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Abstract Large-eddy simulation (LES) runs are performed to understand the influence of a one-dimensional (1D) surface heating heterogeneity on organized vertical motions within and above the atmospheric boundary layer (ABL). Two knowledge gaps are of interest: (i) how updrafts develop in the low free troposphere and (ii) what parameters control updraft location and strength within the ABL? LES runs are performed for a sheared, unstable ABL driven by geostrophic winds of the same magnitude but in various directions relative to a 1D surface-heat-flux heterogeneity. Quasi-steady-state LES results are phase-averaged over time and the horizontal dimension perpendicular to the surface-heat-flux gradient to quantify secondary circulations. Regarding the first knowledge gap, the results show that organized vertical motions in the low free troposphere can be modeled as two-dimensional (2D), stationary gravity waves, whose amplitudes depend on ABL updraft strength and instability development within the free troposphere. For the second gap, the results show that organized updrafts within the ABL may form above warm surfaces or downwind of warm-to-cool transitions. These different locations are well explained by both the relative contributions of horizontal and vertical velocities to the phase-averaged vorticity fluctuations tied to secondary circulations, and the relative importance of horizontal advection and turbulent transport in the phase-averaged internal energy fluctuation equation. The main balances associated with each updraft location are used to propose empirical models of updraft strength, and it is shown that the presence of sufficiently strong organized vertical motions can potentially change parameters used by atmospheric models that do not resolve ABL turbulence. Significance StatementThe purpose of this study is to better understand how heterogeneous surface heating affects updraft location and strength in the lowest kilometers of the atmosphere. We focus on horizontal heterogeneity scales comparable to the most frequently observed cloud size, a necessary step toward the parameterization of cloud shadow effects in weather and climate models. The results show that persistent updrafts may form above either warm or cool surfaces, with their location depending on the relative importance of terms in certain budget equations. Near-surface updrafts become stronger as the background mean wind becomes more perpendicular to the surface-heat-flux gradient, but their potential to influence clouds peaks when the background mean wind is neither parallel nor perpendicular to the surface-heat-flux gradient.