A special DNA computer was designed to solve the vertex coloring problem. The main body of this kind of DNA computer was polyacrylamide gel electrophoresis which could be classified into three parts: melting region, unsatisfied solution region and solution region. This polyacrylamide gel was con- nected with a controllable temperature device, and the relevant temperature was Tm1, Tm2 and Tm3, res- pectively. Furthermore, with emphasis on the encod- ing way, we succeeded in performing the experiment of a graph with 5 vertices. In this paper we introduce the basic structure, the principle and the method of forming the library DNA sequences.
Evolutionary computation techniques have mostly been used to solve various optimization problems, and it is well known that graph isomorphism problem （GIP） is a nondeterministic polynomial problem. A simulated annealing （SA） algorithm for detecting graph isomorphism is proposed, and the proposed SA algorithm is well suited to deal with random graphs with large size. To verify the validity of the proposed SA algorithm, simulations are performed on three pairs of small graphs and four pairs of large random graphs with edge densities 0.5, 0.1, and 0.01, respectively. The simulation results show that the proposed SA algorithm can detect graph isomorphism with a high probability.
