  We study the dynamics of quantum excitations inside macromolecules which can
undergo conformational transitions. In the first part of the paper, we use the
path integral formalism to rigorously derive a set of coupled equations of
motion which simultaneously describe the molecular and quantum transport
dynamics, and obey the fluctuation/dissipation relationship. We also introduce
an algorithm which yields the most probable molecular and quantum transport
pathways in rare, thermally-activated reactions. In the second part of the
paper, we apply this formalism to simulate the propagation of a charge during
the collapse of a polymer from an initial stretched conformation to a final
globular state. We find that the charge dynamics is quenched when the chain
reaches a molten globule state. Using random matrix theory we show that this
transition is due to an increase of quantum localization driven by dynamical
disorder.
