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Using the finite difference model for heat transfer, I am trying to model the heat flow into a heatsink. However, I am unsure of what k value or coefficient of thermal conductivity to use. Should I be using the coefficient for the material of the heatsink, or of the thermal paste in contact with the heatsink? The image below is the equation I am using.

Uniform heat flux node

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    $\begingroup$ If you are using finite element analysis, you can assume that you have perfect contact between the two surfaces or you can include a thermal resistance at the interface. Interface modelling is more complicated and should be done carefully. The losses at the interface can also arise from different values in the speed of sound between the two materials, especially for insulators. $\endgroup$ – mcodesmart Nov 24 '13 at 19:45
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You should be using the coefficient for the metal in the heat sink. The thermal paste is there simply to close a gap between the two surfaces. With a gap you have to worry about extreme inefficiency between the junction of the two surfaces. The thermal paste isn't perfect and there is still some efficiency loss in the interface but you should probably ignore that loss because the thermal paste is there to minimize it.

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