Coherent migration of the single excitation injected into finite-length segment of the biomolecular chain

Abstract

We study the migration of a single excitation excited at a structural element of a finite molecular segment, which is a part of a long biomolecular chain. The excitation cannot leave the segment and is locally coupled to thermal vibrations of the lattice, forming a self-trapped state corresponding to a nonadiabatic polaron. The time-dependent probability distribution of finding the excitation at the nodes of the segment is calculated, with particular emphasis on the role of the initial excitation position. A formal analogy is observed between the present model and continuous-time quantum walk models on finite chains with reflecting boundaries. The results reveal an asymmetry in the probability distribution for nodes symmetrically positioned with respect to the initially excited site, which arises solely from the asymmetric placement of the initial excitation within the finite segment. The only exception occurs when the initially excited node is located at the center of the segment, where the probability distribution becomes symmetric. The complex interference pattern and the absence of well-defined revivals stem from the non-equidistant spectrum of mode frequencies, leading to progressive dephasing of the constituent modes. As a result, the initially well-localized probability maximum fragments into one dominant maximum accompanied by several secondary maxima of lower intensity. These findings highlight the importance of boundary conditions and initial-state geometry in controlling quantum transport in finite molecular systems.