After reviewing the basic modeling framework for simulating battery behavior, three examples relating to mass-transfer effects are presented. Side reactions at the lithium electrode can change the surface concentration of lithium ions, introducing error into measurements of the cell potential as a function of bulk electrolyte concentration (concentration-cell measurements). This error introduced by a continuous side reaction is carried over into calculations of the transference number from the galvanostatic polarization method. Concentration gradients formed during passage of current are associated with a heat-of-mixing effect, which is the cause of heat generation during relaxation after cessation of the current. Finally, molecular dynamics simulations show that the decrease in conductivity with increasing salt concentration in liquid carbonate electrolytes is caused by ion association.