Using sticker to solve the 3-dimensional matching problem in molecular supercomputers

Authors:
Minyi Guo;Weng-Long Chang;Jiannong Cao
Affiliations:
Department of Computer Software, University of Aizu, Aizu-Wakamatsu City, Fukushima 965 8580, Japan.;Department of Information Management, Southern Taiwan University of Technology, Tainan County, Taiwan, 710, ROC.;Department of Computing, Hong Kong Polytechnic University, Hong Kong
Venue:
International Journal of High Performance Computing and Networking
Year:
2004

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Abstract

Adleman demonstrated that DNA (Deoxyribonucleic acid) strands could be applied for dealing with solutions to an instance of the NP-complete Hamiltonian path problem (HPP) (Adleman, 1994). The Adleman techniques could also be used to solve the NP-complete satisfiability (SAT) problem (the first NP-complete problem) (Lipton, 1995). Furthermore, sticker is used for enhancing the Adleman-Lipton model (Roweis et al., 1999). In this paper, we first use sticker to construct solution space of DNA library sequences for the 3-dimensional matching problem. Then, in the Adleman-Lipton model, we propose an algorithm to remove illegal solution and find legal solution for the 3-dimensional matching problem from solution space of sticker. Finally, a simulation result for our algorithm is generated.