
k
jj þ jj
 A
1
jj þ jj
B
1
jj þ jj
#
jj¼
þ
þ
þ
X
e
di
;
d j
2
jj
w
d
i
;
d
 j
jj þ
2
ð
n
À
1
Þ
þ
þ
þ
¼ ð
2
n
þ
4
Þ
þ
X
e
di
;
d j
2
jj
w
d
i
;
d
 j
jj
*
0
6
X
e
di
;
d j
2
jj
w
d
i
;
d
 j
jj
6
)
ð
2
n
þ
4
Þ
6
jj
jj
6
ð
2
n
þ
5
Þ
:
The length of strands which denote passing the other vertices more than once must be longer than
ð
2
n
þ
5
Þ
. So we canget the solution in step
ð
3
Þ
in appropriate length range.
h
Besides, the manipulates of algorithm can be entirely finished in finite operations. Such as step (1), (4) in
O
ð
1
Þ
, step (2) in
O
ð
n
Þ
, Simultaneity step (3) in
O
ð
Þ
. Because
O
ð
n
Þ ¼
O
ð
mn
Þ
and
O
ð
m
Þ ¼
O
ð
1
Þ
, then
O
ð
Þ ¼
O
ð
n
Þ
. In conclusion, We can getthe solution of traveling salesman problem with
n
vertices in
O
ð
n
Þ
.
4. Conclusions
Inthispaper,weproposeaprocedureforthetravelingsalesmanNP-completeproblemintheAdleman–Liptonmodel.Theprocedure works in
O
ð
n
Þ
steps for the travelingsalesman problemof an edge-weightedgraph with
n
vertices. All our results
 Z. Wang et al./Applied Mathematics and Computation 219 (2012) 2267–2270
2269

You're Reading a Free Preview

Download
/*********** DO NOT ALTER ANYTHING BELOW THIS LINE ! ************/ var s_code=s.t();if(s_code)document.write(s_code)//-->