Article on genome-wide analysis of phenylpropanoid defence pathways.

1. Objective: A method to determine whether beryllium (Be) components in surface swipe samples are from a natural source is needed. 2. Methods: Soil samples and surface swipes from area facilities were analyzed for marker elements to identify source pathways for beryllium (Be). To be useful, the natural marker element must be present at reasonably consistent levels across the site, must correlate with the Be concentration, and not have the potential to be present from non-natural sources. 3. Results: The research on marker elements used to identify source pathways for beryllium (Be) concentrations demonstrates a clear correlation between Be and yttrium (Y) in natural soils on the Nevada National Security Site. The Y/Be ratio is proposed as a method to characterize the source of Be in soil and surface swipe samples and to aid in recommendations for follow up actions. Swipe samples are analyzed using an ICP/MS method and compared with results from soil samples. Natural soil constituent levels and the Y/Be Ratio range is determined for the occupied and historical facilities and surrounding areas. Y/Be ratios within the statistical range established indicate the Be is from a natural source. Y/Be ratios lower than this range indicate the presence of …

In the current X-ray crystallographic structural models of photosystem II, Glu354 of the CP43 polypeptide is the only amino acid ligand of the oxygen-evolving Mn4Ca cluster that is not provided by the D1 polypeptide. To further explore the influence of this structurally unique residue on the properties of the Mn4Ca cluster, the CP43-E354Q mutant of the cyanobacterium Synechocystis sp. PCC 6803 was characterized with a variety of biophysical and spectroscopic methods, including polarography, EPR, X-ray Absorption, FTIR, and mass spectrometry. The kinetics of oxygen release in the mutant were essentially unchanged from those in wild-type. In addition, the oxygen flash-yields exhibited normal period-four oscillations having normal S state parameters, although the yields were lower, correlating with the mutant?s lower steady-state rate (approx. 20percent compared to wild-type). Experiments conducted with H218O showed that the fast and slow phases of substrate water exchange in CP43-E354Q thylakoid membranes were accelerated 8.5- and 1.8-fold, respectively, in the S3 state compared to wild-type. Purified oxygen-evolving CP43-E354Q PSII core complexes exhibited a slightly altered S1 state Mn-EXAFS spectrum, a slightly altered S2 state multiline EPR signal, a substantially altered S2-minus-S1 FTIR difference spectrum, and an unusually long lifetime for the S2 state (> 10 hours) in …

We report the results of semiclassical calculations of the asymmetric molecular-frame photoelectron angular distributions for C 1s ionization of CO{sub 2} measured with respect to the CO{sup +} and O{sup +} ions produced by subsequent Auger decay, and show how the decay event can be used to probe ultrafast molecular dynamics of the transient cation. The fixed-nuclei photoionization amplitudes were constructed using variationally obtained electron-molecular ion scattering wave functions. The amplitudes are then used in a semiclassical manner to investigate their dependence on the nuclear dynamics of the cation. The method introduced here can be used to study other core-level ionization events.

The chemical interface structure between phosphorus-doped hydrogenated amorphous silicon and aluminum-doped zinc oxide thin films is investigated with soft x-ray emission spectroscopy (XES) before and after solid-phase crystallization (SPC) at 600C. In addition to the expected SPC-induced phase transition from amorphous to polycrystalline silicon, our XES data indicates a pronounced chemical interaction at the buried Si/ZnO interface. In particular, we find an SPC-enhanced formation of Si-O bonds and the accumulation of Zn in close proximity to the interface. For an assumed closed and homogeneous SiO2 interlayer, an effective thickness of (5+2)nm after SPC could be estimated.

We report time-resolved Kerr effect measurements of magnetization dynamics in ferromagnetic SrRuO{sub 3}. We observe that the demagnetization time slows substantially at temperatures within 15K of the Curie temperature, which is {approx} 150K. We analyze the data with a phenomenological model that relates the demagnetization time to the spin flip time. In agreement with our observations the model yields a demagnetization time that is inversely proportional to T-T{sub c}. We also make a direct comparison of the spin flip rate and the Gilbert damping coefficient showing that their ratio very close to k{sub B}T{sub c}, indicating a common origin for these phenomena.

This work investigated the thermoelectric properties of thin silicon membranes that have been decorated with high density of nanoscopic holes. These ?holey silicon? (HS) structures were fabricated by either nanosphere or block-copolymer lithography, both of which are scalable for practical device application. By reducing the pitch of the hexagonal holey pattern down to 55 nm with 35percent porosity, the thermal conductivity of HS is consistently reduced by 2 orders of magnitude and approaches the amorphous limit. With a ZT value of 0.4 at room temperature, the thermoelectric performance of HS is comparable with the best value recorded in silicon nanowire system.

