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A dynamic simulation method for non-linear systems based on genetic programming (GP) and bond graphs (8G) was developed to improve the design of nonlinear multi-domain energy conversion systems. The genetic operators enable the embryo bond graph to evolve towards the target graph according to the fitness function. Better simulation requires analysis of the optimization of the eigenvalue and the filter circuit evolution. The open topological design and space search ability of this method not only gives a more optimized convergence for the operation, but also reduces the generation time for the new circuit graph for the design of nonlinear multi-domain systems.