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This study presents an approach to the security assessment of the information systems of critical infrastructures. The approach is based on the faithful reconstruction of the evaluated information system in a computer security laboratory followed by simulations of possible threats against the system. The evidence collected during the experiments, stored and organised using a proprietary system InSAW, may later be used for the creation of trust cases which provide valuable information for the end users of the infrastructure. Another new proposal is MAlSim - mobile agent-based simulator of malicious software (viruses, worms, etc). To the best of the authors- knowledge, such a simulator has not been proposed before. The present approach was applied to the verification of the security of industrial control systems and power plants. In the study, one of the experiments related to the security study of an information system of a power plant, a simulation of zero-day worm attack, is described.