| Actually Nigel it is piston area and ratio of piston area to stroke that really determines the power output-because piston SPEED is the real limiting factor-valve area is just a small part of that. You are correct though, small cylinders with short stroke can rev higher and therefore flow more gas for a given piston speed-that is why Ducati has been shortening stroke and increasing bore to get more revs and therefore power whilst not exceeding the limits of piston speed. The problem with that is that there is a limit to how big the bore can go before you start to get the gasflow stalling and therefore again limiting the cylinder filling.
The actual ratio is I believe 1:.736 for a twin versus a 4 in terms of thermodynamic efficiency-in other words a 736cc 4 verses a 1000cc twin-so under the old original Superbike rules the 4 cylinder bikes already had an advantage-the twins should have been allowed to be 1019cc to keep it strictly fair. So with 1000cc 4's the twins should be allowed 1358.7cc!
Nigel just re-read your post and noticed your reference-seems we have read the same work although I am sure it was a Honda engineer-pretty much the same result though. It always hacks me off as well the way that some people keep banging on about Ducati cheating because they have a bigger engine-the same voices will no doubt call it cheating if Ducati decides to race the Desmosedici in Superbike-I have been told they won't but personally wish they would just to shut certain sections up.
John
Growing old-disgracefully! | 
Monty
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