Hi Felix, It is certainly possible, although i do not quite understand your comment about an external circuit to sum the pulses. This sort of circuit:

http://www.analog.com/-/media/images/analog-dialogue/en/volume-45/number-3/articles/applying-dc-to-dc-step-up-boost-regulators/ad45-09_bb_fig_03.jpg?la=en

Will work OK.

Simply switch the FET off and on using one of the timer outputs of the MC. If the voltage is too high, decrease the "output compare value" to shorten the switch on time.

As you commented though the actual PWM frequency will not be particularly fast so you will need a larger inductor, and you will also tie up the micro-controller, preventing it from doing other jobs, as it must continuously adjust the PWM.

You can set up the Micro-controller comparator to monitor the "output-voltage", and compare this with a voltage generated by a simple filtered PWM signal from the controller to allow you to set the output voltage (doing the job of the Feed Back pin on a regular boost IC). This will also free up the microcontroller a little.

Getting such a system to work nicely does take some effort however, and it is very much easier to simply use and off the shelf IC package, with their well explained data sheets, and operating parameters, (they tend to be rather streamlined, and resistant to shorting, overvoltages, undervaoltages etc.) What sort of voltage and currents were you thinking of?

A more flexible "hybrid" method is to simply use an off the shelf boost IC, but to retain the flexibility of being able to set the voltage, using an external comparator. Enclosed is this sort of arrangement with a step down converter. Also illustrating how to use the PWM to produce a reference voltage. This arrangement then frees up the MC to do other tasks.

Which board you are using for programming of Atmega2560? Arduino Mega Board also have Atmega2560 microcontroller and the Arduino Boards can be easily programmed directly using Simulink. So by using Simulink support package for Arduino hardware, you can implement the simple boost control technique for your QZSI.