Exhaust noise comes from the positive pressure in the cylinder being suddenly released by the valve. To tune an engine as you do a potato gun, you can restrict the intake. Ideally, you'd want a short intake stroke and a long expansion stroke, but AFAIK, the Humpfrey pump is the only example of that, so we use things like early closing intake valves to minimize pumping losses. Once the sound is made, there's little hope of gaining on both silence and economy, except perhaps with an exhaust turbine.
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