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

CMB Anomalies from Relic Anisotropy

Most of the analysis of the Cosmic Microwave Background relies on the assumption of statistical isotropy. However, given some recent evidence pointing against isotropy, as for instance the observed alignment of different multipoles on large scales, it is worth testing this assumption against the increasing amount of available data. As a pivot model, we assume that the spectrum of the primordial perturbations depends also on their directionality (rather than just on the magnitude of their momentum, as in the standard case). We explicitly compute the correlation matrix for the temperature anisotropies in the simpler case in which there is a residual isotropy between two spatial directions. As a concrete example, we consider a different initial expansion rate along one direction, and the following isotropization which takes place during inflation. Depending on the amount of inflation, this can lead to broken statistical isotropy on the largest observable scales.Comment: 6 pages, 2 .ps figure

Optimal Clustering under Uncertainty

Classical clustering algorithms typically either lack an underlying probability framework to make them predictive or focus on parameter estimation rather than defining and minimizing a notion of error. Recent work addresses these issues by developing a probabilistic framework based on the theory of random labeled point processes and characterizing a Bayes clusterer that minimizes the number of misclustered points. The Bayes clusterer is analogous to the Bayes classifier. Whereas determining a Bayes classifier requires full knowledge of the feature-label distribution, deriving a Bayes clusterer requires full knowledge of the point process. When uncertain of the point process, one would like to find a robust clusterer that is optimal over the uncertainty, just as one may find optimal robust classifiers with uncertain feature-label distributions. Herein, we derive an optimal robust clusterer by first finding an effective random point process that incorporates all randomness within its own probabilistic structure and from which a Bayes clusterer can be derived that provides an optimal robust clusterer relative to the uncertainty. This is analogous to the use of effective class-conditional distributions in robust classification. After evaluating the performance of robust clusterers in synthetic mixtures of Gaussians models, we apply the framework to granular imaging, where we make use of the asymptotic granulometric moment theory for granular images to relate robust clustering theory to the application.Comment: 19 pages, 5 eps figures, 1 tabl

Quantum Corrections to the Cosmological Evolution of Conformally Coupled Fields

Because the source term for the equations of motion of a conformally coupled scalar field, such as the dilaton, is given by the trace of the matter energy momentum tensor, it is commonly assumed to vanish during the radiation dominated epoch in the early universe. As a consequence, such fields are generally frozen in the early universe. Here we compute the finite temperature radiative correction to the source term and discuss its consequences on the evolution of such fields in the early universe. We discuss in particular, the case of scalar tensor theories of gravity which have general relativity as an attractor solution. We show that, in some cases, the universe can experience an early phase of contraction, followed by a non-singular bounce, and standard expansion. This can have interesting consequences for the abundance of thermal relics; for instance, it can provide a solution to the gravitino problem. We conclude by discussing the possible consequences of the quantum corrections to the evolution of the dilaton.Comment: 24 pages, 7 figure

Grazing impact on soil chemical and biological properties under different plant cover types in a mountain area of Southern Italy.

Grazing can contribute to soil degradation by compaction due to roaming of livestock and loss of herbaceous cover, affecting also soil microbial community. Aim of this study was to assess grazing impact on soil microbial community and nutrient status under different plant cover types (i.e., fernery, chestnut wood, garigue). Grazed and ungrazed soils were analysed for water holding capacity, pH, organic carbon, N, S, K, Mg, Fe, Mn, Zn and Cu content, microbial biomass, fungal mycelium and potential respiration. Moreover, some ecophysiological indices, as microbial quotient, coefficient of endogenous mineralization (CEM), metabolic quotient (qCO2) and fungal fraction of microbial carbon were calculated. The results of present study showed that a moderate intensity grazing had low or no impact on chemical characteristics of soils and affects microbial community mainly in grazed areas with lower vegetation cover and lower content of nutrient and organic carbon, compared to areas with a thick layer of vegetation

Slow-roll Inflation for Generalized Two-Field Lagrangians

We study the slow-roll regime of two field inflation, in which the two fields are also coupled through their kinetic terms. Such Lagrangians are motivated by particle physics and by scalar-tensor theories studied in the Einstein frame. We compute the power spectra of adiabatic and isocurvature perturbations on large scales to first order in the slow-roll parameters. We discuss the relevance of the extra coupling terms for the amplitude and indexes of the power spectra. Beyond the consistency condition which involves the amplitude of gravitational waves, additional relations may be found in particular models based on such Lagrangians: as an example, we find an additional general consistency condition in implicit form for Brans-Dicke theory in the Einstein frame.Comment: 17 pages, 1 figure, accepted for publication in Phys. Rev.

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