In principle, it’s the same atmosphere, and if the conditions were the same between launch and landing, you’d certainly expect there to be the same heating on the spacecraft in both cases. However, there are a few key differences between landing and launch which means that the spacecraft winds up dealing with much more heat on its way back down to the surface than it does going up.
The biggest difference is due to the fact that when you launch a spacecraft, you start out stationary relative to the ground. The major goal of a launch is to speed yourself up to the point where gravity’s downward force is no longer enough to pull you back down to Earth. Any given orbit is simply a matter of falling while moving around the object you would like to not crash into; you’re still falling, but the sideways motion is enough to keep you at the same distance above the surface. A spacecraft’s launch is the slow, rumbling start to building up this speed.
When you’re in orbit, you’re going much faster relative to the ground. The International Space Station, for instance, orbits the Earth once every 90 minutes or so, which means that it’s going slightly over 17,000 miles per hour up there. Any spacecraft which visits the ISS therefore has to start from 0 miles an hour, stationary on a launch pad, and reach 17,000 miles an hour. If you’re starting in space, and trying to land on earth, you need to reverse this; you need to start from zipping around above the planet, and slow yourself down to 0 miles an hour.
In addition to the difference in starting speed, the atmosphere is not evenly dense from top to bottom. The top (i.e., facing outer space) edge is much less dense than the bottom is. And if you’re heating up the spacecraft due to interactions with the atmosphere, those interactions are going to be dependent on both the speed at which you encounter the atmosphere and the density of the atmosphere.
When you’re leaving the planet, your craft will be moving rather slowly while it’s going through the densest parts of the atmosphere, which means that the heat generated will be fairly small. It’s only when the craft leaves the most dense regions and gets into the very thin upper atmosphere that it starts to get up to the orbital speeds that can produce strong heating, but by that point there’s not enough atmosphere left to produce significant heat.
If you’re coming back down from space, you’re hitting an increasingly thick wall of the atmosphere at very high speeds, and the magic combination of dense air and high speeds is present, allowing for the super high temperatures to be produced. The atmosphere is so heated by the re-entering craft that it forms a shock wave of plasma around the spacecraft for at least a few minutes as the craft slows down. This plasma interferes with radio communications between ground and spacecraft, so it’s often an anxious time, as the ground control is unable to communicate with the crew (or the robot) to check on how things are going.
To protect the spacecraft, and its crew if one exists, most crafts are fitted with a heat shield; this is a heat resistant material on the leading edge of the re-entering craft. The heat shield is designed to very slowly vaporize at high temperatures, allowing the hottest parts of the shield to flow away from the craft, and preventing high temperatures from building up near the spacecraft, which could result in the destruction of the entire craft. The partial loss of the integrity of the heat shield on the space shuttle Columbia led to the tragic loss of craft and crew in 2003; the heat shield is a critical component to a safe and successful re-entry.
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