29,794 research outputs found
Helix untwisting and bubble formation in circular DNA
The base pair fluctuations and helix untwisting are examined for a circular
molecule. A realistic mesoscopic model including twisting degrees of freedom
and bending of the molecular axis is proposed. The computational method, based
on path integral techniques, simulates a distribution of topoisomers with
various twist numbers and finds the energetically most favorable molecular
conformation as a function of temperature. The method can predict helical
repeat, openings loci and bubble sizes for specific sequences in a broad
temperature range. Some results are presented for a short DNA circle recently
identified in mammalian cells.Comment: The Journal of Chemical Physics, vol. 138 (2013), in pres
J-factors of short DNA molecules
The propensity of short DNA sequences to convert to the circular form is
studied by a mesoscopic Hamiltonian method which incorporates both the bending
of the molecule axis and the intrinsic twist of the DNA strands. The base pair
fluctuations with respect to the helix diameter are treated as path
trajectories in the imaginary time path integral formalism. The partition
function for the sub-ensemble of closed molecules is computed by imposing chain
ends boundary conditions both on the radial fluctuations and on the angular
degrees of freedom. The cyclization probability, the J-factor, proves to be
highly sensitive to the stacking potential, mostly to its nonlinear parameters.
We find that the J-factor generally decreases by reducing the sequence length (
N ) and, more significantly, below N = 100 base pairs. However, even for very
small molecules, the J-factors remain sizeable in line with recent experimental
indications. Large bending angles between adjacent base pairs and anharmonic
stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page
A Quantum Many-Body Instability in the Thermodynamic Limit
Intrinsic decoherence in the thermodynamic limit is shown for a large class
of many-body quantum systems in the unitary evolution in NMR and cavity QED.
The effect largely depends on the inability of the system to recover the
phases. Gaussian decaying in time of the fidelity is proved for spin systems
and radiation-matter interaction.Comment: 11 pages, 1 figure. Final version accepted for publication in Modern
Physics Letters
Lifetime and polarization of the radiative decay of excitons, biexcitons and trions in CdSe nanocrystal quantum dots
Using the pseudopotential configuration-interaction method, we calculate the intrinsic lifetime and polarization of the radiative decay of single excitons (X), positive and negative trions (X+ and X−), and biexcitons (XX) in CdSe nanocrystal quantum dots. We investigate the effects of the inclusion of increasingly more complex many-body treatments, starting from the single-particle approach and culminating with the configuration-interaction scheme. Our configuration-interaction results for the size dependence of the single-exciton radiative lifetime at room temperature are in excellent agreement with recent experimental data. We also find the following. (i) Whereas the polarization of the bright exciton emission is always perpendicular to the hexagonal c axis, the polarization of the dark exciton switches from perpendicular to parallel to the hexagonal c axis in large dots, in agreement with experiment. (ii) The ratio of the radiative lifetimes of mono- and biexcitons (X):(XX) is ~1:1 in large dots (R=19.2 Å). This ratio increases with decreasing nanocrystal size, approaching 2 in small dots (R=10.3 Å). (iii) The calculated ratio (X+):(X−) between positive and negative trion lifetimes is close to 2 for all dot sizes considered
Laboratory observations of slow earthquakes and the spectrum of tectonic fault slip modes
Slow earthquakes represent an important conundrum in earthquake physics. While regular
earthquakes are catastrophic events with rupture velocities governed by elastic wave speed,
the processes that underlie slow fault slip phenomena, including recent discoveries of tremor,
slow-slip and low-frequency earthquakes, are less understood. Theoretical models and sparse
laboratory observations have provided insights, but the physics of slow fault rupture remain
enigmatic. Here we report on laboratory observations that illuminate the mechanics of
slow-slip phenomena. We show that a spectrum of slow-slip behaviours arises near the
threshold between stable and unstable failure, and is governed by frictional dynamics via the
interplay of fault frictional properties, effective normal stress and the elastic stiffness of the
surrounding material. This generalizable frictional mechanism may act in concert with other
