The present invention relates to system and methods for improving efficiency of an internal combustion engine. This system may include a fuel processor. The system receives instructions for a desired engine output and operating conditions. The system may then determine an operational state corresponding to the desired output. The operational state includes designating the cylinders into one of three categories: working, deactivated and passive. The number of working cylinders is calculated by dividing the desired output by the power provided by one cylinder operating at substantially optimal efficiency. Then the system substantially disables fuel flow to and air flow to the deactivated cylinders, substantially disables fuel flow to and firing of the passive cylinders, and substantially regulates fuel flow to, air flow to and firing of the working cylinders. Firing of the working cylinders is synchronized with engine speed to reduce unwanted engine vibrations. The number of working, passive and deactivated cylinders may be continually altered in response to changes in desired output or operating conditions.