Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton.Comment: 4. Submitted to Phys. Rev.

Anomalous tunneling of bound pairs in crystal lattices

A novel method of solving scattering problems for bound pairs on a lattice is developed. Two different break ups of the hamiltonian are employed to calculate the full Green operator and the wave function of the scattered pair. The calculation converges exponentially in the number of basis states used to represent the non-translation invariant part of the Green operator. The method is general and applicable to a variety of scattering and tunneling problems. As the first application, the problem of pair tunneling through a weak link on a one-dimensional lattice is solved. It is found that at momenta close to \pi the pair tunnels much easier than one particle, with the transmission coefficient approaching unity. This anomalously high transmission is a consequence of the existence of a two-body resonant state localized at the weak link.Comment: REVTeX, 5 pages, 4 eps figure

New records of lichens from the Russian Far East. I. Fuscidea submollis and other arctic-alpine species

Summary. Fuscidea submollis Mas. Inoue is reported for the first time from the Russian Far East. Distinctive features of the taxon are discussed, and a comparison with known saxicolous Fuscidea V. Wirth & Vězda species with amyloid medulla is made. Three arctic-alpine species: Sporastatia testudinea (Ach.) A. Massal., Buellia concinna Th. Fr., Amygdalaria panaeola (Ach.) Hertel et Brodo, and Aspilidea myrinii (Fr.) Hafellner are recorded for the first time in the South Far East from the Sikhote Alin Range (Primorye Territory). Calvitimela aglaea (Sommerf.) Hafellner is reported for the first time from Sikhote Alin Range and Primorye Territory. © 2019 Altai State University. All rights reserved.Japan Society for the Promotion of Science, JSPS: 19-54-50010Russian Foundation for Basic Research, RFBRThe reported study was funded by RFBR and JSPS according to the research project № 19-54-50010

Coherent charge transport through molecular wires: "Exciton blocking" and current from electronic excitations in the wire

We consider exciton effects on current in molecular nanojunctions, using a model comprising a two two-level sites bridge connecting free electron reservoirs. Expanding the density operator in the many-electron eigenstates of the uncoupled sites, we obtain a 16X16 density matrix in the bridge subspace whose dynamics is governed by Liuoville equation that takes into account interactions on the bridge as well as electron injection and damping to and from the leads. Our consideration can be considerably simplified by using the pseudospin description based on the symmetry properties of Lie group SU(2). We study the influence of the bias voltage, the Coulomb repulsion and the energy-transfer interactions on the steady-state current and in particular focus on the effect of the excitonic interaction between bridge sites. Our calculations show that in case of non-interacting electrons this interaction leads to reduction in the current at high voltage for a homodimer bridge. In other words, we predict the effect of \textquotedblleft exciton\textquotedblright blocking. The effect of \textquotedblleft exciton\textquotedblright blocking is modified for a heterodimer bridge, and disappears for strong Coulomb repulsion at sites. In the latter case the exciton type interactions can open new channels for electronic conduction. In particular, in the case of strong Coulomb repulsion, conduction exists even when the electronic connectivity does not exist.Comment: 14 pages, 15 figure

Quantum coherence and carriers mobility in organic semiconductors

We present a model of charge transport in organic molecular semiconductors based on the effects of lattice fluctuations on the quantum coherence of the electronic state of the charge carrier. Thermal intermolecular phonons and librations tend to localize pure coherent states and to assist the motion of less coherent ones. Decoherence is thus the primary mechanism by which conduction occurs. It is driven by the coupling of the carrier to the molecular lattice through polarization and transfer integral fluctuations as described by the hamiltonian of Gosar and Choi. Localization effects in the quantum coherent regime are modeled via the Anderson hamiltonian with correlated diagonal and non-diagonal disorder leading to the determination of the carrier localization length. This length defines the coherent extension of the ground state and determines, in turn, the diffusion range in the incoherent regime and thus the mobility. The transfer integral disorder of Troisi and Orlandi can also be incorporated. This model, based on the idea of decoherence, allowed us to predict the value and temperature dependence of the carrier mobility in prototypical organic semiconductors that are in qualitative accord with experiments

Stability of C20 fullerene chains

The stability of (C20)N chains with N = 3 - 7 is analyzed by numerical simulation using a tight-binding potential and molecular dynamics. Various channels of losing the cluster-chain structure of the (C20)N complexes are observed, including the decay of C20 clusters, their coalescence, and the separation of one C20 fullerene from the chain.Comment: To appear in JETP Letter

Evidence for a Quasi-1D Topological-Excitation Liquid in Bi2212 by Tunneling Spectroscopy

Tunneling measurements have been carried out on heavily underdoped and slightly overdoped Bi2212 single crystals by using a break-junction technique. We find that in-plane tunneling spectra below Tc are the combination of incoherent part from the pseudogap and coherent quasiparticle peaks. There is a correlation between the magnitude of the pseudogap and the magnitude of the superconducting gap in Bi2212. We find that the quasiparticle conductance peaks are caused by condensed solitonlike excitations.Comment: Europysics Lett. (in press

Adiabatic-Nonadiabatic Transition in the Diffusive Hamiltonian Dynamics of a Classical Holstein Polaron

We study the Hamiltonian dynamics of a free particle injected onto a chain containing a periodic array of harmonic oscillators in thermal equilibrium. The particle interacts locally with each oscillator, with an interaction that is linear in the oscillator coordinate and independent of the particle's position when it is within a finite interaction range. At long times the particle exhibits diffusive motion, with an ensemble averaged mean-squared displacement that is linear in time. The diffusion constant at high temperatures follows a power law D ~ T^{5/2} for all parameter values studied. At low temperatures particle motion changes to a hopping process in which the particle is bound for considerable periods of time to a single oscillator before it is able to escape and explore the rest of the chain. A different power law, D ~ T^{3/4}, emerges in this limit. A thermal distribution of particles exhibits thermally activated diffusion at low temperatures as a result of classically self-trapped polaronic states.Comment: 15 pages, 4 figures Submitted to Physical Review