Numerical investigation of the transient, coupled hydrodynamic and thermal behavior of a novel polymerase chain reaction (PCR) centrifugal microfluidic system is presented in this study. The driving mechanism for flow within these devices is modeled as a combination of the capillary forces and rotationally induced pressure gradient working in opposition to viscous forces, which are functions of rotation speed and fluid properties. The physical properties of the working fluid are in turn functions of temperature, some of which can have significant variations over the operating temperature ranges of a PCR thermal cycle. The complex balance of viscous, capillary, and rotationally induced inertial forces are crucial factors in optimizing the design of such devices. Hence, the effects of temperature variation on the filling performance cannot be neglected. A commercial CFD code is utilized to simulate the filling of a microchamber when subjected to thermal conditions typical of a PCR thermal cycle. The numerical model accounts for the temperature dependence of the working fluid’s viscosity and surface tension by simultaneously solving the Navier-Stokes and energy equations. The free surface morphology (position, shape) and total chamber fill fraction as a function of time is predicted by using the volume of fluids (VOF) method. Comparison of the predictions from the temperature dependent numerical model to that which assume said physical properties to be constant, demonstrates the strong effect of the fluid’s viscosity and surface tension on the filling rate for various rotation speeds.

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