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A computational platform has been developed to perform simulation, visualization, and postprocessing analysis of the aggregation process of magnetic particles within a fluid environment such as small arteries and arterioles or fluid-filled cavities of the human body. The mathematical models needed to describe the physics of the system are presented in detail and also computational algorithms needed for efficient computation of these models are described. A number of simulation results demonstrate the simulation capabilities of the platform and preliminary experimental results validate simulation predictions. The platform can be used to design optimal strategies for magnetic steering and magnetic targeting of drug-loaded magnetic microparticles.