We report experimental results on chaotic mass transport induced by alternating topological changes of magnetic particle chains actuated by a rotating magnetic field. Results on the induced fluid flows, through particle tracing experiments and mixing experiments, are obtained for (1) the regime of rigid chain rotation and (2) the regime wherein chains periodically fragment and reform. In the case of rigid rotating chains, the overall tracer particle trajectories are steady slightly modulated circles around the center of the microparticle chains. In the regime of periodic chain breaking and reformation, the tracer particle trajectories become chaotic. The level of mixing is measured by using a mixing index (M) in a water-dye system, i.e. in a perfectly mixed system M = 0 while in an unmixed system M = 1. When particle chains periodically break and reform, we observe that the mixing index M decreases from 1 to 0.1 within 15 rotational cycles. For rigid rotating chains, M reaches a minimum of only 0.5. We also report the effect of the different actuation regimes on a biological binding reaction in the solution, and indeed found that the reaction product (at equal actuation time) is significantly enhanced (3 times) by the dynamic chain regime as compared to the rigid chain regime. We conclude that the alternating topological change of microparticle chains - with repetitive chain breakup and chain reformation - is an effective mechanism to achieve chaotic mixing and thereby promote and homogenize reactions in lab-on-a-chip systems.