There is increasing interest in alternatives to conventional petroleum-derived fuels for piston engines and other applications. A significant issue with alternative fuels is their influence on pollutant emissions. Recent studies have shown that turbulence and turbulence/chemistry interactions affect emissions from compression-ignition engines. To capture the sometimes subtle influences of fuel composition on emissions using CFD-based models, it is expected that these complex interactions will need to be accounted for explicitly. In this research, skeletal chemical mechanisms and a transported composition probability density function (PDF) method are used to capture chemistry and turbulence/chemistry interactions in direct-injection compression-ignition engines. Two examples of applications that explore fuel composition effects are discussed: NOx emissions for hydrogen-assisted diesel combustion, and the increase in NOx emissions that has been observed when biodiesel fuel is substituted for petroleum-derived diesel fuel in common-rail diesel engines. For hydrogen-assisted diesel combustion, the model is able to reproduce the experimentally observed trends for some operating conditions, in spite of the significant simplifications that were made; a model that explicitly accounts for turbulence/chemistry interactions (using a PDF method) does somewhat better than a model that neglects turbulence/chemistry interactions. In the second example, the sensitivity of NOx emissions to variations in the physical properties of the fuel (here density and viscosity) has been explored to assess the origins of the biodiesel-NOx effect; NOx is found to increase with increasing fuel density, with all other parameters held fixed. Complex turbulence/chemistry/soot/radiation interactions are being explored in ongoing work aimed at understanding the biodiesel-NOx effect.