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A cyber-physical system is treated with a collaborative self-organizing knowledge network model, called Vijjana. While traditional communication between users of Vijjana forms a loosely coupled system, in cyber-physical system it is tightly-bound forming a policy-driven knowledge grid. If there is a compromised security in a cyber-physical system, the knowledge grid bootstraps to a subset grid, isolated from other nodes. A model for this bootstrap is proposed, which looks for carefully administered security policies in the cyber-physical system.