Gravitational and axial anomalies for generalized Euclidean Taub-NUT metrics

The gravitational anomalies are investigated for generalized Euclidean Taub-NUT metrics which admit hidden symmetries analogous to the Runge-Lenz vector of the Kepler-type problem. In order to evaluate the axial anomalies, the index of the Dirac operator for these metrics with the APS boundary condition is computed. The role of the Killing-Yano tensors is discussed for these two types of quantum anomalies.Comment: 23 page

Two-phase stretching of molecular chains

While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the extension energy profile of its individual monomer subunits. Namely, if the effective monomer deformation energy as a function of its extension has a non-convex (concave up) region, the stretched polymer chain separates into two phases: the weakly and strongly stretched monomers. Simplified planar and 3D polymer models are used to illustrate the basic principles of the proposed model. Specifically, we show rigorously that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. We then use realistic coarse-grained models to confirm the main findings and make direct connection to the microscopic structure of the monomers. We demostrate in detail how the two-phase scenario is realized in the \alpha-helix, and in DNA double helix. The predicted plateau parameters are consistent with single molecules experiments. Detailed analysis of DNA stretching demonstrates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends at room temperature. The main strengths of the proposed theory are its generality and direct microscopic connection.Comment: 16 pges, 22 figure

Vibrational Tamm states at the edges of graphene nanoribbons

We study vibrational states localized at the edges of graphene nanoribbons. Such surface oscillations can be considered as a phonon analog of Tamm states well known in the electronic theory. We consider both armchair and zigzag graphene stripes and demonstrate that surface modes correspond to phonons localized at the edges of the graphene nanoribbon, and they can be classified as in-plane and out-of-plane modes. In addition, in armchair nanoribbons anharmonic edge modes can experience longitudinal localization in the form of self-localized nonlinear modes, or surface breather solitons.Comment: 10 pages, 10 figure

Reply to comment on "Simple one-dimensional model of heat conduction which obeys Fourier's law"

In this reply we answer the comment by A. Dhar (cond-mat/0203077) on our Letter "Simple one dimensional model of heat conduction which obeys Fourier's law" (Phys. Rev. Lett. 86, 5486 (2001), cond-mat/0104453)Comment: 1 pag., 1 fi

Discrete breathers in polyethylene chain

The existence of discrete breathers (DBs), or intrinsic localized modes (localized periodic oscillations of transzigzag) is shown. In the localization region periodic contraction-extension of valence C-C bonds occurs which is accompanied by decrease-increase of valence angles. It is shown that the breathers present in thermalized chain and their contribution dependent on temperature has been revealed.Comment: 5 pages, 6 figure

Wandering breathers and self-trapping in weakly coupled nonlinear chains: classical counterpart of macroscopic tunneling quantum dynamics

We present analytical and numerical studies of phase-coherent dynamics of intrinsically localized excitations (breathers) in a system of two weakly coupled nonlinear oscillator chains. We show that there are two qualitatively different dynamical regimes of the coupled breathers, either immovable or slowly-moving: the periodic transverse translation (wandering) of low-amplitude breather between the chains, and the one-chain-localization of high-amplitude breather. These two modes of coupled nonlinear excitations, which involve large number of anharmonic oscillators, can be mapped onto two solutions of a single pendulum equation, detached by a separatrix mode. We also study two-chain breathers, which can be considered as bound states of discrete breathers with different symmetry and center locations in the coupled chains, and bifurcation of the anti-phase two-chain breather into the one-chain one. Delocalizing transition of 1D breather in 2D system of a large number of parallel coupled nonlinear chains is described, in which the breather, initially excited in a given chain, abruptly spreads its vibration energy in the whole 2D system upon decreasing breather frequency or amplitude below the threshold one. The threshold breather frequency is above the cut off phonon frequency in 2D system, and the threshold breather amplitude scales as square root of the inter-chain coupling constant. Delocalizing transition of discrete vibrational breather in 2D and 3D systems of coupled nonlinear chains has an analogy with delocalizing transition for Bose-Einstein condensates in 2D and 3D optical lattices.Comment: 33 pages, 16 figure

Heat conductivity of DNA double helix

Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal conductivity. To investigate thermal properties of single molecule DNA we have developed a 3D coarse-grained (CG) model that retains the realism of the full all-atom description, but is significantly more efficient. Within the proposed model each nucleotide is represented by 6 particles or grains; the grains interact via effective potentials inferred from classical molecular dynamics (MD) trajectories based on a well-established all-atom potential function. Comparisons of 10 ns long MD trajectories between the CG and the corresponding all-atom model show similar root-mean-square deviations from the canonical B-form DNA, and similar structural fluctuations. At the same time, the CG model is 10 to 100 times faster depending on the length of the DNA fragment in the simulation. Analysis of dispersion curves derived from the CG model yields longitudinal sound velocity and torsional stiffness in close agreement with existing experiments. The computational efficiency of the CG model makes it possible to calculate thermal conductivity of a single DNA molecule not yet available experimentally. For a uniform (polyG-polyC) DNA, the estimated conductivity coefficient is 0.3 W/mK which is half the value of thermal conductivity for water. This result is in stark contrast with estimates of thermal conductivity for simplified, effectively 1D chains ("beads on a spring") that predict anomalous (infinite) thermal conductivity. Thus, full 3D character of DNA double-helix retained in the proposed model appears to be essential for describing its thermal properties at a single molecule level.Comment: 16 pages, 12 figure