Global pressure to reduce greenhouse gas (GHG) emissions, energy security concerns and increasing demand for liquid fuels incentivize the search for more sustainable and secure alternative methods for producing liquid fuels with improved efficiency and reduced environmental impacts. One of the economically attractive examples of these alternate methods is the gas-to-liquid process, however, its environmental impacts are worse than traditional petroleum refining. Carbon capture and sequestration is an option to reduce greenhouse gas emissions of processes, but it decreases the efficiency of the process and often results in economic infeasibility. Instead, integrating different processes and feedstocks was demonstrated to improve the efficiency, economic and environmental performance of the processes. The focus of this thesis is to design and simulate a novel integrated biomass, gas, nuclear to liquids (BGNTL) process with negative greenhouse gas emissions. In this process, nuclear heat from a high temperature gas-cooled reactor (HTGR) is used as the heat source for a steam methane reforming (SMR) process. The integrated HTGR and SMR process requires detailed analysis and modeling to address key challenges on safety, operability, economic and environmental impacts of the integrated process. To this end, a rigorous first principle based mathematical model was developed in gPROMS modeling environment for the integrated HTGR/SMR process. The results for a large scale design of this system indicate that hydrogen rich syngas with H2/CO ratio in the range of 6.3 can be achieved. To meet the desired H2/CO ratio (around 2) required for the downstream fuel synthesis processes, the HTGR/SMR derived syngas can be blended with a hydrogen lean syngas from biomass gasification. In this thesis, the large scale design of the BGNTL process to synthesize gasoline, diesel and dimethyl ether (DME) is investigated. The results from the gPROMS model of the integrated HTGR/SMR system are used for simulating the BGNTL process in Aspen Plus. The performance of the BGNTL process was compared with a biomass, gas to liquids (BGTL) process. The efficiency, economics, and environmental impact analyses show that the BGNTL process to produce DME is the most efficient, economic and environmentally friendly process among all the considered designs. The results demonstrate that process integration exploits certain synergies that leads to significantly higher carbon and energy efficiencies and lower greenhouse gas emissions. In addition, it was found that all the studied designs yield a net negative greenhouse gas emissions when carbon capture and storage technology is implemented. As another sustainable alternative to meet the required H2/CO ratio of the syngas when biomass resources are not available, it is proposed to apply the nuclear heat to the mixed reforming of methane. This represents using steam and waste CO2 to reform methane into valuable syngas. The developed model for the integrated HTGR/SMR system is extended to the mixed reforming of methane (MRM) process and it was demonstrated that integrated HTGR/MRM process can be a promising option to achieve certain desired H2/CO ratios for the downstream energy conversion processes. Thesis Doctor of Philosophy (PhD)