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New types of synthetic fuels are introduced in internal combustion engine applications to achieve carbon-neutral and ultra-low emission combustion. Dimethyl Ether (DME) and Polyoxymethylene Dimethyl Ethers (OMEn) belong to such kind of synthetic fuels. Recently, Shrestha et al. (2022) have developed a novel detailed chemistry model for OMEn (n=1-3) to predict the ignition delay time, laminar flame speed and species formation for various thermodynamic conditions. The detailed chemistry model is applied in the zero dimensional (0D) stochastic reactor model (DI-SRM) to investigate the non-premixed combustion in a 2-liter diesel engine. Further insights in the formation of unburned hydrocarbons (HC), carbon monoxide and nitrogen oxides during the combustion of OMEn fuels are obtained in this work. The combustion and emission formation of DME and OMEn (n=1-3) are investigated and compared to conventional Diesel combustion. The mixture formation is governed by an earlier vaporization of the DME and OMEn fuels, faster homogenization of the respective air-fuel mixture and higher reactivity. At the same injection pressure, the OMEn fuels obtain higher NOx but lower CO and HC emissions. High amounts of aromatics, ethene, methane formaldehyde and formic acid are found within the Diesel exhaust gas. The DME and OMEn exhaust gas contains higher fractions of formaldehyde and formic acid, and fractions of methane, methyl formate and nitromethane.