This study presents a numerical analysis of Joule heating effect on the electroosmotic flow and species transport, which has a direct application in the capillary electrophoresis based BioChip technology. A rigorous mathematic model for describing the Joule heating in an electroosmotic flow including Poisson-Boltzmann equation, modified Navier-Stokers equations and energy equation is developed. All these equations are coupled together through the temperature-dependent parameters. By numerically solving aforementioned equations simultaneously, the electroosmotic flow field and the temperature distributions in a cylindrical microcapillary are obtained. A systematic study is carried out under influences of different geometry sizes, buffer solution concentrations, applied electric field strengths, and heat transfer coefficients. In addition, sample species transport in a microcapillary is also investigated by numerically solving the mass transfer equation with consideration of temperature-dependant diffusion coefficient and electrophoresis mobility. The characteristics of the Joule heating, electroosmotic flow, and sample species transport in microcapillaries are discussed. The simulations reveal that the presence of the Joule heating could have a great impact on the electroosmotic flow and sample species transport.

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