Improved Covariance Model Parameter Estimation Using RNA Thermodynamic Properties

Covariance models are a powerful description of non-coding RNA (ncRNA) families that can be used to search nucleotide databases for new members of these ncRNA families. Currently, estimation of the parameters of a covariance model (state transition and emission scores) is based only on the observed frequencies of mutations, insertions, and deletions in known ncRNA sequences. For families with very few known members, this can result in rather uninformative models where the consensus sequence has a good score and most deviations from consensus have a fairly uniform poor score. It is proposed here to combine the traditional observed-frequency information with known information about free energy changes in RNA helix formation and loop length changes. More thermodynamically probable deviations from the consensus sequence will then be favored in database search. The thermodynamic information may be incorporated into the models as informative priors that depend on neighboring consensus nucleotides and on loop lengths

The nucleon spin and momentum decomposition using lattice QCD simulations

We determine within lattice QCD, the nucleon spin carried by valence and sea quarks, and gluons. The calculation is performed using an ensemble of gauge configurations with two degenerate light quarks with mass fixed to approximately reproduce the physical pion mass. We find that the total angular momentum carried by the quarks in the nucleon is $J_{u+d+s}{=}0.408(61)_{\rm stat.}(48)_{\rm syst.}$ and the gluon contribution is $J_g {=}0.133(11)_{\rm stat.}(14)_{\rm syst.}$ giving a total of $J_N{=}0.54(6)_{\rm stat.}(5)_{\rm syst.}$ consistent with the spin sum. For the quark intrinsic spin contribution we obtain $\frac{1}{2}\Delta \Sigma_{u+d+s}{=}0.201(17)_{\rm stat.}(5)_{\rm syst.}$. All quantities are given in the $\overline{\textrm{MS}}$ scheme at 2~GeV. The quark and gluon momentum fractions are also computed and add up to $\langle x\rangle_{u+d+s}+\langle x\rangle_g{=}0.804(121)_{\rm stat.}(95)_{\rm syst.}+0.267(12)_{\rm stat.}(10)_{\rm syst.}{=}1.07(12)_{\rm stat.}(10)_{\rm syst.}$ satisfying the momentum sum.Comment: Version published in PR

Universal distribution of threshold forces at the depinning transition

We study the distribution of threshold forces at the depinning transition for an elastic system of finite size, driven by an external force in a disordered medium at zero temperature. Using the functional renormalization group (FRG) technique, we compute the distribution of pinning forces in the quasi-static limit. This distribution is universal up to two parameters, the average critical force, and its width. We discuss possible definitions for threshold forces in finite-size samples. We show how our results compare to the distribution of the latter computed recently within a numerical simulation of the so-called critical configuration.Comment: 12 pages, 7 figures, revtex

Homogeneous versus Spiral Phases of Hole-doped Antiferromagnets: A Systematic Effective Field Theory Investigation

Using the low-energy effective field theory for magnons and holes -- the condensed matter analog of baryon chiral perturbation theory for pions and nucleons in QCD -- we study different phases of doped antiferromagnets. We systematically investigate configurations of the staggered magnetization that provide a constant background field for doped holes. The most general configuration of this type is either constant itself or it represents a spiral in the staggered magnetization. Depending on the values of the low-energy parameters, a homogeneous phase, a spiral phase, or an inhomogeneous phase is energetically favored. The reduction of the staggered magnetization upon doping is also investigated.Comment: 35 pages, 5 figure

Characterization of CoRoT target fields with BEST: Identification of periodic variable stars in the IR01 field

We report on observations of the CoRoT IR01 field with the Berlin Exoplanet Search Telescope (BEST). BEST is a small aperture telescope with a wide field of view (FOV). It is dedicated to search for variable stars within the target fields of the CoRoT space mission to aid in minimizing false-alarm rates and identify potential targets for additional science. CoRoT's observational programm started in February 2007 with the "initial run" field (IR01) observed for about two months. BEST observed this field for 12 nights spread over three months in winter 2006. From the total of 30426 stars observed in the IR01 field 3769 were marked as suspected variable stars and 54 from them showed clear periodicity. From these 19 periodic stars are within the part of the CoRoT FOV covered in our data set

Two Higgs Doublet Model and Lepton Polarization in the B -> K tau+ tau- Decay

The decay width, forward-backward asymmetry and tau lepton longitudinal and transversal polarization for the exclusive (B -> K tau^+ tau^-) decay in a two Higgs doublet model are computed. It is shown that the forward-backward asymmetry and longitudinal polarization of the tau lepton are very effective tools for establishing new physics.Comment: 25 pages, 20 figures, LaTeX formatte

Stability and distortions of liquid crystal order in a cell with a heterogeneous substrate

We study stability and distortions of liquid crystal nematic order in a cell with a random heterogeneous substrate. Modeling this system as a bulk xy model with quenched disorder confined to a surface, we find that nematic order is marginally unstable to such surface pinning. We compute the length scale beyond which nematic distortions become large and calculate orientational correlation functions using the functional renormalization-group and matching methods, finding universal logarithmic and double-logarithmic distortions in two and three dimensions, respectively. We extend these results to a finite-thickness liquid crystal cell with a second homogeneous substrate, detailing crossovers as a function of random pinning strength and cell thickness. We conclude with analysis of experimental signatures of these distortions in a conventional crossed-polarizer-analyzer light microscopy.Comment: 27 pages, 15 figures, Published in PRE, with minor typos correcte

Measuring functional renormalization group fixed-point functions for pinned manifolds

Exact numerical minimization of interface energies is used to test the functional renormalization group (FRG) analysis for interfaces pinned by quenched disorder. The fixed-point function R(u) (the correlator of the coarse-grained disorder) is computed. In dimensions D=d+1, a linear cusp in R''(u) is confirmed for random bond (d=1,2,3), random field (d=0,2,3), and periodic (d=2,3) disorders. The functional shocks that lead to this cusp are seen. Small, but significant, deviations from 1-loop FRG results are compared to 2-loop corrections. The cross-correlation for two copies of disorder is compared with a recent FRG study of chaos.Comment: 4 pages, 4 figure

Quantum vs. Geometric Disorder in a Two-Dimensional Heisenberg Antiferromagnet

We present a numerical study of the spin-1/2 bilayer Heisenberg antiferromagnet with random interlayer dimer dilution. From the temperature dependence of the uniform susceptibility and a scaling analysis of the spin correlation length we deduce the ground state phase diagram as a function of nonmagnetic impurity concentration p and bilayer coupling g. At the site percolation threshold, there exists a multicritical point at small but nonzero bilayer coupling g_m = 0.15(3). The magnetic properties of the single-layer material La_2Cu_{1-p}(Zn,Mg)_pO_4 near the percolation threshold appear to be controlled by the proximity to this new quantum critical point.Comment: minor changes, updated figure