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This study proposes molecular dynamics simulations used to derive guidelines for the design of the superparamagnetic nanocapsules (spherical-like or rod-like) dedicated to cross the brain-blood barrier (BBB) by magnetic forces. We focus our study on capillaries that have opened fenestrations when the integrity of the endothelial barrier is perturbed by tumors. We identified three different categories of governing parameters: geometrical (radius and length of nanocapsules), biophysical (ligand-to-receptor surface density ratio, nonspecific interaction parameters) and biological (ligand/receptor binding affinity). The main novelty of our study is to carry out computational simulations to determine design criteria-the size, charge, and shape of various magnetic nanocapsules (spherical and rod-shaped nanocapsules)-that optimize their penetration into the BBB. Finally, the simulation results show that the superparamagnetic nanorobotic capsules were able to cross the endothelial barrier by using magnetic forces compatible with medical constraints.