PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences

Alignment-based programs are valuable tools for finding potential homologs in genome sequences. Previously, it has been shown that partition function posterior probabilities attuned to local alignment achieve a high accuracy in identifying distantly similar non-coding RNA sequences that are hidden in a large genome. Here, we present an online implementation of that alignment algorithm based on such probabilities. Our server takes as input a query RNA sequence and a large genome sequence, and outputs a list of hits that are above a mean posterior probability threshold. The output is presented in a format suited to local alignment. It can also be viewed within the PLAST alignment viewer applet that provides a list of all hits found and highlights regions of high posterior probability within each local alignment. The server is freely available at http://plastrna.njit.edu

The Single-Particle Structure of Neutron-Rich Nuclei of Astrophysical Interest at the Ornl Hribf

The rapid nuetron-capture process (r process) produces roughly half of the elements heavier than iron. The path and abundances produced are uncertain, however, because of the lack of nuclear strucure information on important neutron-rich nuclei. We are studying nuclei on or near the r-process path via single-nucleon transfer reactions on neutron-rich radioactive beams at ORNL's Holifield Radioactive Ion Beam Facility (HRIBF). Owing to the difficulties in studying these reactions in inverse kinematics, a variety of experimental approaches are being developed. We present the experimental methods and initial results.Comment: Proceedings of the Third International Conference on Fission and Properties of Neutron-Rich Nucle

Direct reaction measurements with a 132Sn radioactive ion beam

The (d,p) neutron transfer and (d,d) elastic scattering reactions were measured in inverse kinematics using a radioactive ion beam of 132Sn at 630 MeV. The elastic scattering data were taken in a region where Rutherford scattering dominated the reaction, and nuclear effects account for less than 8% of the cross section. The magnitude of the nuclear effects was found to be independent of the optical potential used, allowing the transfer data to be normalized in a reliable manner. The neutron-transfer reaction populated a previously unmeasured state at 1363 keV, which is most likely the single-particle 3p1/2 state expected above the N=82 shell closure. The data were analyzed using finite range adiabatic wave calculations and the results compared with the previous analysis using the distorted wave Born approximation. Angular distributions for the ground and first excited states are consistent with the previous tentative spin and parity assignments. Spectroscopic factors extracted from the differential cross sections are similar to those found for the one neutron states beyond the benchmark doubly-magic nucleus 208Pb.Comment: 22 pages, 7 figure

Fermi surface of the colossal magnetoresistance perovskite La_{0.7}Sr_{0.3}MnO_{3}

Materials that exhibit colossal magnetoresistance (CMR) are currently the focus of an intense research effort, driven by the technological applications that their sensitivity lends them to. Using the angular correlation of photons from electron-positron annihilation, we present a first glimpse of the Fermi surface of a material that exhibits CMR, supported by ``virtual crystal'' electronic structure calculations. The Fermi surface is shown to be sufficiently cubic in nature that it is likely to support nesting.Comment: 5 pages, 5 PS figure

How accurate and statistically robust are catalytic site predictions based on closeness centrality?

<p>Abstract</p> <p>Background</p> <p>We examine the accuracy of enzyme catalytic residue predictions from a network representation of protein structure. In this model, amino acid α-carbons specify vertices within a graph and edges connect vertices that are proximal in structure. Closeness centrality, which has shown promise in previous investigations, is used to identify important positions within the network. Closeness centrality, a global measure of network centrality, is calculated as the reciprocal of the average distance between vertex <it>i </it>and all other vertices.</p> <p>Results</p> <p>We benchmark the approach against 283 structurally unique proteins within the Catalytic Site Atlas. Our results, which are inline with previous investigations of smaller datasets, indicate closeness centrality predictions are statistically significant. However, unlike previous approaches, we specifically focus on residues with the very best scores. Over the top five closeness centrality scores, we observe an average true to false positive rate ratio of 6.8 to 1. As demonstrated previously, adding a solvent accessibility filter significantly improves predictive power; the average ratio is increased to 15.3 to 1. We also demonstrate (for the first time) that filtering the predictions by residue identity improves the results even more than accessibility filtering. Here, we simply eliminate residues with physiochemical properties unlikely to be compatible with catalytic requirements from consideration. Residue identity filtering improves the average true to false positive rate ratio to 26.3 to 1. Combining the two filters together has little affect on the results. Calculated p-values for the three prediction schemes range from 2.7E-9 to less than 8.8E-134. Finally, the sensitivity of the predictions to structure choice and slight perturbations is examined.</p> <p>Conclusion</p> <p>Our results resolutely confirm that closeness centrality is a viable prediction scheme whose predictions are statistically significant. Simple filtering schemes substantially improve the method's predicted power. Moreover, no clear effect on performance is observed when comparing ligated and unligated structures. Similarly, the CC prediction results are robust to slight structural perturbations from molecular dynamics simulation.</p

