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We elucidate magnetic effects in the skyrmion system to probe into the dense nuclear matter. We find a deformed dipole structure of a baryon induced by a magnetic field. We then extend our scope to stacked Skyrme crystal layers to scrutinize phases of magnetized nuclear matter. We observe a quantized magnetic flux and identify a phase transition from a crystalline state to a domain wall corresponding to a topological transmutation from to . We establish the phase diagram, which could be explored also in analogous systems with two-component Bose-Einstein condensates.

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