Vibron Self--trapped States in Biological Macromolecules: Comparison of Different Theoretical Approaches

A study of the applicability of the variational treatments based on using of the modified Lang-Firsov unitary transformation (MLF method) in the investigation of the vibron self-trapped states in biological macromolecular chains are presented. We compare the values of the ground state energy predicted by MLF methods with the values of the ground state energy predicted by the standard small-polaron theory, for various values of the basic energy parameters of the system. We obtain regions in system parameter space where MLF approach gives better description of the vibron states.Comment: 8 pages, 4 figures, To appear in the Proceedings of Conference Dubna-Nano2012 (July 9 - 14, 2012

Vibron transport in macromolecular chains

We study the hopping mechanism of the vibron excitation transport in the simple 1D model of biological macromolecular chains. We supposed that the vibron interaction with thermal oscillations of the macromolecular structural elements will result in vibron self -trapping, and the formation of the partial dressed vibron state. With use of the modified Holstein polaron model, we calculate vibron diffusivity in dependence of the basic system parameters and temperature. We obtain that the vibron diffusivity smoothly decreases in non adiabatic limit when the strength of the vibron-phonon coupling grows. However this dependence becomes by discontinuous one in case of growth of the adiabaticity of the system. The value of the critical point depends of the system temperature, and at room temperatures it belongs to the low or intermediate coupling regime. We discuss an application of these results to study of vibron transport to 3D bundles of such macromolecules chains considering it as polymer nanorods and to 2D polymer films organized from such macromolecules.Comment: 4 pages, 6 figures, contribution to the Proceedings of the Conference "Physical mesomechanics of multi-level systems`2014", September 3-5 2014, Tomsk, Russi

On the influence of the "donor"/"acceptor" presence on the excitation states in molecular chains: non-adiabatic polaron approach

In the paper, we considered a molecular structure that consists of a molecular chain and an additional molecule ("donor"/"acceptor") that can inject (or remove) single excitation (vibron, electron, e.t.c.) onto the molecular chain. We assumed that the excitation forms a self-trapped state due to the interaction with mechanical oscillations of 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 non-adiabatic polaron state. The conditions under which the excitation can migrate from one subsystem to another 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 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

Electromagnetic pulse transparency in coupled cavity arrays through dispersion management

We theoretically demonstrated the possible emergence of slow-light self-induced transparency solitons in the infinite one-dimensional coupled cavity array, with each cavity containing a single qubit. We have predicted a substantial dependence of pulse transparency on its dimensionless width $\tau_0$. In particular, short pulses whose widths range from $\tau_0\ll 1$ to $\tau_0\lesssim 1$ exhibit simple, almost linear dispersion law with a finite frequency gap of the order of the cavity array photonic band gap. That is, the medium is opaque for very short pulses with carrier wave frequency below the photonic gap. When the pulse width exceeds the critical one, a twin transparency window separated by a finite band gap appears in the soliton pulse dispersion law. Observation of predicted effects within the proposed setup would be of interest for understanding the properties of self-induced transparency effect in general and future applications in the design of quantum technological devices

Two-vibron bound states in alpha-helix proteins : the interplay between the intramolecular anharmonicity and the strong vibron-phonon coupling

The influence of the intramolecular anharmonicity and the strong vibron-phonon coupling on the two-vibron dynamics in an $\alpha$-helix protein is studied within a modified Davydov model. The intramolecular anharmonicity of each amide-I vibration is considered and the vibron dynamics is described according to the small polaron approach. A unitary transformation is performed to remove the intramolecular anharmonicity and a modified Lang-Firsov transformation is applied to renormalize the vibron-phonon interaction. Then, a mean field procedure is realized to obtain the dressed anharmonic vibron Hamiltonian. It is shown that the anharmonicity modifies the vibron-phonon interaction which results in an enhancement of the dressing effect. In addition, both the anharmonicity and the dressing favor the occurrence of two different bound states which the properties strongly depend on the interplay between the anharmonicity and the dressing. Such a dependence was summarized in a phase diagram which characterizes the number and the nature of the bound states as a function of the relevant parameters of the problem. For a significant anharmonicity, the low frequency bound states describe two vibrons trapped onto the same amide-I vibration whereas the high frequency bound states refer to the trapping of the two vibrons onto nearest neighbor amide-I vibrations.Comment: may 2003 submitted to Phys. Rev.

From Davydov solitons to decoherence-free subspaces: self-consistent propagation of coherent-product states

The self-consistent propagation of generalized $D_{1}$ [coherent-product] states and of a class of gaussian density matrix generalizations is examined, at both zero and finite-temperature, for arbitrary interactions between the localized lattice (electronic or vibronic) excitations and the phonon modes. It is shown that in all legitimate cases, the evolution of $D_{1}$ states reduces to the disentangled evolution of the component $D_{2}$ states. The self-consistency conditions for the latter amount to conditions for decoherence-free propagation, which complement the $D_{2}$ Davydov soliton equations in such a way as to lift the nonlinearity of the evolution for the on-site degrees of freedom. Although it cannot support Davydov solitons, the coherent-product ansatz does provide a wide class of exact density-matrix solutions for the joint evolution of the lattice and phonon bath in compatible systems. Included are solutions for initial states given as a product of a [largely arbitrary] lattice state and a thermal equilibrium state of the phonons. It is also shown that external pumping can produce self-consistent Frohlich-like effects. A few sample cases of coherent, albeit not solitonic, propagation are briefly discussed.Comment: revtex3, latex2e; 22 pages, no figs.; to appear in Phys.Rev.E (Nov.2001

Correlation between acoustic divergence and phylogenetic distance in soniferous European gobiids (Gobiidae; Gobius lineage)

In fish, species identity can be encoded by sounds, which have been thoroughly investigated in European gobiids (Gobiidae, Gobius lineage). Recent evolutionary studies suggest that deterministic and/or stochastic forces could generate acoustic differences among related animal species, though this has not been investigated in any teleost group to date. In the present comparative study, we analysed the sounds from nine soniferous gobiids and quantitatively assessed their acoustic variability. Our interspecific acoustic study, incorporating for the first time the representative acoustic signals from the majority of soniferous gobiids, suggested that their sounds are truly species-specific (92% of sounds correctly classified into exact species) and each taxon possesses a unique set of spectro-temporal variables. In addition, we reconstructed phylogenetic relationships from a concatenated molecular dataset consisting of multiple molecular markers to track the evolution of acoustic signals in soniferous gobiids. The results of this study indicated that the genus Padogobius is polyphyletic, since P. nigricans was nested within the Ponto-Caspian clade, while the congeneric P. bonelli turned out to be a sister taxon to the remaining investigated soniferous species. Lastly, by extracting the acoustic and genetic distance matrices, sound variability and genetic distance were correlated for the first time to assess whether sound evolution follows a similar phylogenetic pattern. The positive correlation between the sound variability and genetic distance obtained here emphasizes that certain acoustic features from representative sounds could carry the phylogenetic signal in soniferous gobiids. Our study was the first attempt to evaluate the mutual relationship between acoustic variation and genetic divergence in any teleost fish