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CannibalSmith comments on UFAI cannot be the Great Filter - Less Wrong Discussion
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Here are my five minutes: nanomachines need to carry a charge to be accelerable, right? Well, it works the other way too - they will decelerate on their own in destination's Van Allen belts.
They don't actually decelerate in the Van Allen belts, though. Magnetic fields apply a force to a charged particle perpendicular to it's direction of motion. F*V = Deceleration Power = 0. Also worth noting that a charged nanomachine has a much higher mass/charge ratio than the usual charged particles (He2+, H+, and e-), so it would be much less affected.
I was actually thinking of neutralizing the seed at the muzzle to avoid troublesome charge effects.