Biological conversion of biomass into gasoline, diesel, and kerosene provides an alternative means to meet liquid transportation fuel demand, going beyond the traditional thermochemical methods involving gasification, Fischer-Tropsch conversion) and methanol synthesis. Process synthesis is an ideal methodology for comparing the developing biological technologies with established thermochemical methods through input-output modeling of biorefinery units and inclusion in a superstructure. The resulting model takes the form of a mixed-integer nonlinear optimization problem with full heat, power, and water integration. In the novel superstructure, the MixAlco process for biological conversion is modeled, in which biomass is fermented into carboxylic acid salts which are further upgraded into liquid transportation fuels. The model is solved to global optimality based on the minimization of the cost of liquid transportation fuels production using a branch-and-bound global optimization algorithm to provide upper bound Solutions, valid lower bound solutions, and an optimality gap. Case studies analyze the performance of the MixAlco process relative to the existing Fischer-Tropsch and methanol synthesis routes when switchgrass is used as the biomass feedstock at capacities ranging from 1000 bbl per day to 200 000 bbl per day of gasoline equivalent liquid transportation fuels by energy content. From an economic perspective, the MixAlco process is not competitive with the existing methods, with break-even oil prices from $102.08/bbl to $169.06/bbl. However, a combined MixAlco thermochemical process is also analyzed, with leftover biomass residue from the fermenter converted into synthesis gas and upgraded to fuels. This proposed process provides break-even oil prices of $79.40/bbl to $144.00/bbl, competitive with and even sometimes outperforming the thermochemical methods for fuel production from biomass. The processes are also analyzed for their greenhouse gas impact, and parametric analysis is conducted on investment cost and switchgrass price parameters to study their impact on the biorefineries.