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This paper predicts programspsila effect of time-domain electromagnetic interference (EMI) on a simple microcontroller. Using the instruction current concept and a modified instruction set simulator (ISS) for this purpose, this paper can predict, in the time domain, accurate conducted EMI behaviors when different programs are running on this system. Different program codespsila EMI behaviors are predicted, and all of these codes fit well with the measurement results. The modified ISS is adapted to estimate the pipeline effect of a microcontroller and to give an accurate current profile of any complex multi-instruction program. By using the instruction current model and the proposed ISS, this paper can predict the EMI behavior of a very complex program-a simple home-made operating system (OS) kernel. To the best of our knowledge, this paper is the first work on observation and prediction of EMI behavior of an embedded system OS kernel.