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

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

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

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 $\sim 10^7 - 10^8$ 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 $h_{pol}$} and the {\em weak polynomial entropy $h_{pol}^*$}. Both are infinite when the topological entropy is positive and they satisfy $h_{pol}^*\leq h_{pol}$. 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 $\phi$ which then decay into $\mu^+\mu^-$ or $e^+e^-$. 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 $\phi$ and show that this indeed gives a rather spectacular broad peak in $E^2d\sigma/dE$, 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