A system, methods and apparatus are described involving the self-organizing dynamics of networks of distributed computers. The system uses intelligent mobile software agents in a multi-agent system to perform numerous functions, including search, analysis, collaboration, negotiation, decision making and structural transformation. Data are continuously input, analyzed, organized, reorganized, used and output for specific commercial and industrial applications. The system uses combinations of AI techniques, including evolutionary computation, genetic programming and evolving artificial neural networks; consequently, the system learns, anticipates and adapts. The numerous categories of applications of the system include optimizing network dynamics, collective robotics systems, automated commercial systems and molecular modeling systems. Given the application of complexity theory and modal and temporal logics to self-organizing dynamic networks, a novel model of intelligent systems is presented.