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The Research on Coding Theory and Methods for DNA Computing

Author: WangYanFeng
Tutor: XuJin
School: Huazhong University of Science and Technology
Course: System Analysis and Integration
Keywords: DNA computing Code design Physical and chemical properties Thermodynamic properties Intelligent Optimization Algorithm Evaluation Model
CLC: Q523
Type: PhD thesis
Year: 2007
Downloads: 348
Quote: 5
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Abstract


DNA computation is a DNA molecule as a carrier, the use of DNA hybridization reaction enormous parallelism characteristics calculated a natural mode of calculation. Coding problem is one of the core issues in the research and development of DNA computer. From the perspective of molecular biology, the physical and chemical properties of the DNA sequence itself determines the form of the presence of the DNA coding sequence; thermodynamic properties of the DNA coding sequence is the power source of the hybridization reaction. Based on this, we focused on the physical and chemical properties of the DNA sequence, and thermodynamic properties encoded in DNA computing theory and design, the main contents are as follows: a detailed discussion of the problem of coding DNA computing; detailed description of the DNA physical and chemical properties of the molecules, the thermodynamic basis of the hybridization reaction and related method of calculation of the thermodynamic parameters. Design optimization of the coding sequence of a DNA computing. The program in on the basis of comprehensive consideration of the constraint condition of the coding sequence in DNA computing, according to the constraint condition between the mutual constraints, using the idea of ??the overall optimization, the first constraint conditions classified; then based on the computation time of each constraint condition of The complexity and binding strength level to optimize the combination sort, - real-time filtering algorithm generates a calculated desired number of DNA coding sequence using randomly generated. The comparison shows that the evaluation of the optimized design is superior to previous literature provided. Calculated on the basis of the relationship between the constraints in the coding sequence of biological constraints, considering the weighting coefficient based on statistical principles, no experiment can be determined for each evaluation method: combination weighting method, which establish a DNA coding sequence of system evaluation model, the simulation results show that the evaluation model coding sequence set reasonable, objective evaluation. In addition, the system evaluation model of the design study of the DNA coding sequence evolution strategy using fitness function has important guiding significance. In a randomly generated set of DNA sequences, looking to meet relevant physico-chemical and thermodynamic constraints encoded can be mapped for Solving the Maximum Clique Problem bedroom and NP-hard problem, so, using heuristic algorithm to solve the The problem will become an inevitable choice. Based on this, try using a Hopfield neural network based on improved algorithm design methodology of DNA coding sequences. Simulation results show that this method can be used for the assessment and pre-filter, the collection of randomly generated DNA sequences ultimately obtain good DNA coding sequence having a guide and reference function. A design method based on the calculation of the coding sequence of the simulated annealing genetic algorithm. The algorithm both global search ability of the genetic algorithm, and both local fast convergence of the simulated annealing algorithm. Simulation results show that this method is effective to the design of the DNA coding sequence, can generate a better quality of the DNA coding sequence. Particle swarm optimization algorithm encoded in DNA computing. A discrete continuous strategy, making only the standard particle swarm optimization algorithm can be used to solve the DNA belonging to the discrete problem in the coding sequence design problem solving continuous optimization problems; proposed a method for DNA sequences design four hex discrete particle swarm optimization algorithm. The simulation results show that these two algorithms has a good effect for smaller encoding DNA sequences design can be quickly and efficiently.

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CLC: > Biological Sciences > Biochemistry > Nucleic acid > Deoxyribonucleic acid (DNA)
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