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Over the course of the past decade, a number of investigations have been conducted to better understand the fluid flow and heat transfer in microchannel heat sinks, particularly as it pertains to applications involving the thermal control of electronic devices. In the current investigation, a detailed numerical simulation of the heat transfer occurring in silicon-based microchannel heat sinks has been conducted in order to optimize the geometric structure using a simplified, three-dimensional (3-D) conjugate heat transfer model [two-dimensional (2-D) fluid flow and 3-D heat transfer]. The micro heat sink modeled in this investigation consists of a 10 mm long silicon substrate with rectangular microchannels fabricated with different geometries. The rectangular microchannels had widths ranging from 20 /spl mu/m to 220 /spl mu/m and a depth ranging from 100 /spl mu/m to 400 /spl mu/m. The effect of the microchannel geometry on the temperature distribution in the microchannel heat sink is presented and discussed assuming a constant pumping power. The model was validated by comparing the predicted results with previously published experimental results and theoretical analyses, and indicated that both the physical geometry of the microchannel and the thermophysical properties of the substrate are important parameters in the design and optimization of these microchannel heat sinks. For the silicon-water micro heat sink, the optimal configuration for rectangular channel heat sinks occurred when the number of channels approached 120 channels per centimeter.