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In recent years, there has been increasing interest in the understanding and application of nanoparticle assemblies driven by external fields. Although these systems can exhibit marked transitions in behavior compared to non-interacting counterparts, it has often proven challenging to connect their dynamics with underlying physical mechanisms or even to verifiably establish their structure under realistic experimental conditions. We have studied colloidal iron oxide nanoparticles that assemble into ordered, few-particle linear chains under the influence of oscillating and pulsed magnetic fields. In this work, our goal has been to answer the following question: by what physical mechanisms does the magnetic switching of a linear chain evolve from the switching of its constituent particles? Cryo-TEM has been used to flash freeze and image the structures formed by oscillatory drive fields, and magnetic relaxometry has been used to extract the multiple time constants associated with magnetic switching of the short chains. Armed with the physical structure from microscopy and the field-dependent switching times from magnetic measurements, we have conducted extensive micromagnetic simulations, revealing probable physical mechanisms for each time constant regime spanning$$10^{6}$$($$\approx$$1 μs to 1 s) in time. These types of magnetic nanomaterials have great potential for biomedical technologies, particularly magnetic particle imaging and hyperthermia, and rigorous elucidation of their physics will hasten their optimization.