Seem like EMP protection in aircraft are mostly in the form of faraday cage and shielded cable, so logically, multiple EMP likely doesn’t degrade it, especially consider that aircraft can take lightning strike and not instantly exploded.
On newer aircraft such as F-16 block 60, F-35 they also seem to use fiber optic instead of copper wire which eliminate the vulnerable to EMP since it can’t conduct current inside fiber optic wire
What I do not know about fibre-optic aircraft control systems would be hard to overestimate. However, I do see a couple of possible problems with these statements, if my minimal knowledge of fibre-optic communications and Faraday cages is applicable.
[1] First, as far as I know, Faraday cages have to be continuous, with no openings that can let an eleectrical field through. This makes them impractical in many settings. For example, as an anti-eavesdropping measure, a secure briefing room that I know of had a Faraday cage implemented in the form of continuous, fine brass screen in the walls. There was a single door, also screened, with all its edges covered by fine brass brushes to bridge gaps when closed. There were no electrical, network, telephone, or plumbing conduits piercing the cage. This so reduced the usability of the room that the customer eventually cut all sorts of holes in the wall, spoiling both the cage and its rather large investment.
In an aircraft, I suspect that practical difficulties are a much bigger obstacle to effective use of Faraday cages. Even with shielded cables interconnecting cages around equipment, it sees like protecting all electronic components would be hard at the very least--and expensive in terms of weight and money. It might work in very large aircraft, like bombers. But in volume-limited aircraft like fighters, it seems less practical. Anything that needs to radiate and receive--radars, radios, GPS, etc--might not be protected at all.
[2] While fibre-optic lines are indeed immune to EMP, the interfaces to electronic components are not. At present, at least, fibre only
transports signals. Vulnerable copper- and silicon-based components generate and interpret the signals. If the sensitive items are Faraday-caged, how do you connect the fibre to them without breaching the cage?
[3] Also, nuclear weapons aren't the only possible EMP sources: solar flares, some currently deployed quasi-conventional weapons, and lightning can have similar effects.
So it seems to me that, realistically, EMP is likely to knock out mission critical components, from radars to flight- and fire-control computers to electronic engine management systems. Even if the electro-mechanical actuators for the control surfaces and engines remain unaffected, the controlling computers will be ruined You'd need mechanical backups for basic flight and engine controls just to fly home.
The benefits of fly-by-wire are not free--even before we talk about software.
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