Ge-substitutional defects and the r3xr3 <--> 3x3 transition in alpha--SnGe(111)

The structure and energetics of Ge substitutional defects on the alpha-Sn/Ge(111) surface are analyzed using Density Functional Theory (DFT) molecular dynamics (MD) simulations. An isolated Ge defect induces a very local distortion of the 3x3 reconstruction, confined to a significant downwards displacement (-0.31 A) at the defect site and a modest upward displacement (0.05 A) of the three Sn nearest neighbours with partially occupied dangling bonds. Dynamical fluctuations between the two degenerate ground states yield the six-fold symmetry observed around a defect in the experiments at room temperature. Defect-defect interactions are controlled by the energetics of the deformation of the 3x3 structure: They are negligible for defects on the honeycomb lattice and quite large for a third defect on the hexagonal lattice, explaining the low temperature defect ordering.Comment: 4 pages, Revtex, 7 Encapsulated Postscript figures, uses epsf.sty. Submitted to Phys. Rev. Let

Identification of novel restriction endonuclease-like fold families among hypothetical proteins

Restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. The lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. Using the consensus fold recognition method Meta-BASIC that combines sequence profiles with predicted protein secondary structure, we identify nine new restriction endonuclease-like fold families among previously uncharacterized proteins and predict these proteins to cleave nucleic acid substrates. Application of transitive searches combined with gene neighborhood analysis allow us to confidently link these unknown families to a number of known restriction endonuclease-like structures and thus assign folds to the uncharacterized proteins. Finally, our method identifies a novel restriction endonuclease-like domain in the C-terminus of RecC that is not detected with structure-based searches of the existing PDB database

Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches

<p>Abstract</p> <p>Background</p> <p>PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes that display little sequence similarity despite retaining a common core fold and a few critical active site residues. This makes identification of new PD-(D/E)XK nuclease families a challenging task as they usually escape detection with standard sequence-based methods. We developed a modified transitive meta profile search approach and to consider the structural diversity of PD-(D/E)XK nuclease fold more thoroughly we analyzed also lower than threshold Meta-BASIC hits to select potentially correct predictions placed among unreliable or incorrect ones.</p> <p>Results</p> <p>Application of a modified transitive Meta-BASIC searches on updated PFAM families and PDB structures resulted in detection of five new PD-(D/E)XK nuclease families encompassing hundreds of so far uncharacterized and poorly annotated proteins. These include four families catalogued in PFAM database as domains of unknown function (DUF506, DUF524, DUF1626 and DUF1703) and YhgA-like family of putative transposases. Three of these families represent extremely distant homologs (DUF506, DUF524, and YhgA-like), while two are newly defined in updated database (DUF1626 and DUF1703). In addition, we also confidently identified an extended AAA-ATPase domain in the N-terminal region of DUF1703 family proteins.</p> <p>Conclusion</p> <p>Obtained results suggest that detailed analysis of below threshold Meta-BASIC hits may push limits further for distant homology detection in the 'midnight zone' of homology. All identified families conserve the core evolutionary fold, secondary structure and hydrophobic patterns common to existing PD-(D/E)XK nucleases and maintain critical active site motifs that contribute to nucleic acid cleavage. Further experimental investigations should address the predicted activity and clarify potential substrates providing further insight into detailed biological role of these newly detected nucleases.</p

Small strange stars and marginally stable orbit in Newtonian theory

It is shown that for very rapidly rotating low mass strange stars the marginally stable orbit is located above the stellar surface. This effect is explained by the very important role of the oblateness of the rotating strange star. The comparison with some ``academic'' examples is presented. This feature is purely Newtonian in its nature and has nothing to do with relativistic marginally stable orbit. The effect is very large and cannot be treated in a perturbative way. It seems that strange stars as a very dense self-bound objects are the only possibility in Nature to represent these toy models.Comment: 4 pages, 5 figures, minor text and Fig.2 changes, references added, Phys. Rev. D, accepte

