Eccentric contraction versus concentric contraction. Cycling uses concentric contraction (exclusively) of the quads to generate power. Concentric contraction is what is used to climb stairs. Eccentric contraction (the negative) is the opposite or going down stairs. Running requires the quad to absorb a foot strike (eccentric) before it pushes off with a concentric contraction. Since you never use the quad in the negative on the bike, when you run, the muscle gets sore until it becomes accustomed to the new motion. The other aspect of concentric versus eccentric contraction is why cyclist are required to endure such pain. One can push very hard using the muscles concentrically as they fatigue. Runners at some point collapse due to the failure of muscles ability to take the negative impact any longer.