Most of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory - still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could overcome these difficulties and facilitate the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures. Here we present StralSV, a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus and demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique or that shared structural similarity with structures that are distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local alignments, one can infer potential structural or functional importance of specific …

The Hf and Nd isotopic compositions of 71 Quaternary lavas collected from locations along the full length of the Aleutian island arc are used to constrain the sources of Aleutian magmas and to provide insight into the geochemical behavior of Nd and Hf and related elements in the Aleutian subduction-magmatic system. Isotopic compositions of Aleutian lavas fall approximately at the center of, and form a trend parallel to, the terrestrial Hf-Nd isotopic array with {var_epsilon}{sub Hf} of +12.0 to +15.5 and {var_epsilon}{sub Nd} of +6.5 to +10.5. Basalts, andesites, and dacites within volcanic centers or in nearby volcanoes generally all have similar isotopic compositions, indicating that there is little measurable effect of crustal or other lithospheric assimilation within the volcanic plumbing systems of Aleutian volcanoes. Hafnium isotopic compositions have a clear pattern of along-arc increase that is continuous from the eastern-most locations near Cold Bay to Piip Seamount in the western-most part of the arc. This pattern is interpreted to reflect a westward decrease in the subducted sediment component present in Aleutian lavas, reflecting progressively lower rates of subduction westward as well as decreasing availability of trench sediment. Binary bulk mixing models (sediment + peridotite) demonstrate that 1-2% of the …

In situ APPES technique demonstrates that the strong metal support interaction effect (SMSI) in the Ni-ceria system is associated with the decoration and burial of metallic particles by the partially reduced support, a phenomenon reversible by evacuation at high temperature of the previously absorbed hydrogen.

A detailed model of the Target Bay (TB) at the National Ignition Facility (NIF) has been developed to estimate the post-shot radiation environment inside the facility. The model includes large number of structures and diagnostic instruments present inside the TB. These structures and instruments are activated by the few nanosecond pulse of neutrons generated during a shot and the resultant gamma dose rates are estimated at various decay times following the shot. The results presented in this paper are based on a low-yield D-T shot of 10{sup 16} neutrons. General environment dose rates drop to below 3 mrem/h within three hours following a shot with higher dose rates observed at contact with some of the components. Dose rate maps of the different TB levels were generated to aid in estimating worker stay-out times following a shot before entry is permitted into the TB.

In many scenarios, an Adaptive Optics (AO) control system operates in the presence of temporally non-white noise. We use a Kalman filter with a state space formulation that allows suppression of this colored noise, hence improving residual error over the case where the noise is assumed to be white. We demonstrate the effectiveness of this new filter in the case of the estimated Gemini Planet Imager tip-tilt environment, where there are both common-path and non-common path vibrations. We discuss how this same framework can also be used to suppress spatial aliasing during predictive wavefront control assuming frozen flow in a low-order AO system without a spatially filtered wavefront sensor, and present experimental measurements from Altair that clearly reveal these aliased components.

The main focus of this work is to synthesize Brassylic Acid (BA) using oxidative cleavage of Erucic Acid (EA). Crambe (Crambe abyssinica) is an industrial oilseed grown in North Dakota. Crambe has potential as an industrial fatty acid feedstock as a source of Erucic acid (EA). It has approximately 50-60 % of EA, a C{sub 22} monounsaturated fatty acid. Oxidative cleavage of unsaturated fatty acids derived from oilseeds produces long chain (9, 11, and 13 carbon atoms) dibasic and monobasic acids. These acids are known commercial feedstocks for the preparation of nylons, polyesters, waxes, surfactants, and perfumes. Other sources of EA are Rapeseed seed oil which 50-60 % of EA. Rapeseed is grown outside USA. The oxidative cleavage of EA was done using a high throughput parallel pressure reactor system. Kinetics of the reaction shows that BA yields reach a saturation at 12 hours. H{sub 2}WO{sub 4} was found to be the best catalyst for the oxidative cleavage of EA. High yields of BA were obtained at 80 C with bubbling of O{sub 2} or 10 bar of O{sub 2} for 12 hours.

