Abstract: In recent years, there has been growing interest in the use of functionalized magnetic beads for biomedical applications due to the outstanding characteristics of these materials. Furthermore, the recent development of microfluidics has enabled the continuous capture of malignant cells or toxins from biofluids for either analysis or treatment. However, the optimization of these processes has been relatively less studied and rational design is often lacking because of the complexity associated to their mathematical description. In this work, the separation of magnetic beads from flowing blood streams inside a multiphase system is analyzed through CFD techniques. The numerical model introduces a coupled magnetic and fluidic analysis that describes the bead trajectories under magnetic gradients generated by permanent magnets. A key feature of this work is that we studied for the first time the interaction between two fluids flowing simultaneously in the device while taking into account the effects of particle-fluid interactions in the flow field. Magnetic and fluidic forces on the particles are studied and optimized through a dimensionless number J. The results show that complete particle separation avoiding any mixing or perturbation of the fluids can be achieved for a certain range of the J number.

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