DNA sequences optimization based on gravitational search algorithm for reliable DNA computing

Proceedings - 2011 6th International Conference on Bio-Inspired Computing: Theories and Applications, BIC-TA 2011

Volumn , Issue , 2011, Pages 103-107

  Xiao, Jianhua ^a   Cheng, Zhen ^b  

^a NANKAI UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

DNA computing; DNA sequences design; Gravitational search algorithm

Indexed keywords

DNA SEQUENCE DESIGN; DNA-COMPUTING; IMPROVED ALGORITHM; LOGICAL CONSTRAINTS; OPTIMIZATION METHOD; RESEARCH TOPICS; SEARCH ALGORITHMS; SIMULATION EXPERIMENTS;

CALCULATIONS; COMPUTATION THEORY; DESIGN; DNA; EVOLUTIONARY ALGORITHMS; LEARNING ALGORITHMS; OPTIMIZATION;

DNA SEQUENCES;

EID: 80155174816     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIC-TA.2011.12     Document Type: Conference Paper

References (28)

1. Adleman L M (1994) Molecular computation of solutions to combinatorial problems. Science 5187: l021-1024.
2. Lipton R (1995) DNA solution of hard computational problems. Science, 268(28): 542-545.
3. Braich R S, Chelyapov N, Johnson C, et al (2002) Solution of a 20-variable 3-SAT problem on a DNA computer. Science 296(5567): 499-502. (Pubitemid 34408664)
4. Zimmermann K (2002) Efficient DNA sticker algorithms for NP-complete graph problems. Computer Physics Communications 144: 397-309.
5. Ouyang Q, Kaplan P D, Liu S, et al (1997) DNA solution of the maximal clique problem. Science 278(10): 446-449. (Pubitemid 27454425)
6. Marathe A, Condon A E, Corn R M (1999) On combinatorial DNA word design. In: Proceedings of 5th DIMACS Workshop on DNA Based Computers Cambridge, MA, USA, pp 75-89.
7. Frutos A G, Thiel A J, Condon A E et al (1997) DNA computing at surfaces: 4 base mismatch word design. In: Proceedings of 3rd DIMACS Workshop on DNA Based Computers, Univ of Penns, pp238-238.
8. Arita M, Nishikawa A, Hagiya M et al (2000) Improving sequence design for DNA computing. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO-2000), pp875-882.
9. Tanaka F, Nakatsugawa M, Yamamoto M et al (2001) Developing support system for sequence design in DNA computing. In: Preliminary Proceedings of 7th International Workshop on DNA-Based Computers, pp340-349.
10. Deaton R, Murphy R C, Rose J A et al (1997) A DNA based implementation of an evolutionary search for good encodings for DNA computation. In: Proceedings of the 1997 IEEE International Conference on Evolutionary Computation, pp267-272.
11. Cui G Z, Niu Y Y, Wang Y F et al (2007) A new approach based on PSO algorithm to find good computational encoding sequences. Progress in Natural Science 17(6): 712-716.
12. Khalid, N K, Ibrahim Z, Kurniawan T B (2008) DNA sequence optimization based on continuous particle swarm optimization. Journal of Computer Science. 4(11): 942-950.
13. Wang W, Zheng X D, Zhang Q et al (2007) The optimization of DNA encodings based on GA/SA algorithm. Progress in Natural Science 17(6): 739-744. (Pubitemid 46947658)
14. Qiu Q R, Mukre P, Bishop M et al (2008) Hardware acceleration for thermodynamic constrained DNA code generation. DNA13, LNCS 4848, pp201-210.
15. D'yachkov A G, Macula A, Rykov V et al (2008) DNA codes based on stem similarities between DNA sequences. DNA13, LNCS 4848, pp146-151.
16. Kawashimo S, Ono H, Sadakane K et al (2008) Dynamic neighborhood searches for thermodynamically designing DNA sequence. DNA13, LNCS 4848, pp130-139.
17. Rashedi E, Nezamabadi-pour H, Saryazdi S (2009) GSA: agravitationalsearch algorithm. InformationSciences. 179(13): 2232-2248.
18. Rashedi E, Nezamabadi-pour H, Saryazdi S (2009) BGSA: binary gravitational search algorithm. Natural Computing. 9(3): 727-745.
19. Hassanzadeh, H R, Rouhani M (2010) A Multi-objective Gravitational Search Algorithm. 2010 International Conference on Computational Intelligence, Communication Systems and Networks. 24, pp117-122.
20. Ghalambaz M, Noghrehabadi A R, Behrang M A (2011) A hybrid neural network and gravitational search algorithm (HNNGSA) method to solve well known Wessinger's equation. World Academy of Science, Engineering and Technology. 73, 803-807.
21. Rashedi E, Nezamabadi-pour H, Saryazdi S (2011) Filter modeling using gravitational search algorithm. Engineering Applicaitons of Artifical Intelligence. 24, 117-122.
22. Gu W X, Li X T, Zhu L (2010) A gravitational search algorithm for flow shop schduling. CAAI Transctions on Intelligent Systems. 5(5): 411-418.
23. Li C S, Zhou J Z (2011) Parameters identification of hybdraulic turbine governing system using improved gravitational search algorithm. Energy Conversion and Management. 52, 374-381.
24. Tanaka F, Nakatsugawa N, Yamamoto M et al (2002) Toward a general-purpose sequence design system in DNA computing. 2002 IEEE Congress on Evolutionary Computation. USA pp73-78.
25. Cui G Z, Niu Y Y, Wang Y F et al (2007) A new approach base on PSO to find good computaition encoding sequences. Progress in Natural Science. 17(6): 712-716.
26. Shin S Y, Lee I H, Kim D et al (2005) Multi-objective evolutionary optimization of DNA sequences for reliable DNA computing. IEEE Transactions on Evolutionary Computation 9(2): 143-158. (Pubitemid 40573248)
27. Deaton R, Murphy R C, Garzon M et al (1996) Good encodings for DNA-based solutions to combinatorial problems. The 2nd Annu Meeting DNA Based Comput, pp247-258.
28. Xiao J H, Xu J, Chen Z H et al (2009) A hybrid quantum chaotic swarm evolutionary algorithm for DNA encoding. Computers and Mathematics with Applications. 57(12): 1949-1958.