bruce marshall, a 54 year old male from Davie asks on June 23, 2003,In energy transformations, even on the subatomic level, is some energy always lost as thermal energy?
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At a detailed level, your question invites considerable digression -- you have cleverly pointed out the discrepancy between large-scale phenomena (where we say that friction and loss of energy to heat makes any "engine" imperfect) and microscopic phenomena, which in fact do exhibit in one sense "perfect" behavior.
Science often boils down to finding sufficiently detailed, and not always obvious definitions of what seem to be commonplace circumstances to make consistency appear in phenomena. So it is with heat, which is probably identified as the easiest visualization of "energy" by most people. In one sense, heat is motion -- but heat is intimately related to another concept called entropy, which describes, in a way, the disorder of a physical system.
On the microscopic scale, things are simpler -- in a subatomic transformation of the simplest type, a decay, one object splits into two objects, which move away in opposite directions with velocities proportionate to the inverse of their mass, and scaling with the energy released in the decay. Assuming this takes place in a vacuum, then all the energy of the decay is manifest in the motion of the two daughter objects nothing else intervenes, and there is nothing to interact to transfer the energy inherent in the motion of these particles -- until they hit something. That said, not all subatomic particles are "simple" -- an atom may split into two atoms which are themselves said to be "excited" and which only later radiate energy or further split -- in one sense these atoms are "hot". A subatomic particle in a decay may not decay into fundamental particles, but into excited particles which also may be said to be "hot" in the sense that they can further decay.
However, the point is that one is faced with relatively limited choices -- while in one sense measuring the beginning and ending states of a decay is limited by the uncertainty principle -- we need not even make the measurement to say in principle what must occur, and our inventory of forces in a thought experiment may all be balanced. In any experiment involving ponderable masses, however, there is much more wiggle room for some aspect of the interaction involved in a transformation to start a chain of interactions between all the fundamental elements in an object(s) -- and thus something initially simple must always transform some small part of itself into random motions -- that we call "thermal". Remember the little executive-desk toys that consists of suspended steel balls -- such that when one ball at one end is released the opposite ball will arc up, returning to repeat the cycle? These work for a few repetitions, but slowly devolve to chaotic behavior. But at the subatomic world, things are *sometimes* perfect enough that this need not happen.
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