This study presents a numerical simulation of Joule heating effect on electroosmotic flow and mass species transport in microchannels, which has direct applications in the capillary electrophoresis based Biochip technology. The proposed model includes the Poisson-Boltzmann equation, the modified Navier-Stokes equations, the conjugate energy equation, and the mass species transport equation. The numerical predictions show that the time development for both the electroosmotic flow field and the Joule heating induced temperature field are less than 1 second. The Joule heating induced temperature field is strongly dependent on channel size, electrolyte concentration, and applied electric field strength. The simulations reveal that the presence of Joule heating can result in significantly different characteristics of the electroosmotic flow and electrokinetic mass transport in microchannels.

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