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Jason is correct that co-simulation will provide a more general approach that allows you to directly incorporate filters in airflow paths. I suppose (I have not done this) you could also implement one of the contaminant removal methods offered by EnergyPlus, e.g., deposition velocity or rate. I'm not sure if EnergyPlus tracks the amount of removal, but CONTAM will. Further, CONTAM will enable you to partition the particles into more size bins and associate these bins with different filtration and deposition rates.