Some genes produce transcripts that function directly in regulatory, catalytic, or structural roles in the cell. These non-coding RNAs are prevalent in all living organisms, and methods that aid the understanding of their functional roles are essential. RNA secondary structure, the pattern of base-pairing, contains the critical information for determining the three dimensional structure and function of the molecule. In this work we examine whether the basic geometric and topological properties of secondary structure are sufficient to distinguish between RNA families in a learning framework. First, we develop a labeled dual graph representation of RNA secondary structure by adding biologically meaningful labels to the dual graphs proposed by Gan et al [1]. Next, we define a similarity measure directly on the labeled dual graphs using the recently developed marginalized kernels [2]. Using this similarity measure, we were able to train Support Vector Machine classifiers to distinguish RNAs of known families from random RNAs with similar statistics. For 22 of the 25 families tested, the classifier achieved better than 70% accuracy, with much higher accuracy rates for some families. Training a set of classifiers to automatically assign family labels to RNAs using a one vs. all multi-class scheme also yielded encouraging …

The most commonly discussed measures of microstructure in composite materials are the spatial correlation functions, which in a porous medium measure either the grain-to-grain correlations, or the pore-to-pore correlations in space. Improved bounds based on this information such as the Beran-Molyneux bounds for bulk modulus and the Beran bounds for conductivity are well-known. It is first shown here how to make direct use of this information to provide estimates that always lie between these upper and lower bounds for any microstructure whenever the microgeometry parameters are known. Then comparisons are made between these estimates, the bounds, and two new types of estimates. One new estimate for elastic constants makes use of the Peselnick-Meister bounds (based on Hashin-Shtrikman methods) for random polycrystals of laminates to generate self-consistent values that always lie between the bounds. A second new type of estimate for conductivity assumes that measurements of formation factors (of which there are at least two distinct types in porous media, associated respectively with pores and grains) are available, and computes new bounds based on this information. The paper compares and contrasts these various methods in order to clarify just what microstructural information and how precisely that information needs to be known …

Carbon dioxide (CO{sub 2}) injection into deep geologic formations could decrease the atmospheric accumulation of this gas from anthropogenic sources. Furthermore, by co-injecting H{sub 2}S or SO{sub 2}, the products respectively of coal gasification or combustion, with captured CO{sub 2}, problems associated with surface disposal would be mitigated. We developed models that simulate the co-injection of H{sub 2}S or SO{sub 2} with CO{sub 2} into an arkose formation at a depth of about 2 km and 75 C. The hydrogeology and mineralogy of the injected formation are typical of those encountered in Gulf Coast aquifers of the United States. Six numerical simulations of a simplified 1-D radial region surrounding the injection well were performed. The injection of CO{sub 2} alone or co-injection with SO{sub 2} or H{sub 2}S results in a concentrically zoned distribution of secondary minerals surrounding a leached and acidified region adjacent to the injection well. Co-injection of SO{sub 2} with CO{sub 2} results in a larger and more strongly acidified zone, and alteration differs substantially from that caused by the co-injection of H{sub 2}S or injection of CO{sub 2} alone. Precipitation of carbonates occurs within a higher pH (pH > 5) peripheral zone. Significant quantities of CO{sub …

Plasma oxidation was used to obtain radiocarbon dates on six different materials from a naturally mummified baby bundle from the Lower Pecos River region of southwest Texas. This bundle was selected because it was thought to represent a single event and would illustrate the accuracy and precision of the plasma oxidation method. Five of the materials were clearly components of the original bundle with 13 dates combined to yield a weighted average of 2135 {+-} 11 B.P. Six dates from a wooden stick of Desert Ash averaged 939 {+-} 14 B.P., indicating that this artifact was not part of the original burial. Plasma oxidation is shown to be a virtually non-destructive alternative to combustion. Because only sub-milligram amounts of material are removed from an artifact over its exposed surface, no visible change in fragile materials has been observed, even under magnification. The method is best applied when natural organic contamination is unlikely and serious consideration of this issue is needed in all cases. If organic contamination is present, it will have to be removed before plasma oxidation to obtain accurate radiocarbon dates.

Current designs for inertial confinement fusion capsules for the National Ignition Facility (NIF) consist of a solid deuterium-tritium (D-T) fuel layer inside of a copper doped beryllium capsule. Phase contrast enhanced x-ray imaging is shown to render the D-T layer visible inside the Be(Cu) capsule. Phase contrast imaging is experimentally demonstrated for several surrogate capsules and validates computational models. Polyimide and low density divinyl benzene foam capsules were imaged at the Advanced Photon Source synchrotron. The surrogates demonstrate that phase contrast enhanced imaging provides a method to characterize surfaces when absorption imaging cannot be used. Our computational models demonstrate that a rough surface can be accurately reproduced in phase contrast enhanced x-ray images.