A primary goal in the design and synthesis of molecular hosts has been the selective recognition and binding of a variety of guests using non-covalent interactions. Supramolecular catalysis, which is the application of such hosts towards catalysis, has much in common with many enzymatic reactions, chiefly the use of both spatially appropriate binding pockets and precisely oriented functional groups to recognize and activate specific substrate molecules. Although there are now many examples which demonstrate how selective encapsulation in a host cavity can enhance the reactivity of a bound guest, all have failed to reach the degree of increased reactivity typical of enzymes. We now report the catalysis of the Nazarov cyclization by a self-assembled coordination cage, a carbon-carbon bond-forming reaction which proceeds under mild, aqueous conditions. The acceleration in this system is over a million-fold, and represents the first example of supramolecular catalysis that achieves the level of rate enhancement comparable to that observed in several enzymes. We explain the unprecedented degree of rate increase as due to the combination of (a) preorganization of the encapsulated substrate molecule, (b) stabilization of the transition state of the cyclization by constrictive binding, and (c) increase in the basicity of the complexed alcohol …

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The National Spherical Torus Experiment (NSTX) is a low aspect ratio, spherical torus (ST) configuration device which is located at Princeton Plasma Physics Laboratory (PPPL) This device is presently being updated to enhance its physics by doubling the TF field to 1 Tesla and increasing the plasma current to 2 Mega-amperes. The upgrades include a replacement of the centerstack and addition of a second neutral beam. The upgrade analyses have two missions. The first is to support design of new components, principally the centerstack, the second is to qualify existing NSTX components for higher loads, which will increase by a factor of four. Cost efficiency was a design goal for new equipment qualification, and reanalysis of the existing components. Showing that older components can sustain the increased loads has been a challenging effort in which designs had to be developed that would limit loading on weaker components, and would minimize the extent of modifications needed. Two areas representing this effort have been chosen to describe in more details: analysis of the current distribution in the new TF inner legs, and, second, analysis of the out-of-plane support of the existing TF outer legs.

Algebraic multigrid (AMG) solvers have proven to be extremely efficient on distributed-memory architectures. However, when executed on modern multicore cluster architectures, we face new challenges that can significantly harm AMG's performance. We discuss our experiences on such an architecture and present a set of techniques that help users to overcome the associated problems, including thread and process pinning and correct memory associations. We have implemented most of the techniques in a MultiCore SUPport library (MCSup), which helps to map OpenMP applications to multicore machines. We present results using both an MPI-only and a hybrid MPI/OpenMP model.

We study finite temperature properties of a generic spin-orbital model relevant to transition metal compounds, having coupled quantum Heisenberg-spin and Ising-orbital degrees of freedom. The model system undergoes a phase transition, consistent with that of a 2D Ising model, to an orbitally ordered state at a temperature set by short-range magnetic order. At low temperatures the orbital degrees of freedom freeze-out and the model maps onto a quantum Heisenberg model. The onset of orbital excitations causes a rapid scrambling of the spin spectral weight away from coherent spin-waves, which leads to a sharp increase in uniform magnetic susceptibility just below the phase transition, reminiscent of the observed behavior in the Fe-pnictide materials.

We have made an experimental study of the tunneling density of states (DOS) in strong ferromagnetic thin films (CoFe) in proximity with a thick superconducting film (Nb) as a function of d{sub F}, the ferromagnetic thickness. Remarkably, we find that as d{sub F} increases, the superconducting DOS exhibits a scaling behavior in which the deviations from the normal-state conductance have a universal shape that decreases exponentially in amplitude with characteristic length d* {approx} 0.4 nm. We do not see oscillations in the DOS as a function of d{sub F}, as expected from predictions based on the Usadel equations, although an oscillation in T{sub c}(d{sub F}) has been seen in the same materials.

We present the prospects for a future joint gamma-ray and radio survey of southern hemisphere sources using the Fermi Large Area Telescope (LAT) and the upcoming Australian Square Kilometre Array Pathfinder (ASKAP) radio telescope. ASKAP is a next generation radio telescope designed to perform surveys at GHz frequencies at a much higher survey speed than previous radio telescopes, and is scheduled to start engineering observations in 2011. The survey capabilities of both Fermi LAT and ASKAP are described, and the planned science surveys for ASKAP are summarized. We give some expected details of the Variable and Slow Transient (VAST) survey using ASKAP, which will search for transients on timescales from 5 seconds to years. Some observational properties of faint and transient sources seen at gamma-ray and radio wavelengths are summarized, and prospects and strategies for using ASKAP survey data for LAT source counterpart identification are summarized.

