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<p>The Multi-sensor Cloud and Aerosol Retrieval Simulator (MCARS) presently produces synthetic radiance data from Goddard Earth Observing System version 5 (GEOS-5) model output as if the Moderate Resolution Imaging Spectroradiometer (MODIS) were viewing a combination of atmospheric column inclusive of clouds, aerosols, and a variety of gases and land–ocean surface at a specific location. In this paper we use MCARS to study the MODIS Above-Cloud AEROsol retrieval algorithm (MOD06ACAERO). MOD06ACAERO is presently a regional research algorithm able to retrieve aerosol optical thickness over clouds, in particular absorbing biomass-burning aerosols overlying marine boundary layer clouds in the southeastern Atlantic Ocean. The algorithm's ability to provide aerosol information in cloudy conditions makes it a valuable source of information for modeling and climate studies in an area where current clear-sky-only operational MODIS aerosol retrievals effectively have a data gap between the months of June and October. We use MCARS for a verification and closure study of the MOD06ACAERO algorithm. The purpose of this study is to develop a set of constraints a model developer might use during assimilation of MOD06ACAERO data.</p> <p>Our simulations indicate that the MOD06ACAERO algorithm performs well for marine boundary layer clouds in the SE Atlantic provided some specific screening rules are observed. For the present study, a combination of five simulated MODIS data granules were used for a dataset of 13.5 million samples with known input conditions. When pixel retrieval uncertainty was less than 30 %, optical thickness of the underlying cloud layer was greater than 4, and scattering angle range within the cloud bow was excluded, MOD06ACAERO retrievals agreed with the underlying ground truth (GEOS-5 cloud and aerosol profiles used to generate the synthetic radiances) with a slope of 0.913, offset of 0.06, and <span class="inline-formula">RMSE=0.107</span>. When only near-nadir pixels were considered (view zenith angle within <span class="inline-formula">±20</span><span class="inline-formula">^∘</span>) the agreement with source data further improved (0.977, 0.051, and 0.096 respectively). Algorithm closure was examined using a single case out of the five used for verification. For closure, the MOD06ACAERO code was modified to use GEOS-5 temperature and moisture profiles as an ancillary. Agreement of MOD06ACAERO retrievals with source data for the closure study had a slope of 0.996 with an offset of <span class="inline-formula">−0.007</span> and RMSE of 0.097 at a pixel uncertainty level of less than 40 %, illustrating the benefits of high-quality ancillary atmospheric data for such retrievals.</p>