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Abstract Observations from the third campaign of the National Aeronautics and Space Administration Airborne Tropical Tropopause Experiment (ATTREX 3) field mission and Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observations satellite mission are used to evaluate simulations of tropical tropopause layer (TTL) cirrus clouds in the Community Earth System Model's (CESM) Community Atmosphere Model, CAM5. In this study, CAM5 is coupled with a sectional ice cloud model, the Community Aerosol and Radiation Model for Atmospheres (CARMA). We find that both model variants underrepresent cloud frequency along the ATTREX 3 flight path and both poorly represent relative humidity in the TTL. Furthermore, simulated in‐cloud ice size distributions contained erroneous amounts of ice crystals throughout the distribution. In response, we present a modified ice cloud fraction scheme that boosts the cloud fraction within the TTL. Due to coarse vertical model resolution in the TTL, we also prescribe a 2‐K decrease in cold point tropopause temperatures to better align with observed temperatures. Our modifications improve both CAM5 and CAM5/CARMA's in‐cloud ice size and mass distributions. However, only CAM5/CARMA has a significant improvement in cloud frequency and relative humidity. An investigation of cloud extinction in the ATTREX 3 region found that each model variant struggles to reproduce observed extinctions. As a first‐order approximation, we introduce randomly generated temperature perturbations to simulate the effect of gravity waves into the CAM5/CARMA simulation. These gravity waves significantly increase the incidence of low extinction (<0.02 km⁻¹) values, ice cloud fraction between 16 and 18 km, and ice crystal smaller than 100‐μm concentrations but provided only small changes to high extinction values. 

Abstract Convective systems dominate the vertical transport of aerosols and trace gases. The most recent in situ aerosol measurements presented here show that the concentrations of primary aerosols including sea salt and black carbon drop by factors of 10 to 10,000 from the surface to the upper troposphere. In this study we show that the default convective transport scheme in the National Science Foundation/Department of Energy Community Earth System Model results in a high bias of 10–1,000 times the measured aerosol mass for black carbon and sea salt in the middle and upper troposphere. A modified transport scheme, which considers aerosol activation from entrained air above the cloud base and aerosol‐cloud interaction associated with convection, dramatically improves model agreement with in situ measurements suggesting that deep convection can efficiently remove primary aerosols. We suggest that models that fail to consider secondary activation may overestimate black carbon's radiative forcing by a factor of 2.