6,532 research outputs found
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
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