You're using an N-channel MOSFET, for it to come into an "on" (low-resistance) state Vgs must be large, let's say 5V. The highest voltage you have is 36 V (+ node of battery). Even this will not fully turn-on the NMOS. You would need at least 41 V on the gate.
Instead I would use a PMOS, then you can just pull the gate low.
But to switch it OFF the gate of the PMOS must be pulled to 36 V !
An AVR cannot handle this so you would need an additional transistor to pull the gate of the PMOS down.
A 1n4001 is not fast enough for these type of applications, better use a Schottky diode.
There is a fundamental flaw in your circuit! It has no current limiting !
This is an issue, especially when the battery pack has a low voltage and the inductor saturates. The current would only be limited by the series resistance of the batteries and this is BAD, avoid at all cost ! (Your wires could melt !)
Have a look at this document form TI and learn how it's done !
If you want to actually build this then I strongly advise you to use an IC for that but pay attention to the 36V battery voltage, not all ICs can handle that.
Also there are a lot of ready-built modules for sale on eBay, that would be more convenient as the layout of a switched converter is not something for a beginner.
In general, you don't want an AVR or any micro Controller to control a DC-DC converter switch. They're too slow, software could get stuck with the switch turned on. The current will be uncontrolled. AVOID !!!
I do not understand what you mean by "designed for bridges" ?