There is a small component of nuclear energy in DOE, and an even smaller component of alternatives and fossil fuel ( DOE FY2013 budget) but most of this is for basic scientific research.
In this case, the main contractor is given total responsibility for the entire project, selecting even the component suppliers, and checking everything before handing over the finished vehicle to the customer.
The result was that the cost per mile for consumers on the ethanol component of their fuel was double or even triple the cost of the gasoline component.