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We examine the dependence of the inferred isoprene surface emission flux from atmospheric concentration on the diurnalvariability of the convective boundary layer (CBL). A series of systematic numerical experimentscarried out using the mixed-layer technique enabled us to study the sensitivity ofisoprene fluxes to the entrainment process, the partition of surface fluxes, the horizontaladvection of warm/cold air masses and subsidence. Our findings demonstrate the key role played by the evolution of boundary layer heightin modulating the retrieved isoprene flux. More specifically, inaccurate valuesof the potential temperature lapse rate lead to changes in the dilution capacity of the CBLand as a result the isoprene flux may be overestimated or underestimated by as much as 20%. The inferredemission flux estimated in the early morning hours is highly dependent on theaccurate estimation of the discontinuity of the thermodynamic values between the residual layerand the rapidly forming CBL.Uncertainties associated with the partition of the sensible and latent heat fluxalso yield large deviations in the calculation of the isoprene surface flux. Similar resultsare obtained if we neglect the influence of warm or cold advection in the development of the CBL.We show that all the above-mentioned processes are non-linear, for which reasonthe dynamic and chemical evolutions of the CBL must be solved simultaneously. Based on the discussion of our results, we suggest themeasurements needed to correctly apply the mixed-layer technique in order to minimize theuncertainties associated with the diurnal variability of the convective boundary layer

On inferring isoprene emission surface flux from atmospheric boundary layer concentration measurements