A system, methods and apparatus are described involving the self-organizing dynamics of networks of distributed computers. The system is comprised of complex networks of databases. The system presents a novel database architecture called the distributed transformational spatio-temporal object relational (T-STOR) database management system (dbms). Data is continuously input, analyzed, organized, reorganized and used for specific commercial and industrial applications. The system uses intelligent mobile software agents in a multi-agent system in order to learn, anticipate, and adapt and to perform numerous functions, including search, analysis, collaboration, negotiation, decision making and structural transformation. The system links together numerous complex systems involving distributed networks to present a novel model for dynamic adaptive computing systems, which includes plasticity of collective behavior and self-organizing behavior in intelligent system structures.