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What are your measured NO and NO2 concentrations? If your target concentration is around 1 to 2 ppm, you may be at the lowest attainable NOx concentration for the designed SCR system, as well as unable to observe any sine waves from the individual pollutants that make up NOx.

A sine wave occurs routinely in control logic. The older style derivative based controllers may create prominent sine waves due to the response times between measured and corrected parameters.

In brief, it could either be the controller for the SCR system, or the control logic of your instrumentation system. Determination of the time interval between the peaks of the sine wave, and examination of the equipment involved should allow you to target the problem. Another option might be the use of a FTIR, since it would measure all three pollutants simultaneously.