Modeling of engine-out heat release (HR) is of great importance for engine combustion research. Variations in fuel properties bring about changing combustion behavior within the cylinder, which may be captured by modeling of the rate of heat release (RHR). This is particularly true for biodiesel fuels, where changes in fuel behavior are linked to viscosity, density, and energy content. HR may also be expanded into an analysis using the second law of thermodynamics, which may ascertain the pathways through which availability is either captured as useful work, unused as thermal availability of the exhaust gas, or wasted as heat transfer. In specific, the second-law model identifies the period of peak availability, and thus the ideal period to extract work, and is of use for power optimization. A multizone (fuel, burned, and unburned) diagnostic model using a first law of thermodynamics analysis is utilized as a foundation for a second-law analysis, allowing for a simultaneous energy and exergy analysis of engine combustion from a captured pressure trace. The model calibrates the rate and magnitude of combustion through an Arrhenius equation in place of a traditional Wiebe function, calibrated using exhaust emission measurements. The created model is then utilized to categorize combustion of diesel and palm biodiesel fuels as well as their blends. The second-law analysis is used to highlight the effects of increasing biodiesel usage on engine efficiency, particularly with respect to fuel viscosity and combustion temperature. The second-law model used is found to provide a more clear understanding of combustion than the original first-law model, particularly with respect to the relationships between biodiesel content, viscosity, temperature, and diffusion-dominated combustion.