Why is there less helium in Jupiter’s upper atmosphere than expected?

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The observation that Jupiter’s upper atmosphere contains less helium than expected—approximately 24 percent by mass compared to the 28 percent predicted from the original solar nebula—is explained by the planet's internal cooling process.1

As Jupiter continues to cool, helium that was previously dissolved in the planet's fluid hydrogen interior has precipitated out of solution. These helium droplets have sunk toward the planet's center, effectively depleting the upper atmosphere of the gas. This process is also believed to have carried neon downward along with it. Furthermore, the liberation of thermal energy resulting from this helium precipitation is considered a significant contributor to Jupiter's internal heat source.1