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Concrete contains numerous pores that allow degradation when chloride ions migrate through these paths and make contact with the steel reinforcement in a structure. Chlorides come mainly from the sea or de-icing salts. To keep the reinforcement from being exposed to chlorides, it is possible to electrokinetically force nanoparticles into the pores, blocking access. This procedure is called electrokinetic nanoparticle treatment. When the particles used are reactive in nature, the process becomes both structural and chemical in nature. We use the term electromutagenic processing to describe such extensive electrochemical remodeling. Filling the pores in a block of concrete with solid materials or nanoparticles tends to improve the strength significantly. In this paper, results obtained from modeling and simulation were aimed at multi-scale porosity reduction of concrete. Since nanoparticles and pores were modeled with spheres and cylinders having different sizes, the results were compared with traditional sphere packing problems in mathematics. There were significant differences observed related to the sizes of spheres and allowable boundary conditions. From traditional sphere packing analysis the highest porosity reduction anticipated was 74%. In contrast, the highest pore reduction obtained in this work was approximately 50%, which matched results from actual electrokinetic nanoparticle treatments. This work also compared the analytical and simulation methods used for several sizes of nanoparticles and pores.