Efficient initial pool generation for weighted graph problems using parallel overlap assembly

Authors:
Ji Youn Lee;Hee-Woong Lim;Suk-In Yoo;Byoung-Tak Zhang;Tai Hyun Park
Affiliations:
School of Chemical Engineering;School of Computer Science and Engineering, Seoul National University, Seoul, Korea;School of Computer Science and Engineering, Seoul National University, Seoul, Korea;School of Computer Science and Engineering, Seoul National University, Seoul, Korea;School of Chemical Engineering
Venue:
DNA'04 Proceedings of the 10th international conference on DNA computing
Year:
2004

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Abstract

Most DNA computing algorithms for mathematical problems start with combinatorial generation of an initial pool. Several methods for initial-pool generation have been proposed, including hybridization/ligation and mix/split methods. Here, we implement and compare parallel overlap assembly with the hybridization/ligation method. We applied these methods to the molecular algorithm to solve an instance of the graph problem with weighted edges. Our experimental results show that parallel overlap assembly is a better choice in terms of generation speed and material consumption than the hybridization/ligation method. Simulation of parallel overlap assembly was performed to investigate the potential and the limitation of the method.