1. A fuel cell system comprising: a fuel cell stack; a cooling fluid pump pumping a cooling fluid through the fuel cell stack; a temperature sensor measuring the temperature of the cooling fluid out of the fuel cell stack; a radiator for cooling the cooling fluid from the fuel cell stack before it is returned to the fuel cell stack; a by-pass valve that selectively allows a portion of the cooling fluid to by-pass the radiator; and a controller programmed to control the position of the by-pass valve, said controller receiving a temperature signal from the temperature sensor, said controller also programmed with a dead-time plant model to calculate a plurality of variables and a dead-time value that are used to set the position of the by-pass valve so that the temperature of the cooling fluid exiting the fuel cell stack moves towards a desired temperature set-point, wherein the plurality of variables include control parameters that are recalculated for new operating conditions and wherein the recalculated control parameters are used to estimate new plant model parameters, and wherein the controller estimates a first dead-time plant model having a time delay greater than a current estimate of the dead-time value, a second dead-time plant model including a time-delay less than the current estimate of the dead-time value and a third dead-time plant model including the current estimate of the dead-time value, wherein the first dead-time plant model is compared to the third dead-time plant model and the second dead-time plant model is compared to the third dead-time plant model by calculating variances in the estimates to determine whether the dead-time value should be increased or decreased.