DNA codewords design using the improved NSGA-II algorithms

BIC-TA 2009 - Proceedings, 2009 4th International Conference on Bio-Inspired Computing: Theories and Applications

Volumn , Issue , 2009, Pages 48-52

  Wang, Yanfeng ^a   Shen, Yongpeng ^a   Zhang, Xuncai ^a   Cui, Guangzhao ^a  

^a ZHENGZHOU UNIVERSITY OF LIGHT INDUSTRY   (China)

Author keywords

DNA codewords design; DNA computing; NSGA II algorithms

Indexed keywords

CODE-WORDS; CONVERGENCE SPEED; DNA COMPUTING; ENGINEERING APPLICATIONS; IMPROVED NSGA-II; IN-SILICO; NON-DOMINATED SORTING GENETIC ALGORITHMS; NSGA-II ALGORITHM; OTHER ALGORITHMS; POPULATION DIVERSITY; SORTING PROCESS;

ALGORITHMS; CALCULATIONS; CONVERGENCE OF NUMERICAL METHODS; DNA; GENES; GENETIC PROGRAMMING;

COMPUTATION THEORY;

EID: 73949105197     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BICTA.2009.5338158     Document Type: Conference Paper

References (20)

1. Garzon M H, Deaton R J. Codeword Design and Information Encoding in DNA Ensembles. Natural Computing, 2004, 3(3): 253-292.
2. Deaton R J, Garzon M H. Thermodynamic constraints on DNA based computing. Computing with Bio-Molecus: Theory and Experiments, Singapore: Springe-Verlag, 1998, 138-152.
3. Deaton R J, Franceschetti D R, Garzon M H, et al. Information transfer through hybridization reaction in DNA based computing. Proceedings of the Second Annual Conference, 1997, 463-471.
4. Frutos A G. Demonstration of a Word Design Strategy for DNA Computing on Surface. Nucleic Acids Research, 1997, 25: 4748-4757.
5. Feldkamp U, Banzhaf W, Rauhe H, et al. A DNA sequence compiler. In: the Proceedings of 6th DIMACS Workshop on DNA Based Computers,2000
6. Deaton R J. DNA Based Implementation of an Evolutionary Search for Good Encodings for DNA Computation. In: Kennedy J, ed. the Proceedings of 1997 IEEE International Conference on Evolutionary Computation[C], IEEE Press, Piscataway, NJ, 1997: 267-271.
7. Deaton R J, Murphy R C, Garzon M H, et al. Good encodings for DNA-based solutions to combinatorial problems. DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 1999, 44: 247-258.
8. Kalyanmoy D, Amrit P, Sameer A, et al. A Fast and Elitist Multiobjective Genetic Algorithm: NSGA-II. IEEE Transactions on Evolutionary Computation, 2002, 6(2): 182-197.
9. Sager J, Stefanovic D. Designing nucleotide sequences for computation: a survey of constraints. In: the Preliminary Proceedings of the 11th International Meeting on DNA Computing, London, ON, Canada, June 2005, 275-289.
10. Tanaka F, Nakatsugawa M, Yamamoto M, et al. Developing support system for sequence design in DNA computing. In: the Proceedings of the 7th International Workshop DNA-Based Computers, Tampa, FL, USA, June 2001, 340-349.
11. Hartemink A J, Gifford D K, Khodor J. Automated constraint based nucleotide sequence selection for DNA computation. Biosystems, 1999, 52(1-3): 227-235.
12. Arita M, Kobayashi S. DNA sequence design using templates. New Generation Computer, 2002, 20(3): 263-277.
13. Feldkamp U, Saghafi S, Rauhe H. DNA sequence generator: A program for the construction of DNA sequences. In: the Proceedings of the 7th International Workshop DNA-Based Computers, Tampa, FL, USA, June 2001, 179-188.
14. Wallace R B, Shaffer J, Murphy R F, et al. Hybridization of synthetic oligodeoxyribonucleotides to phi chi 174 DNA: The effect of single base pair mismatch. Nucleic Acids Res., 1979, 6(11): 3543-3557.
15. Wetmur J G. DNA probes: Applications of the principles of nucleic acid hybridization. Critical Rev. Biochem. Molecular Bio., 1991, 26: 227-259.
16. SantaLucia J. A Unified View of Polymer, Dumbbell, and Oligonucleotide DNA Nearest-neighbor Thermodynamics. Proc Natl Acid Sic USA, 1998, 95: 1460-1465.
17. Srinivas N, Deb K. Multiobjective optimization using nondominated sorting in genetic algorithms. Evolution Computation, 2(3): 221-248.
18. Deb K, Pratap A, Agarwal S, et al. A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Transaction on Evolutionary Computation, 2002, 6: 182-197.
19. Shin S Y, Lee I H, Kim D, et al. Multiobjective evolutionary optimization of DNA sequences for reliable DNA computing. IEEE Transactions on Evolutionary Computation, 2005, 9: 143-158.
20. Shin S Y, Kim D M, Lee I H, et al. Evolutionary Sequence Generation for Reliable DNA Computing. In: the Proceedings of the 2002 Congress on Evolutionary Computing (CEC2002), Honolulu, HI, USA, 2002, 79-84.