Perturbations on an interface driven by a strong blast wave grow in time due to a combination of Rayleigh-Taylor, Richtmyer-Meshkov, and decompression effects. In this paper, we present the first results from a computational study of such a system under drive conditions to be attainable on the National Ignition Facility. Using the multiphysics, AMR, higher order Godunov Eulerian hydrocode, Raptor, we consider the late nonlinear instability evolution for multiple amplitude and phase realizations of a variety of multimode spectral types. We show that compressibility effects preclude the emergence of a regime of self-similar instability growth independent of the initial conditions by allowing for memory of the initial conditions to be retained in the mix-width at all times. The loss of transverse spectral information is demonstrated, however, along with the existence of a quasi-self-similar regime over short time intervals. The initial conditions are shown to have a strong affect on the time to transition to the quasi-self-similar regime.

The effect of preparation conditions on the structural and optical properties of silicon nanoparticles is investigated. Nanoscale reconstructions, unique to curved nanosurfaces, are presented for silicon nanocrystals and shown to have lower energy and larger optical gaps than bulk-derived structures. We find that high-temperature synthesis processes can produce metastable non-crystalline nanostructures with different core structures than bulk-derived crystalline clusters. The type of core structure that forms from a given synthesis process may depend on the passivation mechanism and time scale. The effect of oxygen on the optical of different types of silicon structures is calculated. In contrast to the behavior of bulk-like nanostructures, for non-crystalline and reconstructed crystalline structures surface oxygen atoms do not decrease the gap. In some cases, the presence of oxygen atoms at the nanocluster surface can significantly increase the optical absorption gap, due to decreased angular distortion of the silicon bonds. The relationship between strain and the optical gap in silicon nanoclusters is discussed.

Models with low-scale breaking of global symmetries in the neutrino sector provide an alternative to the seesaw mechanism for understanding why neutrinos are light. Such models can easily incorporate light sterile neutrinos required by the LSND experiment. Furthermore, the constraints on the sterile neutrino properties from nucleosynthesis and large scale structure can be removed due to the non-conventional cosmological evolution of neutrino masses and densities. We present explicit, fully realistic supersymmetric models, and discuss the characteristic signatures predicted in the angular distributions of the cosmic microwave background.

Grain size is a critically important aspect of polycrystalline materials and experimental observations on Cu and Al polycrystals have shown that a Hall-Petchtype phenomenon does exist at the onset of plastic deformation. In this work, a parametric study is conducted to investigate the effect of microstructural and deformation-related length scales on the behavior of such FCC polycrystals. It relies on a recently proposed non-local dislocation-mechanics based crystallographic theory to describe the evolution of dislocation mean spacings within each grain, and on finite element techniques to incorporate explicitly grain interaction effects. Polycrystals are modeled as representative volume elements (RVEs) containing up to 64 randomly oriented grains. Predictions obtained from RVEs of Cu polycrystals with different grain sizes are shown to be consistent with experimental data. Furthermore, mesh sensitivity studies revealed that, when there is a predominance of geometrically necessary dislocations (GNDs) relative to statistically-stored dislocations (SSDs), the polycrystal response becomes increasingly mesh sensitive. This was found to occur specially during the early stages of deformation in polycrystals with small grains.

This report describes the focusing solenoid for the proposed Muon Ionization Cooling Experiment (MICE) [1]. The focusing solenoid consists of a pair of superconducting solenoids that are on a common bobbin. The two coils, which have separate leads, may be operated in the same polarity or at opposite polarity. This report discusses the superconducting magnet design and the cryostat design for the MICE focusing module. Also discussed is how this superconducting magnet can be integrated with a pair of small 4.2 K coolers.

The focusing solenoids for MICE surround energy absorbers that are used to reduce the transverse momentum of the muon beam that is being cooled within MICE. The focusing solenoids will have a warm-bore diameter of 470 mm. Within this bore is a flask of liquid hydrogen or a room temperature beryllium absorber. The focusing solenoid consists of two coils wound with a copper matrix Nb-Ti conductor originally designed for MRI magnets. The two coils have separate leads, so that they may be operated at the same polarity or at opposite polarity. The focusing magnet is designed so that it can be cooled with a pair of 1.5 W (at 4.2 K) coolers. The MICE cooling channel has three focusing magnets with their absorbers. The three focusing magnets will be hooked together in series for a circuit stored-energy of about 9.0 MJ. Quench protection for the focusing magnets is discussed. This report presents the mechanical and thermal design parameters for this magnet, including the results of finite element calculations of mechanical forces and heat flow in the magnet cold mass.

