Fast Enough - S1-E23
Corrected entry: Particle accelerators have to be a perfect vacuum in order to work properly, otherwise the particles inside would constantly collide with the air molecules. This means Barry couldn't possibly be running inside, because he doesn't have any breathing apparatus with him.
Correction: As seen in many episodes, Barry's cells can rapidly reproduce new cells even with no oxygen (as seen in season 1 where the man could create a poisonous gas) and Barry survived. Therefore he would not have to have a breathing aid.