Nucleon structure from mixed action calculations using 2+1 flavors of asqtad sea and domain wall valence fermions

We present high statistics results for the structure of the nucleon from a mixed-action calculation using 2+1 flavors of asqtad sea and domain wall valence fermions. We perform extrapolations of our data based on different chiral effective field theory schemes and compare our results with available information from phenomenology. We discuss vector and axial form factors of the nucleon, moments of generalized parton distributions, including moments of forward parton distributions, and implications for the decomposition of the nucleon spin.Comment: 68 pages, 47 figures. Main revision points: improved discussion of chiral fits and systematic uncertainties, several minor refinements. Accepted for publication in Phys.Rev.

Nucleon Generalized Parton Distributions from Full Lattice QCD

We present a comprehensive study of the lowest moments of nucleon generalized parton distributions in N_f=2+1 lattice QCD using domain wall valence quarks and improved staggered sea quarks. Our investigation includes helicity dependent and independent generalized parton distributions for pion masses as low as 350 MeV and volumes as large as (3.5 fm)^3, for a lattice spacing of 0.124 fm. We use perturbative renormalization at one-loop level with an improvement based on the non-perturbative renormalization factor for the axial vector current, and only connected diagrams are included in the isosinglet channel.Comment: 40 pages, 49 figures; Revised chiral extrapolations in sections A-K, main conclusions unchange

Nucleon axial and pseudoscalar form factors from the covariant Faddeev equation

We compute the axial and pseudoscalar form factors of the nucleon in the Dyson-Schwinger approach. To this end, we solve a covariant three-body Faddeev equation for the nucleon wave function and determine the matrix elements of the axialvector and pseudoscalar isotriplet currents. Our only input is a well-established and phenomenologically successful ansatz for the nonperturbative quark-gluon interaction. As a consequence of the axial Ward-Takahashi identity that is respected at the quark level, the Goldberger-Treiman relation is reproduced for all current-quark masses. We discuss the timelike pole structure of the quark-antiquark vertices that enters the nucleon matrix elements and determines the momentum dependence of the form factors. Our result for the axial charge underestimates the experimental value by 20-25% which might be a signal of missing pion-cloud contributions. The axial and pseudoscalar form factors agree with phenomenological and lattice data in the momentum range above Q^2 ~ 1...2 GeV^2.Comment: 17 pages, 7 figures, 1 tabl

Spin structure of the nucleon: QCD evolution, lattice results and models

The question how the spin of the nucleon is distributed among its quark and gluon constituents is still a subject of intense investigations. Lattice QCD has progressed to provide information about spin fractions and orbital angular momentum contributions for up- and down-quarks in the proton, at a typical scale \mu^2~4 GeV^2. On the other hand, chiral quark models have traditionally been used for orientation at low momentum scales. In the comparison of such model calculations with experiment or lattice QCD, fixing the model scale and the treatment of scale evolution are essential. In this paper, we present a refined model calculation and a QCD evolution of lattice results up to next-to-next-to-leading order. We compare this approach with the Myhrer-Thomas scenario for resolving the proton spin puzzle.Comment: 11 pages, 6 figures, equation (9) has been corrected leading to a revised figure 1b. Revision matches published versio

Identification of Key Residues for pH Dependent Activation of Violaxanthin De-Epoxidase from Arabidopsis thaliana

Plants are often exposed to saturating light conditions, which can lead to oxidative stress. The carotenoid zeaxanthin, synthesized from violaxanthin by Violaxanthin De-Epoxidase (VDE) plays a major role in the protection from excess illumination. VDE activation is triggered by a pH reduction in the thylakoids lumen occurring under saturating light. In this work the mechanism of the VDE activation was investigated on a molecular level using multi conformer continuum electrostatic calculations, site directed mutagenesis and molecular dynamics. The pKa values of residues of the inactive VDE were determined to identify target residues that could be implicated in the activation. Five such target residues were investigated closer by site directed mutagenesis, whereas variants in four residues (D98, D117, H168 and D206) caused a reduction in enzymatic activity indicating a role in the activation of VDE while D86 mutants did not show any alteration. The analysis of the VDE sequence showed that the four putative activation residues are all conserved in plants but not in diatoms, explaining why VDE in these algae is already activated at higher pH. Molecular dynamics showed that the VDE structure was coherent at pH 7 with a low amount of water penetrating the hydrophobic barrel. Simulations carried out with the candidate residues locked into their protonated state showed instead an increased amount of water penetrating the barrel and the rupture of the H121–Y214 hydrogen bond at the end of the barrel, which is essential for VDE activation. These results suggest that VDE activation relies on a robust and redundant network, in which the four residues identified in this study play a major role

Brane-World Gravity

The observable universe could be a 1+3-surface (the "brane") embedded in a 1+3+\textit{d}-dimensional spacetime (the "bulk"), with Standard Model particles and fields trapped on the brane while gravity is free to access the bulk. At least one of the \textit{d} extra spatial dimensions could be very large relative to the Planck scale, which lowers the fundamental gravity scale, possibly even down to the electroweak ($\sim$ TeV) level. This revolutionary picture arises in the framework of recent developments in M theory. The 1+10-dimensional M theory encompasses the known 1+9-dimensional superstring theories, and is widely considered to be a promising potential route to quantum gravity. At low energies, gravity is localized at the brane and general relativity is recovered, but at high energies gravity "leaks" into the bulk, behaving in a truly higher-dimensional way. This introduces significant changes to gravitational dynamics and perturbations, with interesting and potentially testable implications for high-energy astrophysics, black holes, and cosmology. Brane-world models offer a phenomenological way to test some of the novel predictions and corrections to general relativity that are implied by M theory. This review analyzes the geometry, dynamics and perturbations of simple brane-world models for cosmology and astrophysics, mainly focusing on warped 5-dimensional brane-worlds based on the Randall--Sundrum models. We also cover the simplest brane-world models in which 4-dimensional gravity on the brane is modified at \emph{low} energies -- the 5-dimensional Dvali--Gabadadze--Porrati models. Then we discuss co-dimension two branes in 6-dimensional models.Comment: A major update of Living Reviews in Relativity 7:7 (2004) "Brane-World Gravity", 119 pages, 28 figures, the update contains new material on RS perturbations, including full numerical solutions of gravitational waves and scalar perturbations, on DGP models, and also on 6D models. A published version in Living Reviews in Relativit