We discuss energy efficiency and renewable energy investments in Eritrea from the strategic long-term economic perspective of meeting Eritrea's sustainable development goals and reducing greenhouse gas emissions. Energy efficiency and renewable energy are potentially important contributors to national productive capital accumulation, enhancement of the environment, expansion of energy services, increases in household standard of living, and improvements in health. In this study we develop a spreadsheet model for calculating some of the national benefits and costs of different levels of investment in energy efficiency and renewable energy. We then present the results of the model in terms of investment demand and investment scenario curves. These curves express the contribution that efficiency and renewable energy projects can make in terms of reduced energy sector operating expenses, and reduced carbon emissions. We provide demand and supply curves that show the rate of return, the cost of carbon emissions reductions vs. supply, and the evolution of the marginal carbon emissions per dollar of GDP for different investment levels and different fuel-type subsectors.

This report discusses the results from the rupture of a thin window that is part of a 20-liter liquid hydrogen vessel. This rupture will spill liquid hydrogen onto the walls and bottom of a 300 K cylindrical vacuum vessel. The spilled hydrogen goes into film boiling, which removes the thermal energy from the vacuum vessel wall. This report analyzes the transient heat transfer in the vessel and calculates the thermal deflection and stress that will result from the boiling liquid in contact with the vessel walls. This analysis was applied to aluminum and stainless steel vessels.

In the process of Savannah River Site (SRS) operations limited amounts of waste are generated containing petroleum, and radiological contaminated soils. Currently, this combination of radiological and petroleum contaminated waste does not have an immediate disposal route and is being stored in low activity vaults. SRS developed and implemented a successful plan for clean up of the petroleum portion of the soils in situ using simple, inexpensive, bioreactor technology. Treatment in a bioreactor removes the petroleum contamination from the soil without spreading radiological contamination to the environment. This bioreactor uses the bioventing process and bioaugmentation or the addition of the select hydrocarbon degrading bacteria. Oxygen is usually the initial rate-limiting factor in the biodegradation of petroleum hydrocarbons. Using the bioventing process allowed control of the supply of nutrients and moisture based on petroleum contamination concentrations and soil type. The results of this work have proven to be a safe and cost-effective means of cleaning up low level radiological and petroleum-contaminated soil. Many of the other elements of the bioreactor design were developed or enhanced during the demonstration of a ''biopile'' to treat the soils beneath a Polish oil refinery's waste disposal lagoons. Aerobic microorganisms were isolated from the aged refinery's …

As part of the vibration budget study for the NLC Main Linac components, the vibration sources in the NLC modules (Girder) are under investigation. The activity is focused on the effect of cooling water flow on the structures (FXB type) stability, the transmission of vibrations to the adjacent components, and the effect of different materials of construction used for the supports. Experimental data and ANSYS simulations have been compared. This paper reports on the ongoing work.

Operating and improving the understanding of the Fermilab Accelerator Complex for the colliding beam experiments requires advanced software methods and tools. The Shot Data Acquisition and Analysis (SDA) has been developed to fulfill this need. The SDA takes a standard set of critical data at relevant stages during the complex series of beam manipulations leading to {radical}(s) {approx} 2 TeV collisions. Data is stored in a relational database, and is served to programs and users via Web based tools. Summary tables are systematically generated during and after a store. Written entirely in Java, SDA supports both interactive tools and application interfaces used for in-depth analysis. In this talk, we present the architecture and described some of our analysis tools. We also present some results on the recent Tevatron performance as illustrations of the capabilities of SDA.

The acceleration of the expansion of the universe, ascribed to a dark energy, is one of the most intriguing discoveries in science. In addition to precise, systematics controlled data, clear, robust interpretation of the observations is required to reveal the nature of dark energy. Even for the simplest question: is the data consistent with the cosmological constant? there are important subtleties in the reconstruction of the dark energy properties. We discuss the roles of analysis both in terms of the Hubble expansion rate or dark energy density {rho}DE(z) and in terms of the dark energy equation of state w(z), arguing that each has its carefully defined place. Fitting the density is best for learning about the density, but using it to probe the equation of state can lead to instability and bias.

