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Pions are created when high energy cosmic particles collide with atoms in Earth's atmosphere and also in particle accelerators that smash hadrons together. It's clear that that positive, negative and zero charge pions can be created with probabilities that we can calculate.

But, is there a method through which one could control or at the very least predictably influence the charge of pions produced is such way?

Has there been any work (experimental or purely theoretical) done that you can point me to? Is this even possible?

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Elementary particles and hadrons are produced by scattering, and this as you say depends on the probability of generating the various particles, hadrons, pion included.

After creation though, each charged pion ( in this case) which has a life time of some nanoseconds can be guided using magnetic fields to form a beam of pions . Also a beam of other hadrons, and these beams have been used to study, for example, pion proton scattering, or kaon proton scattering. A number of experiments have been carried out in the various high energy laboratories, (example) .

Neutral beams are harder .

But, is there a method through which one could control or at the very least predictably influence the charge of pions produced is such way?

There is no way before, since the interaction is probabilistic, only after the interaction particles can be separated if their lifetime is long enough.

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