As part of the Idaho National Laboratory's (INL's) Secure Energy Initiative, the INL is performing research in areas that are vital to ensuring clean, secure energy supplies for the future. The INL Hybrid Energy Systems Testing (HYTEST) Laboratory is being established to develop and test hybrid energy systems with the principal objective to safeguard U.S. Energy Security by reducing dependence on foreign petroleum. HYTEST involves producing liquid fuels in a Hybrid Energy System (HES) by integrating carbon-based (i.e., bio-mass, oil-shale, etc.) with non-carbon based energy sources (i.e., wind energy, hydro, geothermal, nuclear, etc.). Advances in process development, control and modeling are the unifying vision for HES. This paper describes new modeling tools and methodologies to simulate advanced energy processes. Needs are emerging that require advanced computational modeling of multiphase reacting systems in the energy arena, driven by the 2007 Energy Independence and Security Act, which requires production of 36 billion gal/yr of biofuels by 2022, with 21 billion gal of this as advanced biofuels. Advanced biofuels derived from microalgal biomass have the potential to help achieve the 21 billion gal mandate, as well as reduce greenhouse gas emissions. Production of biofuels from microalgae is receiving considerable interest due to their potentially high oil yields (around 600 gal/acre). Microalgae have a high lipid content (up to 50%) and grow 10 to 100 times faster than terrestrial plants. The use of environmentally friendly alternatives to solvents and reagents commonly employed in reaction and phase separation processes is being explored. This is accomplished through the use of hydrothermal technologies, which are chemical and physical transformations in high-temperature (200-600 C), high-pressure (5-40 MPa) liquid or supercritical water. Figure 1 shows a simplified diagram of the production of biofuels from algae. Hydrothermal processing has significant advantages over other biomass processing methods with respect to separations. These 'green' alternatives employ a hybrid medium that, when operated supercritically, offers the prospect of tunable physicochemical properties. Solubility can be rapidly altered and phases partitioned selectively to precipitate or dissolve certain components by altering temperature or pressure in the near-critical region. The ability to tune the solvation properties of water in the highly compressible near-critical region facilitates partitioning of products or by-products into separate phases to separate and purify products. Since most challenges related to lipid extraction are associated with the industrial scale-up of integrated extraction systems, the new modeling capability offers the prospect of addressing previously untenable scaling issues.