Research On Optimization Method Of DNA Sequence Design In DNA Computing

DNA computing is a brand news computing mode which is based on DNA molecular and biological enzyme and uses biochemical reaction as its information processing tool. DNA encoding problem which usually is mentioned is DNA encoding set computed problem.High quality DNA sequences can prevent the interference between different DNA molecules, and improve the reliability and effectiveness of DNA computation. The scalability of a lab experiment is the effective reproducibility of the experiment with longer or more numerous molecules that can encode larger problem instances while still obtaining equally reliable results under comparable efficiency. Nucleic acid sequences design is an important problem in DNA computing. This doctoral thesis mainly focuses on the nucleic acid encoding theory and DNA sequences design algorithm for DNA computing, the detailed contents are as follows:The main restrictions which have influences on the DNA codes designing is studied, the various types of mathematical restrictions are analysised and summarized, an optimal model for DNA coding with a multi-objective evaluation system is established. In the paper, the evaluation system is realized as Fitness function.An optimal algorithm for DNA coding named Global Artificial Fish Swarm (GAFS) is researched. This paper includes the coding sequence of artificial fish swarm algorithm for the optimization model framework, taking advantage of artificial fish swarm algorithm with parallel processing capabilities and global search capability, so that DNA encoding quality is more stable and reliable.A General Sequence Design System(GSDS) is designed and realized using JAVA language. The system structure consists of four main modules:GSDS/Seq for sequence generation, GSDS/Report, GSDS/Plot for analysis and visualization, and GSDS/Sim for bio-lab simulation. Four structures can help to add or delete the independent modules. The good traits contribute to an agile, extendable and general-purposed system. Through the realization of the GSDS system, different optimal model for DNA coding can be implemented, and the respective DNA code sequence acquired.