Over the past decades, it has been well established that the mechanical behavior of materials changes when they are confined geometrically at least in one dimension to small scale. It is the aim of the 2010 Gordon Conference on 'Thin Film and Small Scale Mechanical Behavior' to discuss cutting-edge research on elastic, plastic and time-dependent deformation as well as degradation mechanisms like fracture, fatigue and wear at small scales. As in the past, the conference will benefit from contributions from fundamental studies of physical mechanisms linked to material science and engineering reaching towards application in modern applications ranging from optical and microelectronic devices and nano- or micro-electrical mechanical systems to devices for energy production and storage. The conference will feature entirely new testing methodologies and in situ measurements as well as recent progress in atomistic and micromechanical modeling. Particularly, emerging topics in the area of energy conversion and storage, such as material for batteries will be highlighted. The study of small-scale mechanical phenomena in systems related to energy production, conversion or storage offer an enticing opportunity to materials scientists, who can provide new insight and investigate these phenomena with methods that have not previously been exploited.

We present a state-of-the-art compilation of the existing bottom production cross sections in elementary collisions, from fixed-target to collider experiments. We then discuss the theoretical uncertainties on the total and differential bottom cross sections in the FONLL approach. In particular, we show total cross sections and kinematical distributions of the bottom hadrons and their decays: B {yields} e/{mu}X, B {yields} D {yields} e/{mu}, and B {yields} J/{psi}X. After seeing that the calculations give a good description of the existing measurements, we present detailed predictions for the LHC experiments in their specific phase space windows. Recent improvements in heavy quark production theory and experimental measurements at colliders, especially for bottom production, have shown that the perturbative QCD framework seems to work rather well, see Refs. [1, 2]. It is important to continue to validate this theoretical framework and its phenomenological inputs, extracted from other measurements, with new data such as that obtained by the CMS collaboration in pp collisions at {radical}s = 7 TeV. We validate the FONLL approach with lower energy data and also compare the results with preliminary LHC data. By showing good agreement between the calculations and the data, we demonstrate we can confidently extrapolate our results to …

The level of 'anomalous' charmonium suppression in high-energy heavy-ion collisions and its interpretation as a signal of quark-gluon plasma formation requires a robust understanding of charmonium production and absorption in proton-nucleus collisions. In a previous study we have shown that, contrary to common belief, the so-called J/{psi} 'absorption cross section', {sigma}{sub abs}{sup J/{psi}}, is not a 'universal constant' but, rather, an effective parameter that depends very significantly on the charmonium rapidity and on the collision energy. Here we present ugraded Glauber calculations with the EPS09 parameterization of nuclear modifications of the parton densities. We confirm that the effective 'absorption cross section' depends on the J/{psi} kinematics and the collision energy. We also make further steps towards understanding the physics of the mechanisms behind the observed 'cold nuclear matter' effects.

The Environmental Management (EM) mission is to complete the safe cleanup of the environmental legacy brought about from five decades of nuclear weapons development and government-sponsored nuclear energy research. The EM program has embraced a mission completion philosophy based on reducing risk and environmental liability over a 40-50 year lifecycle. The Department has made great progress toward safely disposing of its legacy nuclear waste. EM Research and Development (R&D) program management strategies have driven numerous technology and engineering innovations to reduce risk, minimize cleanup costs, and reduce schedules. Engineering and technology investments have provided the engineering foundation, technical assistance, approaches, and technologies that have contributed to moving the cleanup effort forward. These successes include start-up and operation of several waste treatment facilities and processes at the sites.

The GRC series on Membranes: Materials and Processes have gained significant international recognition, attracting leading experts on membranes and other related areas from around the world. It is now known for being an interdisciplinary and synergistic meeting. The next summer's edition will keep with the past tradition and include new, exciting aspects of material science, chemistry, chemical engineering, computer simulation with participants from academia, industry and national laboratories. This edition will focus on cutting edge topics of membranes for addressing several grand challenges facing our society, in particular, energy, water, health and more generally sustainability. During the technical program, we want to discuss new membrane structure and characterization techniques, the role of advanced membranes and membrane-based processes in sustainability/environment (including carbon dioxide capture), membranes in water processes, and membranes for biological and life support applications. As usual, the informal nature of the meeting, excellent quality of the oral presentations and posters, and ample opportunity to meet many outstanding colleagues make this an excellent conference for established scientists as well as for students. A Gordon Research Seminar (GRS) on the weekend prior to the GRC meeting will provide young researchers an opportunity to present their work and network with outstanding experts. …

We describe our new methodology for Adaptive Smoothed Particle Hydrodynamics (ASPH) and its application to problems in modeling material failure. We find that ASPH is often crucial for properly modeling such experiments, since in most cases the strain placed on materials is non-isotropic (such as a stretching rod), and without the directional adaptability of ASPH numerical failure due to SPH nodes losing contact in the straining direction can compete with or exceed the physical process of failure.

