A physics-based single particle model was used to simulate the life cycling data of a lithium ion cell. The simulation indicates that there are probably three stages of capacity fade in a lithium ion cell used at low rates. In the first stage, lithium ions are lost to a film formation reaction (e.g. SEI formation) and, consequently, the cathode becomes less intercalated during cycling. In the second stage, the loss of active cathode material outpaces the loss of lithium ions and the cathode gradually becomes more intercalated at the end of discharge. The anode is the limiting electrode in stages one and two and the change in the anode voltage causes the cell to reach end of discharge voltage. In the third stage, the limiting electrode shifts from the anode to the cathode, and the anode becomes increasingly less discharged at the end of discharge. Thus, more and more “cyclable” lithium ions are left inside the anode, which causes additional capacity fade.