Magnetic micro-beads can facilitate many functions in lab-on-a-chip systems, such as bio-chemical labeling, selective transport, magnetic sensing and mixing. In order to investigate potential applications of magnetic micro-beads for mixing in micro fluidic systems, we developed a pin-jointed mechanism model that allows analysing the behaviour of rotating superparamagnetic bead chains. Our numerical model revealed the response of the chains on a rotating magnetic field over time. We could demonstrate that the governing parameters are the Mason number and number of beads in the chain. The results are in agreement with the simplified analytical model, assuming a straight chain, but also allow prediction of the transient chain shape. The modelled chains develop an anti-symmetric S-shape that is stable, if the Mason number for a given chain length does not surpass a critical value. Above that value, rupture occurs in the vicinity of the chain centre. However, variations in bead susceptibility can shift the location of rupture. Moreover, we performed experiments with superparamagnetic micro-beads in a small fluid volume exposed to a uniform rotating magnetic field. Our simulation could successfully predict the observed transient chain form and the time for chain rupture. The developed model can be used to design optimised bead based mixers in micro fluidic systems.