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I've seen a lot of questions on this topic so please don't misunderstand, I understand E = mc^2 and SEMF and so on. I specifically want to know how internal forces within lets say a nucleus make it more difficult to accelerate said nucleus by an outside force.

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I can provide you a better point of view, in which case the result becomes intuitive. However, it does not constitute as a complete explanation, because, in the end, it is really about accepting the physics rather than a detailed mechanism.

In old Newtonian mechanics, the phenomenon of both inertia (difficulty to accelerate) and gravity (pulls at you) are ascribed to mass. It is discovered that in relativity, this ascribing is wrong. Instead, both inertia and gravity are due to energy(-momentum). That is, all appearances of mass in old Newtonian mechanics is really that the phenomena is dependent upon the total amount of energy in a system, and the total amount of energy in a system in Newtonian mechanics is always being dominated by the rest mass contribution to the energy budget. Old Newtonian energies are only just differences in total energy, the differences after subtracting off this rest mass contribution to total energy.

This then makes intuitive sense that, if the energy of a system is increased by any means, then it will be harder to push (inertia) and will gravitationally pull at you stronger. This includes when you simply increase the kinetic energy of a system. Be it by heating it, or by giving it orderly overall linear momentum. It is the relativistic viewpoint that makes far more sense of this.

However, you are incredibly confused, so much so that you are getting even the signs wrong. Binding energy, the internal forces inside a nucleus, is acting to subtract the energy of stuff being bound inside a nucleus, so that they do not have enough energy to fly apart. As such, they actually make the nucleus easier to accelerate, not harder.

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You might also ask how mass makes it hard to accelerate an object. It just does. And it is the same for how energy makes it hard to accelerate on object.

You might take a look at this PBS Space Time video - The Real Meaning of E=mc². It makes the point you already know that adding energy increases mass, or resistance to acceleration. But also that mass arises from energy.

It also has a link to an English translation of Einstein's original short paper, Does the inertia of a body depend on its energy content?, which also does not propose a mechanism.

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