A fuel separation system includes a fuel separator configured to receive a fuel stream and separate the fuel stream, based on a volatility of the fuel stream, into a vapor stream defined by a first auto-ignition characteristic value and a first liquid stream defined by a second auto-ignition characteristic value, the second auto-ignition characteristic value greater than the first auto-ignition characteristic value; and a control system communicably coupled to the fuel separator and operable to receive an input from an engine, the input including an engine operating condition, the control system configured to adjust an operating parameter of the fuel separator, based at least in part on the engine operating condition, to vary at least one of the first or second auto-ignition characteristic values.