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The megasmasher is a particule accelerator of sorts, imo. Guyver energy is used to power the accelerator mechanism (megasmasher) to draw in and accelerate atmospheric/molecular particles. Once the charge is at a certain speed/mass, it's released in the form of the megablast/heatblast. I would say theres a minimum capacity required before a discharge and it takes slightly longer for a full capacity discharge as it's been shown a few times in the magna/anime.

I don't think Arkanfel (Alkanphel ) is a Prototype. Prototyping is by a full bodied test subject. You test the result and see how it works. Then you make another Prototype compare and see how it goes. Each prototype being it's own thing until you eventually reach the final product and are happy with the design. Alkanphel (I'm too used to the Viz spelling of his name ) is either a final Prototype or the final product, the difference being not important. He is too complex a design to be anything else and the story has a much earlier Prototype in it to support this. Waferdanos is a prototype of Alkanphel. He is the combined bio-mass of an island full of intelligent complex plant based creatures. He is a test in control, you've the primary core and then you have the lower followers in support controlled by the core (the King). What's even more amazing in the way Takaya shows us this is that is not only do we see the early form of Waferdanos we saw his evolved form first. When given access to more advanced Creator technology (a Zoacrystal) Waferdanos was able to collect his complete bio-mass together into one form, named by Balcus after the island where he discovered him. Zoalord crystals also repair themselves over time, (Alkanphel stated as much himself) Imakarum's would have done so, but after the death of Prug'stall at the hands of the Rogues that Alkanphel triggers the Ark to use its energy to heal him. Book 15 gives us a good explanation as to why Alkanphel is so damaged, it wasn't using his shield (though that would have drained him for awhile) it was the attack from the God's themselves and being ordered to shut down. Something Alkanphel rebelled against when he saw Earth about to be destroyed,