hypothesized processes that damp dynamic ruptures, and is consistent with the broad range
of geologic environments where slow earthquakes are observed
Molecular Lines as Diagnostics of High Redshift Objects
Models are presented for CO rotational line emission by high redshift
starburst galaxies. The influence of the cosmic microwave background on the
thermal balance and the level populations of atomic and molecular species is
explicitly included. Predictions are made for the observability of starburst
galaxies through line and continuum emission between z=5 and z=30. It is found
that the Millimeter Array could detect a starburst galaxy with ~10^5 Orion
regions, corresponding to a star formation rate of about 30 Mo yr^{-1}, equally
well at z=5 or z=30 due to the increasing cosmic microwave background
temperature with redshift. Line emission is a potentially more powerful probe
than dust continuum emission of very high redshift objects.Comment: 15 pages LaTex, uses aasms4.sty, Accepted by ApJ
Thermodynamics of Twisted DNA with Solvent Interaction
The imaginary time path integral formalism is applied to a nonlinear
Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing
solvent interaction term. Torsional effects are modeled by a twist angle
between neighboring base pairs stacked along the molecule backbone. The base
pair displacements are described by an ensemble of temperature dependent paths
thus incorporating those fluctuational effects which shape the multisteps
thermal denaturation. By summing over base pair paths, a
large number of double helix configurations is taken into account consistently
with the physical requirements of the model potential. The partition function
is computed as a function of the twist. It is found that the equilibrium twist
angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal
geometry against thermal disruption of the base pair hydrogen bonds. This
result is corroborated by the computation of thermodynamical properties such as
fractions of open base pairs and specific heat.Comment: The Journal of Chemical Physics (2011) in pres
Polynomial growth of volume of balls for zero-entropy geodesic systems
The aim of this paper is to state and prove polynomial analogues of the
classical Manning inequality relating the topological entropy of a geodesic
flow with the growth rate of the volume of balls in the universal covering. To
this aim we use two numerical conjugacy invariants, the {\em strong polynomial
entropy } and the {\em weak polynomial entropy }. Both are
infinite when the topological entropy is positive and they satisfy
. We first prove that the growth rate of the volume of
balls is bounded above by means of the strong polynomial entropy and we show
that for the flat torus this inequality becomes an equality. We then study the
explicit example of the torus of revolution for which we can give an exact
asymptotic equivalent of the growth rate of volume of balls, which we relate to
the weak polynomial entropy.Comment: 22 page
Gamma-ray and Radio Constraints of High Positron Rate Dark Matter Models Annihilating into New Light Particles
The possibility of explaining the positron and electron excess recently found
by the PAMELA and ATIC collaborations in terms of dark matter (DM) annihilation
has attracted considerable attention. Models surviving bounds from, e.g,
antiproton production generally fall into two classes, where either DM
annihilates directly with a large branching fraction into light leptons, or, as
in the recent models of Arkani-Hamed et al., and of Nomura and Thaler, the
annihilation gives low-mass (pseudo)scalars or vectors which then decay
into or . While the constraints on the first kind of
models have recently been treated by several authors, we study here
specifically models of the second type which rely on an efficient Sommerfeld
enhancement in order to obtain the necessary boost in the annihilation cross
section. We compute the photon flux generated by QED radiative corrections to
the decay of and show that this indeed gives a rather spectacular broad
peak in , that for these extreme values of the cross section
violate gamma-ray observations of the Galactic center for DM density profiles
steeper than that of Navarro, Frenk and White. The most stringent constraint
comes from the comparison of the predicted synchrotron radiation in the central
part of the Galaxy with radio observations of Sgr A*. For the most commonly
adopted DM profiles, the models that provide a good fit to the PAMELA and ATIC
data are ruled out, unless there are physical processes that boost the local
anti-matter fluxes more than one order of magnitude, while not affecting the
gamma-ray or radio fluxes.Comment: 5 pages, 3 figures, matches published versio
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