In-cylinder engine modeling is a necessary aspect of combustion research. In particular, simulating heat release connects variable combustion behavior to fuel properties through the 1st Law of Thermodynamics. One extension of such models is to evaluate changes to in-cylinder behavior using the Second Law of Thermodynamics in order to identify the peak period of availability for work extraction. Thus, Second Law models are a useful tool to augment research into alternative fuel usage and optimization. These models also help identify internal irreversibilities that are separate from heat transfer and exhaust gas losses.This study utilizes a multi-zone 1st and 2nd Law Heat Release model to characterize the changes in combustion behavior of a number of neat fuels used in a single-cylinder compression ignition (CI) engine. This includes standard Ultra Low Sulfur Diesel (ULSD), biodiesels derived from jatropha and tallow feedstocks, Jet A aviation fuel, and a synthetic aviation fuel derived from renewable sources. In all cases, fuel injection timing was adjusted to align the peak pressure timing of each fuel with that of ULSD.Overall, variations in fuel properties were found to bring about considerable changes in engine operation when investigating the 2nd Law. Most prominently, fuel density, energy content, cetane number, and viscosity serve as the primary fuel characteristics that drive combustion timing, duration, and intensity. In particular, it is shown that large viscosities (a characteristic of biodiesels) lead to delayed and prolonged combustion, which serves to add availability to the working fluid later in the expansion stroke, subsequently making it more difficult to extract that availability as useful work. In addition, the strengths of incorporating the 2nd Law analysis are expressed, both alone and in tandem with the traditional 1st Law analysis.