Spin Wave Theory of Double Exchange Ferromagnets

We construct the 1/S spin-wave expansion for double exchange ferromagnets at T=0. It is assumed that the value of Hund's rule coupling, J_H, is sufficiently large, resulting in a fully saturated, ferromagnetic half-metallic ground state. We evaluate corrections to the magnon dispersion law, and we also find that, in contrast to earlier statements in the literature, magnon-electron scattering does give rise to spin wave damping. We analyse the momentum dependence of these quantities and discuss the experimental implications for colossal magnetoresistance compounds.Comment: 4 pages, Latex-Revtex, 2 PostScript figures. Minor revisions, references added. See also cond-mat/990921

The magic nature of 132Sn explored through the single-particle states of 133Sn

Atomic nuclei have a shell structure where nuclei with 'magic numbers' of neutrons and protons are analogous to the noble gases in atomic physics. Only ten nuclei with the standard magic numbers of both neutrons and protons have so far been observed. The nuclear shell model is founded on the precept that neutrons and protons can move as independent particles in orbitals with discrete quantum numbers, subject to a mean field generated by all the other nucleons. Knowledge of the properties of single-particle states outside nuclear shell closures in exotic nuclei is important for a fundamental understanding of nuclear structure and nucleosynthesis (for example the r-process, which is responsible for the production of about half of the heavy elements). However, as a result of their short lifetimes, there is a paucity of knowledge about the nature of single-particle states outside exotic doubly magic nuclei. Here we measure the single-particle character of the levels in 133Sn that lie outside the double shell closure present at the short-lived nucleus 132Sn. We use an inverse kinematics technique that involves the transfer of a single nucleon to the nucleus. The purity of the measured single-particle states clearly illustrates the magic nature of 132Sn.Comment: 19 pages, 5 figures and 4 table

Nesting properties and anisotropy of the Fermi surface of LuNi2_{2}B2_{2}C

The rare earth nickel borocarbides, with the generic formula $R$Ni$_{2}$B$_{2}$C, have recently been shown to display a rich variety of phenomena. Most striking has been the competition between, and even coexistence of, antiferromagnetism and superconductivity. We have measured the Fermi surface (FS) of LuNi$_{2}$B$_{2}$C, and shown that it possesses nesting features capable of explaining some of the phenomena experimentally observed. In particular, it had previously been conjectured that a particular sheet of FS is responsible for the modulated magnetic structures manifest in some of the series. We report the first direct experimental observation of this sheet.Comment: 4 pages, 4 PS figure

First proton-transfer study of 18F+p resonances relevant for novae

The 18F(p,α)15O reaction is the predominant destruction mechanism in novae of the radionuclide F18, a target of γ-ray observatories. Thus, its rate is important for understanding F18 production in novae. We have studied resonances in the 18F+p system by making a measurement of a proton-transfer reaction 18F(d,n). We have observed 15 Ne19 levels, 5 of which are below the proton threshold, including a subthreshold state, which has significant l p=0 strength. Our data provide a direct determination of the spectroscopic strength of these states and new constraints on their spins and parities, thereby resolving a controversy, which involves the 8- and 38-keV resonances. The 18F(p,α)15O reaction rate is reevaluated, which takes the subthreshold resonance and other new information determined in this experiment into account. © 2011 American Physical Society