Hey Seth, OpenStudio does understand the important of natural ventilation and addition of airflow network to OpenStudio is in the design stages. That work is being led by @Jason DeGraw at the Consortium for Building Energy Innovation. In the meantime, there are a few options in OpenStudio. The simplest would be to write EnergyPlus measures as Matt suggested, you could use either airflow network objects (http://bigladdersoftware.com/epx/docs...) or the simpler ventilation design flow rate objects (http://bigladdersoftware.com/epx/docs...). If you are familiar with CONTAM, you could try the OpenStudio->CONTAM translator, you could contact Jason for more information about that.

What I have been doing with OpenStudio is I created a script to import either a ZoneVentilation:DesignFlowRate or ZoneVentilation:WindandStackOpenArea object with arguments for the thermal zone, schedule, etc. for any inputs I want as variables. You could create this script using the Measure Writing Guide for EnergyPlus measures or copy one from the BCL and modify to fit your measure needs. There is also a AvailabilityManager:HybridVentilation object I have not tried yet but may be worth looking into as well to import as a measure.