Nature of the vibron self-trapped states in hydrogen-bonded macromolecular chains

Influence of donor or acceptor presence on excitation states in molecular chains: Nonadiabatic polaron approach

In this paper, we considered a molecular structure that consists of a molecular chain and an additional molecule (donor or acceptor) that can inject (or remove) single excitation (vibron, electron, etc.) onto the molecular chain. We assumed that the excitation forms a self-trapped state due to the interaction with mechanical oscillations of the chain structure elements. We analyzed the energy spectra of the excitation and showed that its state (when it migrates to the molecular chain) has the properties of the nonadiabatic polaron state. The conditions under which the excitation can migrate from one subsystem to another one were considered. It was shown that the presence of a "donor" molecule cannot significantly change the properties of the excitation located on the molecular chain. At the same time, the molecular chain can affect the position of the energy level of the excitation localized on the donor subsystem. Indirectly, this can influence the process of excitation migration from one subsystem to another one. The influence of the basic energy parameters of the system and the environment temperature on this process are discussed. The entire system was assumed to be in thermal equilibrium with the environment.

A review on nonlinear DNA physics

The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

A qubit coupled with confined phonons: the interplay between true and fake decoherence

The decoherence of a qubit coupled with the phonons of a finite-size lattice is investigated. The confined phonons no longer behave as a reservoir. They remain sensitive to the qubit so that the origin of the decoherence is twofold. First, a qubit-phonon entanglement yields an incomplete true decoherence. Second, the qubit renormalizes the phonon frequency resulting in fake decoherence when a thermal average is performed. To account for the initial thermalization of the lattice, the qua- ntum Langevin theory is applied so that the phonons are viewed as an open system coupled with a thermal bath of harmonic oscillators. Consequently, it is shown that the finite lifetime of the phonons does not modify fake decoherence but strongly affects true decoherence. Depending on the values of the model parameters, the interplay between fake and true decoherence yields a very rich dynamics with various regimes.