A note on the Jarzynski equality

The Jarzynski equality relates the free energy difference between two equilibrium states of a system to the average of the work over all irreversible phase space trajectories for going from one state to the other. We claim that the derivation of this equality is flawed, introducing an ad hoc and unjustified weighting factor which handles improperly the heat exchange with a heat bath. Therefore the experiment of Liphardt et al cannot be viewed as a confirmation of this equality, although the numerical deviations between the two are small. However, the Jarzynski equality may well be a useful approximation, e.g. in measurements on single molecules in solution.