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One-dimensional models of column liquid chromatography are today widely applied due to some obvious advantages. These models are easy to set up, they can be computed very fast, and they can often predict experimental results reasonably well. However, one-dimensional chromatography models also have some serious disadvantages, mainly because the applied homogeneity assumptions neglect important information on flow conditions and concentration distributions over cross sections of the chromatography column. This information can be highly advantageous for analyzing existing systems and for designing future processes. We hence developed a three-dimensional model for packed bed liquid chromatography in micro-columns. The system geometry is given by a cylindrical vessel that is randomly packed with spherical beads. The equations for convective solute transport in the interstitial volume, for diffusive transport within the porous beads, and for adsorption at the inner bead surfaces, are adapted from the well known general rate model and generalized to three spatial dimensions. Simulations were performed with COMSOL Multiphysics. This tool is especially suitable for systems that feature a mix of several underlying physical principles, such as the system at hand. COMSOL has interfaces to MATLAB that have been used for composing the geometry and for visualization purposes.