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The combustion properties of a fuel are a function of many variables, including things like bulk modulus (compressibility), vapor pressure, viscosity, surface tension, melting point/cloud point, flash point, heat capacity etc, etc, etc. These physical properties are in turn, closely related to molecular structure. Moreover they can vary with temperature, and in the case of some kinds of conceivable fuels - wood oils come to mind - with the age of the fuel. (Not all fuels have equal shelf lives - the most stable fuels are petroleum based.)
The interesting thing about diesel engines is that the types of fuels that can operate the engine vary considerably over a wide range of molecular structures.
One can control to a certain extent how these properties interplay by varying the physical arrangement of the engine, the size of the injector ports, the speed at which fuels are injected, the precise timing of injection, stroke length, etc. Obviously most engines are now optimized to handle petroleum diesel and not biodiesel. Were engines to be fueled with DME or some other type of fuel, these variables would be yet again different.
Obviously if one is attempting to operate engines with variable fuels, say B100 in summer or in warm climates where issues of flowability and cloud point do not play much of a role, and B20 in winter, when these issues become very important. Whether the B20 is petroleum or FT (Fischer-Tropsch) based, one must engage in a process of combinatorial optimization in selecting the engine design. That is, adjustment for one variable that may minimize problems or drawbacks under one set of circumstances may elevate problems under another set of circumstances. Thus one is seeking to maximize the performance characteristics while minimizing the pollution properties over the average fueling conditions. It is possible than under localized conditions, say cold days, these properties may prove quite poor depending on the engine design chosen but excellent on, say, hot days. One would attempt to choose engine design so that the lifetime environmental impact of the engine is lower over all.
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