Application of a novel IWO to the design of encoding sequences for DNA computing

  • Authors:

  • Xuncai Zhang;Yanfeng Wang;Guangzhao Cui;Ying Niu;Jin Xu

  • Affiliations:

  • Research Institute of Biomolecular Computer, Huazhong University of Science and Technology, Wuhan, 430074, China and School of Electrical and Electronic Engineering, Zhengzhou University of Light ...;School of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China;School of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China;School of Electrical and Electronic Engineering, Zhengzhou University of Light Industry, Zhengzhou, 450002, China;Research Institute of Biomolecular Computer, Huazhong University of Science and Technology, Wuhan, 430074, China

  • Venue:
  • Computers & Mathematics with Applications
  • Year:
  • 2009

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Abstract

Encoding and processing information in DNA-, RNA- and other biomolecule-based devices is an important requirement for DNA based computing with potentially important applications. To make DNA computing more reliable, much work has focused on designing the good DNA sequences. However, this is a bothersome task as encoding problem is an NP problem. In this paper, a new methodology based on the IWO algorithm is developed to optimize encoding sequences. Firstly, the mathematics models of constrained objective optimization design for encoding problems based on the thermodynamic criteria are set up. Then, a modified IWO method is developed by defining the colonizing behavior of weeds to overcome the obstacles of the original IWO algorithm, which cannot be applied to discrete problems directly. The experimental results show that the proposed method is effective and convenient for the user to design and select effective DNA sequences in silicon for controllable DNA computing.