In this paper, a two-dimensional dynamic model describing the separation behaviors of magnetic particles in magnetophoretic chip microchannels integrated with double-side symmetric and asymmetric soft magnets is proposed and solved with the combining use of the finite element method and the fourth-order Runge-Kutta method. The dynamic characteristics of magnetic particles during the separation process, including the trajectories of magnetic particles, the capture time and capture efficiency are analyzed. The impacts of the geometrical configurations, fluid velocity and magnetic field intensity are also studied. The results show that the trajectories of the magnetic particles in microchannels are oscillatory because of the alternative magnetic force and this oscillation is more obvious for asymmetric positions of the soft magnets. The oscillatory motion of the particle leads to the increase of the moving distance and delay of the capture time. The capture time depends on the geometrical configurations, the initial positions and the dynamic characteristics of the particles. It is also found that under the same strength of magnetic fields there is nearly no difference on the capture efficiency for symmetric and asymmetric configurations. With the increase of fluid velocity, the capture efficiency drops drastically at low flow rates and decreases slowly at high flow rates. The distance between soft magnets and microchannel walls has the similar influence on capture efficiency. It is expected that the results presented in this paper are helpful for the design and optimization of magnetophoretic separation microsystems.

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