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A thermodynamic model has been employed to study the effect of changing injection timing, spray angle, fuel density, fuel viscosity, chemical reaction rate constants and air entrainment on the combustion performance of seed oils and their methyl esters in an open chamber diesel engine. It is shown that the most important valuables affecting the performance are fuel density and fuel viscosity. It is deduced that modification of these physical properties can lead to substantial improvement in the combustion performance of the seed oils.