As discovered by Ohtomo et al., a large sheet charge density with high mobility exists at the interface between SrTiO{sub 3} and LaAlO{sub 3}. Based on transport, spectroscopic and oxygen-annealing experiments, we conclude that extrinsic defects in the form of oxygen vacancies introduced by the pulsed laser deposition process used by all researchers to date to make these samples is the source of the large carrier densities. Annealing experiments show a limiting carrier density. We also present a model that explains the high mobility based on carrier redistribution due to an increased dielectric constant.

We explore the general phenomenology of resonant inelastic scattering (RIXS) using CuB{sub 2}O{sub 4}, a network of CuO{sub 4} plaquettes electronically isolated by B{sup +3} ions. Spectra show a small number of well-separated features, and we exploit the simple electronic structure to explore RIXS phenomenology by developing a calculation which allows for intermediate-state effects ignored in standard approaches. These effects are found to be non-negligible and good correspondence between our model and experiment leads to a simple picture of such phenomenology as the genesis of d {yields} d excitations at the K edge and intermediate-state interference effects.

Extra dimensions provide a very useful tool in addressing a number of the fundamental problems faced by the Standard Model. The following provides a very basic introduction to this very broad subject area as given at the VIII School of the Gravitational and Mathematical Physics Division of the Mexican Physical Society in December 2009. Some prospects for extra dimensional searches at the 7 TeV LHC with {approx}1 fb{sup -1} of integrated luminosity are provided.

A search for the neutrinoless, lepton-flavor violating decay of the {tau} lepton into three charged leptons has been performed using an integrated luminosity of 468 fb{sup -1} collected with the BABAR detector at the PEP-II collider. In all six decay modes considered, the numbers of events found in data are compatible with the background expectations. Upper limits on the branching fractions are set in the range (1.8-3.3) x 10{sup -8} at 90% confidence level.

We examine the nucleated (with barrier) activation of perfectly wetting (zero contact angle) particles ranging from bulk size down to one nanometer. Thermodynamic properties of the particles, coated with liquid layers of varying thickness and surrounded by vapor, are analyzed. Nano-size particles are predicted to activate at relative humidity below the Kelvin curve on crossing a nucleation barrier, located at a critical liquid layer thickness such that the total particle size (core + liquid layer) equals the Kelvin radius (Fig. 1). This barrier vanishes precisely as the critical layer thickness approaches the thin layer limit and the Kelvin radius equals the radius of the particle itself. These considerations are similar to those included in Fletcher's theory (Fletcher, 1958) however the present analysis differs in several important respects. Firstly, where Fletcher used the classical prefactor-exponent form for the nucleation rate, requiring separate estimation of the kinetic prefactor, we solve a diffusion-drift equation that is equivalent to including the full Becker-Doering (BD) multi-state kinetics of condensation/evaporation along the growth coordinate. We also determine the mean first passage time (MFPT) for barrier crossing (Wedekind et al., 2007), which is shown to provide a generalization of BD nucleation kinetics especially useful for barrier heights …

The combination of Anti-de Sitter space (AdS) methods with light-front (LF) holography provides a remarkably accurate first approximation for the spectra and wavefunctions of meson and baryon light-quark bound states. The resulting bound-state Hamiltonian equation of motion in QCD leads to relativistic light-front wave equations in terms of an invariant impact variable {zeta} which measures the separation of the quark and gluonic constituents within the hadron at equal light-front time. These equations of motion in physical space-time are equivalent to the equations of motion which describe the propagation of spin-J modes in anti-de Sitter (AdS) space. The eigenvalues give the hadronic spectrum, and the eigenmodes represent the probability distributions of the hadronic constituents at a given scale. A positive-sign confining dilaton background modifying AdS space gives a very good account of meson and baryon spectroscopy and form factors. The light-front holographic mapping of this model also leads to a non-perturbative effective coupling {alpha}{sub s}{sup Ads} (Q{sup 2}) which agrees with the effective charge defined by the Bjorken sum rule and lattice simulations. It displays a transition from perturbative to nonperturbative conformal regimes at a momentum scale {approx} 1 GeV. The resulting {beta}-function appears to capture the essential characteristics of the …