Recursive representation of the torus 1-point conformal block

The recursive relation for the 1-point conformal block on a torus is derived and used to prove the identities between conformal blocks recently conjectured by R. Poghossian. As an illustration of the efficiency of the recurrence method the modular invariance of the 1-point Liouville correlation function is numerically analyzed.Comment: 14 pages, 1 eps figure, misprints corrected and a reference adde

Experimental and numerical investigation of the reflection coefficient and the distributions of Wigner's reaction matrix for irregular graphs with absorption

We present the results of experimental and numerical study of the distribution of the reflection coefficient P(R) and the distributions of the imaginary P(v) and the real P(u) parts of the Wigner's reaction K matrix for irregular fully connected hexagon networks (graphs) in the presence of strong absorption. In the experiment we used microwave networks, which were built of coaxial cables and attenuators connected by joints. In the numerical calculations experimental networks were described by quantum fully connected hexagon graphs. The presence of absorption introduced by attenuators was modelled by optical potentials. The distribution of the reflection coefficient P(R) and the distributions of the reaction K matrix were obtained from the measurements and numerical calculations of the scattering matrix S of the networks and graphs, respectively. We show that the experimental and numerical results are in good agreement with the exact analytic ones obtained within the framework of random matrix theory (RMT).Comment: 15 pages, 8 figure

Second-order electronic correlation effects in a one-dimensional metal

The Pariser-Parr-Pople (PPP) model of a single-band one-dimensional (1D) metal is studied at the Hartree-Fock level, and by using the second-order perturbation theory of the electronic correlation. The PPP model provides an extension of the Hubbard model by properly accounting for the long-range character of the electron-electron repulsion. Both finite and infinite version of the 1D-metal model are considered within the PPP and Hubbard approximations. Calculated are the second-order electronic-correlation corrections to the total energy, and to the electronic-energy bands. Our results for the PPP model of 1D metal show qualitative similarity to the coupled-cluster results for the 3D electron-gas model. The picture of the 1D-metal model that emerges from the present study provides a support for the hypothesis that the normal metallic state of the 1D metal is different from the ground state.Comment: 21 pages, 16 figures; v2: small correction in title, added 3 references, extended and reformulated a few paragraphs (detailed information at the end of .tex file); added color to figure

Metric gravity theories and cosmology:II. Stability of a ground state in f(R) theories

A fundamental criterion of viability of any gravity theory is existence of a stable ground-state solution being either Minkowski, dS or AdS space. Stability of the ground state is independent of which frame is physical. In general, a given theory has multiple ground states and splits into independent physical sectors. All metric gravity theories with the Lagrangian being a function of Ricci tensor are dynamically equivalent to Einstein gravity with a source and this allows us to study the stability problem using methods developed in GR. We apply these methods to f(R) theories. As is shown in 13 cases of Lagrangians the stability criterion works simply and effectively whenever the curvature of the ground state is determined. An infinite number of gravity theories have a stable ground state and further viability criteria are necessary.Comment: A modified and expanded version of a second part of the paper which previously appeared as gr-qc/0702097v1. The first, modified part is now published as gr-qc/0702097v2 and as a separate paper in Class. Qu. Grav. The present paper matches the published versio

High rate operation of micro-strip gas chambers on diamond-coated glass

Very high rate operation of micro­strip gas chambers can be achieved using slightly conducting substrates. We describe preliminary measurements realized with detectors manufactured on boro-silicate glass coated, before the photo-lithographic processing, with a diamond layer having a surface resistivity of around 1014 /o. Stable medium-term operation, and a rate capability largely exceeding the one obtained with identical plates manufactured on uncoated glass are demonstrated. If these results are confirmed by long-term measurements the diamond coating technology appears very attractive since it allows, with a moderate cost overhead, to use thin, commercially available glass with the required surface quality for the large-scale production of gas micro-strip detectors