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IANAEE but is there some way to integrate peltier junctions into a 3D microchip design so that the heat all gets funneled out of the CPU in a regulated and controlled manner?

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Not my area of expertise, but I believe most research today is on microfluidics, introducing microchannels into 3D interconnect layers alongside the TSVs to cool the device. For example, http://deepaksekar.weebly.com/uploads/1/9/8/6/1986457/3d_mic...

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