The Simulation Of Basic Biology Operation Of DNA Computing

With the rapid development of biotechnology, a new discipline named DNA computing has come into being. Because of the massive parallelism, high-density storage and low energy cost, DNA computer will overcome the disadvantages of electronic computer in some special area. DNA computing is a type of computing. DNA computing is a kind of biological computing. It code the information using the double helix structure and the base pairing complementary principle of DNA, map the objects to be computed into DNA chains, and then compute the original problem in high parallel using the coded DNA chains with the catalysis of enzyme, generating a data pool containing all kinds of data. And at last, detection the required results from the data pool using molecular biology techniques, such as polymerase chain reaction, ultrasonic degradation, affinity chromatography, cloning, mutagenesis, molecular purification, electrophoresis, magnetic separation, etc.This paper mainly focuses on the following three subjects: the extracting of basic biology operation of DNA computing, the encoding problem and the analog of basic biology operation of DNA computingThe extraction of basic biology operation is the prerequisite for the analog. Just in the condition of exaction of the basic biology operations and making certain the real terms of every basic operation, we can analog the basic operations on an electronic computer. In this paper, the extraction of basic operation is based on the tube-based DNA computing model, where the operation is divided into two parts, the operation of DNA chains and tubes.Encoding problem is the key to DNA computing and the most difficult problem. In this thesis, the definition of encoding problem is given, and the factors that affect the stability of DNA chain are summarized. In the simulated experiment, several of the factors are take considered to encode the objects, and the results can meet the requirement of the experiment perfectly.The analog experiment is based on the Object-Oriented Technology, there are three classes defined in this paper, which are TDNAChain, TTube and TControler. All the three classes express the basic factors in the tube-based model, DNA chains, tubes and the process of the experiment.Finally, we computed and a 7 vertexes TSP problem and the 7 vertexes Hamilton Path Problem used in Adleman's experiment with the classes designed. The detail steps of the HPP experiment are given, and the results computed are expressed, too.