1) No idea how the computers did it.
2) Energy creates mass if there's enough of it. This is the whole
principle behind the LHC, it creates high enough energies that large
particles are created.
3) Assume you have two quarks. If you try to separate them, the strong
force between them will be so great, that 2 new quarks will be created
by the energy of the strong force. This process creates 2 new quark
pairs. This is analogous to separating a magnet and consequently
creating two new magnets, each with a north and south pole.