Theoretical perfect Newton's Cradle (where does the sound really come from?)

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Mediocrates
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If the spheres of a Newton's Cradle were perfectly spherical I assume "contact" would be some minimal distance between the outer electrons of one atom of each sphere? Pulling one sphere back and releasing would result in a modest plastic deformation and subsequent minimal distance between more electrons? Anybody got a good explanation for where the sound really comes from?
 
I've always thought that the sound waves come from vibrations of the spheres as a result of the collision. The sphere oscillations cause the surrounding air to vibrate thus generating sound waves that reach your ear. The characteristic sharp sound suggests the superposition of many frequencies over a relatively short time interval.
 
You're making it more difficult than necessary by combining ideal concepts like "perfect sphere" with nitty gritty real life like atomic spacing. The picture shows a scan of a "perfect" steel surface. To make your life easier, stick either with the "ideal" or the "real" and don't try to mix the two.

Grayscale electron micrograph of a densely packed field of sharp, tapered micro-scale spikes or pillars rising from a surface, viewed at an oblique angle.
 
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