To define these particles, one has to bombard it with energy, causing it to fly apart. You start with one particle and create fragments that are themselves particles. So far these fragments behave predictably and reinforce the idea of the universe being made of these particles. But all is not well.

The reason for all this energy is that these atomic particles are thought to be to held together by forces that must be overcome by even stronger force. This seems like a overly complicated arrangement since we really only need one the force that fragments the atom and it comes from outside the atom. It is just as plausible to suppose that an atom has it's structure because its constituent parts are clustered in a small space.

In this case, there is no force needed to explain why these atoms hold together, since plain old inertia will account for their stability. To upset this state you have to introduce something from the outside.

This is generally what is called a particle with high energy but it's only a particle in the sense of having high energy in a small space. For this energy to affect an atom it has to have a wavelength less than the size of the atom which, for all practical purposes, behaves as if it is a particle.

This may be significant. If energy is focused into a small enough space, it is, effectively, the same as a particle. This makes the idea of "particle" merely a description for some region of space with high energy; there is no such "thing" as a particle. Thinking in terms of particles is just an explanatory convenience.

What may be happening is there are regions in space where "things" accumulate into stable arrangements. They are stable because there's nothing disturbing them. If something enters the the system that can disrupt it. For something to disturb this stability, it must have sufficient energy. It doesn't matter what holds the stable region together, all we need to know is how much energy it takes to disrupt it. There doesn't have to be a "force" holding atoms together, just a force (energy) great enough to fragment them.

There is probably no difference in how we work with atoms, but the above does radically simplify how we understand them. Since there are no forces at work holding an atom together, all we need to know is the force (energy) it takes to split it apart. This same simplification applies to the "particles" within an atom. A proton, for instance, isn't a “thing” but the force required to affect its position.

Particle accelerators can strip an atom of its electrons and isolate protons that can then be made to collide with other atom or protons. From these collisions, physicists can produce sub-proton particles. Collisions at the same energy level will produce the same particles. Increasing the energy produces different particles. This is a clue. What's being observed are the results of different energies interacting; no particles are necessary to explain any of this. Particles are focused energy.