Achievement of atomic-resolution electron-beam tomography will allow determination of the three-dimensional structure of nanoparticles (and other suitable specimens) at atomic resolution. Three-dimensional reconstructions will yield ''section'' images that resolve atoms overlapped in normal electron microscope images (projections), resolving lighter atoms such as oxygen in the presence of heavier atoms, and atoms that lie on non-lattice sites such as those in non-periodic defect structures. Our first demonstrations of 3-D reconstruction to atomic resolution used five zone-axis images from test specimens of staurolite consisting of a mix of light and heavy atoms. We propose combining ultra-high (sub-Angstrom) resolution zone-axis images with off-zone images by first using linear reconstruction of the off-zone images while excluding images obtained within a small range of tilts (of the order of 60 milliradian) of any zone-axis orientation, since it has been shown that dynamical effects can be mitigated by slight off-axis tilt of the specimen. The (partial) reconstruction would then be used as a model for forward calculation by image simulation in zone-axis directions and the structure refined iteratively to achieve satisfactory fits with the experimental zone-axis data. Another path to atomic-resolution tomography would combine ''zone-axis tomography'' with high-resolution dark-field hollow-cone (DFHC) imaging. Electron diffraction theory indicates …

In T-duality invariant effective supergravity with gaugino condensation as the mechanism for supersymmetry breaking, there is a residual discrete symmetry that could play the role of R-parity in supersymmetric extensions of the Standard Model.

We present the first data on e{sup +}e{sup -} pair production accompanied by nuclear breakup in ultra-peripheral gold-gold collisions at a center of mass energy of 200 GeV per nucleon pair. The nuclear breakup requirement selects events at small impact parameters, where higher-order corrections to the pair production cross section should be enhanced. We compare the pair kinematic distributions with two calculations: one based on the equivalent photon approximation, and the other using lowest-order quantum electrodynamics (QED); the latter includes the photon virtuality. The cross section, pair mass, rapidity and angular distributions are in good agreement with both calculations. The pair transverse momentum, p{sub T}, spectrum agrees with the QED calculation, but not with the equivalent photon approach. We set limits on higher-order contributions to the cross section. The e{sup +} and e{sup -} p{sub T} spectra are similar, with no evidence for interference effects due to higher-order diagrams.

Detailed STRUCT simulations are performed on beam loss rates in the vicinity of the BTeV detector in the Tevatron CO interaction region due to beam-gas nuclear elastic interactions and out-scattering from the collimation system. Corresponding showers induced in the machine components and background rates in BTeV are modeled with the MARS14 code. It is shown that the combination of a steel collimator and concrete shielding wall located in front of the detector can reduce the accelerator-related background rates in the detector by an order of magnitude.

GaAs Blocked-Impurity-Band (BIB) photoconductor detectors have the potential to become the most sensitive, low noise detectors in the far-infrared below 45.5 cm{sup -1} (220 {micro}m). We have studied the characteristics of liquid phase epitaxial GaAs films relevant to BIB production, including impurity band formation and the infrared absorption of the active section of the device. Knowledge of the far-infrared absorption spectrum as a function of donor concentration combined with variable temperature Hall effect and resistivity studies leads us to conclude that the optimal concentration for the absorbing layer of a GaAs BIB detector lies between 1 x 10{sup 15} and 6.7 x 10{sup 15} cm{sup -3}. At these concentrations there is significant wavefunction overlap which in turn leads to absorption beyond the 1s ground to 2p bound excited state transition of 35.5 cm{sup -1} (282 {micro}m). There still remains a gap between the upper edge of the donor band and the bottom of the conduction band, a necessity for proper BIB detector operation.

Since about 5 years, Apple-II type Elliptically Polarizing Undulators (EPU) have been used very successfully at the ALS to generate high brightness photon beams with arbitrary polarization. However, both EPUs installed so far cause significant changes of the vertical beamsize, especially when the row phase is changed to change the polarization of the photons emitted. Detailed measurements indicate this is caused by a row phase dependent skew quadrupole term in the EPUs. Magnetic measurements revealed the same effect for the third EPU to be installed later this year. All measurements to identify and quantify the effect with beam will be presented, as well as some results of magnetic bench measurements and numeric field simulations.

The nature of dark energy is of such fundamental importance -- yet such a mystery -- that a dedicated dark energy experiment should be as comprehensive and powerfully incisive as possible. The Supernova/Acceleration Probe robustly controls for a wide variety of systematic uncertainties, employing the Type Ia supernova distance method, with high signal to noise light curves and spectra over the full redshift range from z=0.1-1.7, and the weak gravitational lensing method with an accurate and stable point spread function.