The operational characteristics of a cyber-physical system (CPS) may deviate from the certified system due to intended (in case of cheating) or unintended (wear and tear) reasons. A computer-implemented certification system makes test case search aware of the multidimensional interactions between the cyber and physical subsystems and addresses practical dynamical system problems like Zeno behavior and dynamical model divergence. The system dynamically modulates an input search space by predicting and limiting input variations that can potentially cause divergence or Zeno behavior.