Isotopically-pure Si-28 has a higher heat conductivity than native Si because isotopic "defects," i.e. nuclei of Si-29 (4.7% of native Si) or Si-30 (3.1%) act as phonon scattering centers and thereby create thermal resistance.
Basically, the greater the distance the phonons (heat quanta) can travel before bouncing off a site in the lattice that is different from most of the others, the faster heat can travel from one side (the hot side) of the chip to the other (the cooled side). With so many scattering centers around in native Si, it is far from a straight shot, so the phonons bounce from site to site, only slowly diffusing from hotter to cooler regions. Semiconductor-grade Si has usually been so highly purified and so carefully crystallized that there are essentially no lattice defects other than the minority isotopes. Eliminating these can improve cooling dramatically, although there is still phonon-phonon scattering to slow things down.
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Basically, the greater the distance the phonons (heat quanta) can travel before bouncing off a site in the lattice that is different from most of the others, the faster heat can travel from one side (the hot side) of the chip to the other (the cooled side). With so many scattering centers around in native Si, it is far from a straight shot, so the phonons bounce from site to site, only slowly diffusing from hotter to cooler regions. Semiconductor-grade Si has usually been so highly purified and so carefully crystallized that there are essentially no lattice defects other than the minority isotopes. Eliminating these can improve cooling dramatically, although there is still phonon-phonon scattering to slow things down.