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We describe the baseline model configuration and simulation characteristics of the Geophysical Fluid Dynamics Laboratory (GFDL)'s Atmosphere Model version 4.1 (AM4.1), which builds on developments at GFDL over 2013–2018 for coupled carbon‐chemistry‐climate simulation as part of the sixth phase of the Coupled Model Intercomparison Project. In contrast with GFDL's AM4.0 development effort, which focused on physical and aerosol interactions and which is used as the atmospheric component of CM4.0, AM4.1 focuses on comprehensiveness of Earth system interactions. Key features of this model include doubled horizontal resolution of the atmosphere (~200 to ~100 km) with revised dynamics and physics from GFDL's previous‐generation AM3 atmospheric chemistry‐climate model. AM4.1 features improved representation of atmospheric chemical composition, including aerosol and aerosol precursor emissions, key land‐atmosphere interactions, comprehensive land‐atmosphere‐ocean cycling of dust and iron, and interactive ocean‐atmosphere cycling of reactive nitrogen. AM4.1 provides vast improvements in fidelity over AM3, captures most of AM4.0's baseline simulations characteristics, and notably improves on AM4.0 in the representation of aerosols over the Southern Ocean, India, and China—even with its interactive chemistry representation—and in its manifestation of sudden stratospheric warmings in the coldest months. Distributions of reactive nitrogen and sulfur species, carbon monoxide, and ozone are all substantially improved over AM3. Fidelity concerns include degradation of upper atmosphere equatorial winds and of aerosols in some regions.

Recent observations show a distinct cooling of the tropical lower stratosphere, and chemistry-climate models (CCMs) suggest a link to a strengthening tropical upwelling, arguably related to increases in greenhouse gas concentrations from anthropogenic activity. The present study explores the strengthening of tropical upwelling by comparing ensemble realisations of two different transient scenarios with the CCM E39/C. Both scenarios share the same boundary conditions, including concentrations of ozone-depleting substances, but differ in their climate forcing via prescribed sea surface temperatures (SSTs) and well-mixed greenhouse gas concentrations. In the summer hemisphere tropics, higher SSTs amplify deep convection locally and hence the convective excitation of quasistationary waves. These waves propagate upward through the region of easterly winds while dissipating, but still carry enough of the signal into the low-latitude lower stratosphere to induce an anomalous low-latitude Brewer-Dobson (BD) cell. The transport change in turn increases the flux of ozone-poor tropospheric air into the tropical lower stratosphere.