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We aim to understand the correlation between cloud formation and alkali line formation in substellar atmospheres.We perform line profile calculations for Na I and K I based on the coupling of our kinetic model for the formation and composition of dust grains with 1D radiative transfer calculations in atmosphere models for brown dwarfs and giant gas planets. The Na I and K I line profiles sensibly depend on the way clouds are treated in substellar atmosphere simulations. The kinetic dust formation model results in the highest pseudo-continuum compared to the limiting cases., Comment: 5 pages, Accepted for publication in MNRAS

We present comparisons which show good agreement between observed and synthetic spectra for water vapour transitions in a range of M dwarfs, The observations were made from 2.85 to 3.40 mu m where water vapour transitions are strong in cool stars but relatively weak in the Earth's atmosphere, allowing reliable observations to be made, The synthetic spectra were computed using a stellar atmosphere code and include preliminary ab initio calculations for re-vibrational bands up to J = 30, Synthetic spectra indicate that changes in metallicity and gravity have a small effect on the strength of the observed water bands whereas temperature changes produce large differences in strength, Formally, we find similar effective temperatures to those found in previous work. However, since the molecular opacity at the peak of the flux distribution is not well determined, uncertainties in the model atmosphere structure and the effective temperature scale remain.Detailed line profiles can be modelled for atomic lines because their damping constants are known, but they are not known for molecular transitions, Atomic lines computed with Voigt profiles and Van der Waals pressure broadening give an averaged full width half maximum of around 50 km s(-1), For the observed water vapour transitions to match this generation of synthetic spectra we use Gaussian profiles with a full width half maximum of 2 km s(-1) to model the pressure broadening of water vapour transitions, Examination of the model structure indicates that water vapour lines are formed relatively high in the photosphere at pressures about an order of magnitude lower than those of atomic lines, These results strongly suggest that water vapour transitions are not pressure broadened sufficiently to overlap; as previously assumed when modelling molecular transitions in cool dwarfs using the Just Overlapping Line Approximation, The inferred lack of pressure broadening allows flux to escape between water lines, even within a region of strong water vapour absorption, and leads to weaker water band strengths. We demonstrate that this result is likely to explain much of the past discrepancy between observed and theoretical spectral energy distributions for M dwarfs