Constraints on the IR behaviour of gluon and ghost propagator from Ward-Slavnov-Taylor identities

We consider the constraints of the Slavnov-Taylor identity of the IR behaviour of gluon and ghost propagators and their compatibility with solutions of the ghost Dyson-Schwinger equation and with the lattice picture.Comment: 5 pages, 2 figure

Infrared Features of the Landau Gauge QCD

The infrared features of Landau gauge QCD are studied by the lattice simulation of $\beta=6.0, 16^4, 24^4, 32^4$ and $\beta=6.4, 32^4, 48^4$. We adopt two definitions of the gauge field; 1) $U-$linear 2) $\log U$ and measured the gluon propagator and ghost propagator. Infrared singularity of the gluon propagator is less than that of tree level result but the gluon propagator at 0 momentum remains finite. The infrared singularity of ghost propagator is stronger than the tree level. The QCD running coupling measured by using the gluon propagator and the ghost propagator has a maximum $\alpha_s(p)\simeq 1$ at around $p=0.5GeV$ and decreases as $p$ approaches 0. The data are analyzed in use of formula of the principle of minimal sensitivity(PMS), the effective charge method and the contour-improved perturbation method, which suggest necessity of the resummation of perturbation series in the infrared region together with existence of the infrared fixed point. Kugo-Ojima parameter saturates at about -0.8 in contrast to the theoretically expected value -1.Comment: RevTex4, 9 pages, 10 eps figures, Typos corrected. To be published in Phys. Rev. D(2004

Quark propagator and vertex: systematic corrections of hypercubic artifacts from lattice simulations

This is the first part of a study of the quark propagator and the vertex function of the vector current on the lattice in the Landau gauge and using both Wilson-clover and overlap actions. In order to be able to identify lattice artifacts and to reach large momenta we use a range of lattice spacings. The lattice artifacts turn out to be exceedingly large in this study. We present a new and very efficient method to eliminate the hypercubic (anisotropy) artifacts based on a systematic expansion on hypercubic invariants which are not SO(4) invariant. A simpler version of this method has been used in previous works. This method is shown to be significantly more efficient than the popular ``democratic'' methods. It can of course be applied to the lattice simulations of many other physical quantities. The analysis indicates a hierarchy in the size of hypercubic artifacts: overlap larger than clover and propagator larger than vertex function. This pleads for the combined study of propagators and vertex functions via Ward identities.Comment: 14 pags., 9 fig

On the leading OPE corrections to the ghost-gluon vertex and the Taylor theorem

This brief note is devoted to a study of genuine non-perturbative corrections to the Landau gauge ghost-gluon vertex in terms of the non-vanishing dimension-two gluon condensate. We pay special attention to the kinematical limit which the bare vertex takes for its tree-level expression at any perturbative order, according to the well-known Taylor theorem. Based on our OPE analysis, we also present a simple model for the vertex, in acceptable agreement with lattice data.Comment: Final version published in JHE

The Gluon Propagator without lattice Gribov copies

We study the gluon propagator in quenched lattice QCD using the Laplacian gauge which is free of lattice Gribov copies. We compare our results with those obtained in the Landau gauge on the lattice, as well as with various approximate solutions of the Dyson Schwinger equations. We find a finite value $\sim (445 \rm{MeV})^{-2}$ for the renormalized zero-momentum propagator (taking our renormalization point at 1.943 GeV), and a pole mass $\sim 640 \pm 140$ MeV.Comment: Discussion of the renormalized gluon propagator and of the Laplacian gauge fixing procedure extended. Version to appear in Phys. Rev. D. 15 pages, 8 figure

Influence of Neutron Enrichment on Disintegration Modes of Compound Nuclei

Cross sections, kinetic energy and angular distributions of fragments with charge 6$\le$Z$\le$28 emitted in 78,82Kr+40C at 5.5 MeV/A reactions were measured at the GANIL facility using the INDRA apparatus. This experiment aims to investigate the influence of the neutron enrichment on the decay mechanism of excited nuclei. Data are discussed in comparison with predictions of transition state and Hauser-Feshbach models.Comment: 8 pages, 1 figure, paper presented at the First Workshop on "State of the Art in Nuclear Cluster Physics" 13-16 May, 2008, at Strasbourg, France (SOTANCP2008) and accepted for publication at International Journal of Modern Physics E (Special Issue), Proceedings of SOTANCP2008 (to be published

Confinement and Chiral Symmetry Breaking via Domain-Like Structures in the QCD Vacuum

A qualitative mechanism for the emergence of domain structured background gluon fields due to singularities in gauge field configurations is considered, and a model displaying a type of mean field approximation to the QCD partition function based on this mechanism is formulated. Estimation of the vacuum parameters (gluon condensate, topological susceptibility, string constant and quark condensate) indicates that domain-like structures lead to an area law for the Wilson loop, nonzero topological susceptibility and spontaneous breakdown of chiral symmetry. Gluon and ghost propagators in the presence of domains are calculated explicitly and their analytical properties are discussed. The Fourier transforms of the propagators are entire functions and thus describe confined dynamical fields.Comment: RevTeX, 48 pages (32 pages + Appendices A-E), new references added [1,2,4,5] and minor formulae corrected for typographical error

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein