We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS.

Abstract. In this paper, we present the implementation and evaluation of the aerosol microphysics module SALSA2.0 in the framework of the aerosol–chemistry–climate model ECHAM-HAMMOZ. It is an alternative microphysics module to the default modal microphysics scheme M7 in ECHAM-HAMMOZ. The SALSA2.0 implementation within ECHAM-HAMMOZ is evaluated against observations of aerosol optical properties, aerosol mass, and size distributions, comparing also to the skill of the M7 implementation. The largest differences between the implementation of SALSA2.0 and M7 are in the methods used for calculating microphysical processes, i.e., nucleation, condensation, coagulation, and hydration. These differences in the microphysics are reflected in the results so that the largest differences between SALSA2.0 and M7 are evident over regions where the aerosol size distribution is heavily modified by the microphysical processing of aerosol particles. Such regions are, for example, highly polluted regions and regions strongly affected by biomass burning. In addition, in a simulation of the 1991 Mt. Pinatubo eruption in which a stratospheric sulfate plume was formed, the global burden and the effective radii of the stratospheric aerosol are very different in SALSA2.0 and M7. While SALSA2.0 was able to reproduce the observed time evolution of the global burden of sulfate and the effective radii of stratospheric aerosol, M7 strongly overestimates the removal of coarse stratospheric particles and thus underestimates the effective radius of stratospheric aerosol. As the mode widths of M7 have been optimized for the troposphere and were not designed to represent stratospheric aerosol, the ability of M7 to simulate the volcano plume was improved by modifying the mode widths, decreasing the standard deviations of the accumulation and coarse modes from 1.59 and 2.0, respectively, to 1.2 similar to what was observed after the Mt. Pinatubo eruption. Overall, SALSA2.0 shows promise in improving the aerosol description of ECHAM-HAMMOZ and can be further improved by implementing methods for aerosol processes that are more suitable for the sectional method, e.g., size-dependent emissions for aerosol species and size-resolved wet deposition.

Abstract. Challenges in understanding the aerosol-cloud interactions and their impacts on global climate highlight the need for improved knowledge of the underlying physical processes and feedbacks as well as their interactions with cloud and boundary layer dynamics. To pursue this goal, increasingly sophisticated cloud-scale models are needed to complement the limited supply of observations of the interactions between aerosols and clouds. For this purpose, a new large-eddy simulation (LES) model, coupled with an interactive sectional description for aerosols and clouds, is introduced. The new model builds and extends upon the well-characterized UCLA Large-Eddy Simulation Code (UCLALES) and the Sectional Aerosol module for Large-Scale Applications (SALSA), hereafter denoted as UCLALES-SALSA. Novel strategies for the aerosol, cloud and precipitation bin discretisation are presented. These enable tracking the effects of cloud processing and wet scavenging on the aerosol size distribution as accurately as possible, while keeping the computational cost of the model as low as possible. The model is tested with two different simulation set-ups: a marine stratocumulus case in the DYCOMS-II campaign and another case focusing on the formation and evolution of a nocturnal radiation fog. It is shown that, in both cases, the size-resolved interactions between aerosols and clouds have a critical influence on the dynamics of the boundary layer. The results demonstrate the importance of accurately representing the wet scavenging of aerosol in the model. Specifically, in a case with marine stratocumulus, precipitation and the subsequent removal of cloud activating particles lead to thinning of the cloud deck and the formation of a decoupled boundary layer structure. In radiation fog, the growth and sedimentation of droplets strongly affect their radiative properties, which in turn drive new droplet formation. The size-resolved diagnostics provided by the model enable investigations of these issues with high detail. It is also shown that the results remain consistent with UCLALES (without SALSA) in cases where the dominating physical processes remain well represented by both models.