The Linac Coherent Light Source (LCLS) at the Stanford Linear Accelerator Center is a pioneer fourth generation hard x-ray free electron laser that shall start to deliver laser pulses in 2009. Among other components of LCLS that present radiation protection concerns, the tune up dump (tdund) is of special interest because it also constitutes an issue for machine protection, as it is placed close to radiation sensitive components, like electronic devices and permanent magnets in the undulators. This paper first introduces the stopper of tdund looking at the heat load, and then it describes the shielding around the dump necessary to maintain the prompt and residual dose within design values. Next, preliminary comparisons of the magnetization loss in a dedicated on-site magnet irradiation experiment with FLUKA simulations serve to characterize the magnetic response to radiation of magnets like those of LCLS. The previous knowledge, together with the limit for the allowed demagnetization, are used to estimate the lifetime of the undulator. Further simulations provide guidelines on which lifetime can be expected for an electronic device placed at a given distance of tdund.

Angle Resolved Photoemission Spectroscopy (ARPES) probes the momentum-space electronic structure of materials, and provides invaluable information about the high-temperature superconducting cuprates. Likewise, cuprates real-space, inhomogeneous electronic structure is elucidated by Scanning Tunneling Spectroscopy (STS). Recently, STS has exploited quasiparticle interference (QPI) - wave-like electrons scattering off impurities to produce periodic interference patterns - to infer properties of the QP in momentum-space. Surprisingly, some interference peaks in Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} (Bi-2212) are absent beyond the antiferromagnetic (AF) zone boundary, implying the dominance of particular scattering process. Here, we show that ARPES sees no evidence of quasiparticle (QP) extinction: QP-like peaks are measured everywhere on the Fermi surface, evolving smoothly across the AF zone boundary. This apparent contradiction stems from different natures of single-particle (ARPES) and two-particle (STS) processes underlying these probes. Using a simple model, we demonstrate extinction of QPI without implying the loss of QP beyond the AF zone boundary.

Using x-ray absorption and resonant inelastic x-ray scattering, charge dynamics at and near the Fe L edges is investigated in Fe pnictide materials, and contrasted to that measured in other Fe compounds. It is shown that the XAS and RIXS spectra for 122 and 1111 Fe pnictides are each qualitatively similar to Fe metal. Cluster diagonalization, multiplet, and density-functional calculations show that Coulomb correlations are much smaller than in the cuprates, highlighting the role of Fe metallicity and strong covalency in these materials. Best agreement with experiment is obtained using Hubbard parameters U {approx}< 2eV and J {approx} 0.8eV.

The U.S. Department of Energy Office of Environmental Management (DOE-EM) is responsible for the Decontamination and Decommissioning (D&D) of nuclear facilities throughout the DOE Complex. Some of these facilities will be completely dismantled, while others will be partially dismantled and the remaining structure will be stabilized with cementitious fill materials. The latter is a process known as In-Situ Decommissioning (ISD). The ISD decision process requires a detailed understanding of the existing facility conditions, and operational history. System information and material properties are need for aged nuclear facilities. This literature review investigated the properties of aged concrete structures affected by radiation. In particular, this review addresses the Savannah River Site (SRS) isotope production nuclear reactors. The concrete in the reactors at SRS was not seriously damaged by the levels of radiation exposure. Loss of composite compressive strength was the most common effect of radiation induced damage documented at nuclear power plants.

The main focus of this work is to estimate Brassylic Acid (BA) using gas chromatography-mass spectrometry (GC-MS). BA is a product obtained from the oxidative cleavage of Erucic Acid (EA). BA has various applications for making nylons and high performance polymers. BA is a 13 carbon compound with two carboxylic acid functional groups at the terminal end. BA has a long hydrocarbon chain that makes the molecule less sensitive to some of the characterization techniques. Although BA can be characterized by NMR, both the starting material (EA) and products BA and nonanoic acid (NA) have peaks at similar {delta}, ppm values. Hence it becomes difficult for the quick estimation of BA during its synthesis.