ERROR-TOLERANT MINIMUM FINDING WITH DNA COMPUTING

In the past decade, DNA computing has become one of the powerful approaches to solve a class of intractable computational problems such as Hamiltonian path problem and SAT problem. The power of DNA computing comes from the fact that it has great potential of massive data storage and processing computation over data in parallel. In this paper, an algorithm for solving the minimum finding problem is proposed in theory with a randomized scheme – the broadcasting scheme on the broadcast communication model. Our method is a novel strategy for optimization in DNA computing, since it can tolerate some chemistry reaction and experiment errors. The less errors are, the less the number of required iterations is. A series of computer simulations are also performed and analyzed to demonstrate the feasibility of the algorithm and the designed experiment.

[1]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[2]  John Capetanakis,et al.  Tree algorithms for packet broadcast channels , 1979, IEEE Trans. Inf. Theory.

[3]  Steven P. Levitan,et al.  Finding an extremum in a network , 1982, ISCA '82.

[4]  Selim G. Akl,et al.  Design and analysis of parallel algorithms , 1985 .

[5]  Leonard Kleinrock,et al.  Broadcast Communications and Distributed Algorithms , 1986, IEEE Transactions on Computers.

[6]  Gerald F. Joyce,et al.  Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA , 1990, Nature.

[7]  Richard C. T. Lee,et al.  Parallel Graph Algorithms Based Upon Broadcast Communications , 1990, IEEE Trans. Computers.

[8]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[9]  W. Stemmer.  Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[10]  R J Lipton,et al.  DNA solution of hard computational problems. , 1995, Science.

[11]  Chang-Biau Yang,et al.  A Fast Maximum Finding Algorithm on Broadcast Communication , 1995, Inf. Process. Lett..

[12]  Alan Dove,et al.  From bits to bases: Computing with DNA , 1998, Nature Biotechnology.

[13]  Lila Kari,et al.  Towards a DNA Solution to the Shortest Common Superstring Problem , 1999, Int. J. Artif. Intell. Tools.

[14]  Masami Hagiya,et al.  From Molecular Computing to Molecular Programming , 2000, DNA Computing.

[15]  Chang-Biau Yang,et al.  The Design of Sorters Based on DNA for Bio-Computers , 2002 .

[16]  Satoru Miyano,et al.  Identification of genetic networks by strategic gene disruptions and gene overexpressions under a boolean model , 2003, Theor. Comput. Sci..

[17]  Chang-Biau Yang,et al.  A DNA solution of SAT problem by a modified sticker model. , 2005, Bio Systems.

[18]  Chang-Biau Yang,et al.  A Fast Initialization Algorithm for Single-Hop Wireless Networks , 2005, IEICE Trans. Commun..

[19]  Akimitsu Okamoto,et al.  Public-key system using DNA as a one-way function for key distribution. , 2005, Bio Systems.

[20]  Junzo Watada,et al.  REDESIGNING SUBGROUPS IN A PERSONNEL NETWORK BASED ON DNA COMPUTING , 2006 .

[21]  Chinchen Chang,et al.  REVERSIBLE DATA HIDING SCHEMES FOR DEOXYRIBONUCLEIC ACID (DNA) MEDIUM , 2007 .

[22]  Chang-Biau Yang,et al.  Solving satisfiability problems using a novel microarray-based DNA computer , 2007, Biosyst..