The National Ignition Facility (NIF), the world's largest and most energetic laser system, is now operational at Lawrence Livermore National Laboratory. A key goal of the NIF is to demonstrate fusion ignition for the first time in the laboratory. Its flexibility allows multiple target designs (both indirect and direct drive) to be fielded, offering substantial scope for optimization of a robust target design. In this paper we discuss an approach to generating gigawatt levels of electrical power from a laser-driven source of fusion neutrons based on these demonstration experiments. This 'LIFE' concept enables rapid time-to-market for a commercial power plant, assuming success with ignition and a technology demonstration program that links directly to a facility design and construction project. The LIFE design makes use of recent advances in diode-pumped, solid-state laser technology. It adopts the paradigm of Line Replaceable Units utilized on the NIF to provide high levels of availability and maintainability and mitigate the need for advanced materials development. A demonstration LIFE plant based on these design principles is described, along with the areas of technology development required prior to plant construction. A goal-oriented, evidence-based approach has been proposed to allow LIFE power plant rollout on a time scale …

The new ohmic heating (OH) coil and center stack for the National Spherical Torus Experiment (NSTX) upgrade are required to meet cooling and structural requirements for operation at the enhanced 1 Tesla toroidal field and 2 MA plasma current. The OH coil is designed to be cooled in the time between discharges by water flowing in the center of the coil conductor. We performed resistive heating and thermal hydraulic analyses to optimize coolant channel size to keep the coil temperature below 100 C and meet the required 20 minute cooling time. Coupled electromagnetic, thermal and structural FEA analyses were performed to determine if the OH coil meets the requirements of the structural design criteria. Structural response of the OH coil to its self-field and the field from other coils was analyzed. A model was developed to analyze the thermal and electromagnetic interaction of centerstack components such as the OH coil, TF inner legs and the Bellville washer preload mechanism. Torsional loads from the TF interaction with the OH and poloidal fields are transferred through the TF flag extensions via a torque transfer coupling to the rest of the tokamak structure. A 3D FEA analysis was performed to qualify this design. …

We give an overview of a number of algebraic multigrid methods targeting finite element discretization problems. The focus is on the properties of the constructed hierarchy of coarse spaces that guarantee (two-grid) convergence. In particular, a necessary condition known as 'weak approximation property', and a sufficient one, referred to as 'strong approximation property' are discussed. Their role in proving convergence of the TG method (as iterative method) and also on the approximation properties of the AMG coarse spaces if used as discretization tool is pointed out. Some preliminary numerical results illustrating the latter aspect are also reported.

A plasma lens, consisting of a solenoid and potential-defining ring electrodes, has been placed between a magnetron and substrates to be coated. Photography reveals qualitative information on excitation, ionization, and the transport of plasma to the substrate.

GyPSuM is a tomographic model fo mantle seismic shear wave (S) speeds, compressional wave (P) speeds and detailed density anomalies that drive mantle flow. the model is developed through simultaneous inversion of seismic body wave travel times (P and S) and geodynamic observations while considering realistic mineral physics parameters linking the relative behavior of mantle properties (wave speeds and density). Geodynamic observations include the (up to degree 16) global free-air gravity field, divergence of the tectonic plates, dynamic topography of the free surface, and the flow-induced excess ellipticity of the core-mantle boundary. GyPSuM is built with the philosophy that heterogeneity that most closely resembles thermal variations is the simplest possible solution. Models of the density field from Earth's free oscillations have provided great insight into the density configuration of the mantle; but are limited to very long-wavelength solutions. Alternatively, simply scaling higher resolution seismic images to density anomalies generates density fields that do not satisfy geodynamic observations. The current study provides detailed density structures in the mantle while directly satisfying geodynamic observations through a joint seismic-geodynamic inversion process. Notable density field observations include high-density piles at the base of the superplume structures, supporting the fundamental results of past normal mode …

A series of ceramic waste forms were developed and characterized for the immobilization of a Cesium/Lanthanide (CS/LN) waste stream anticipated to result from nuclear fuel reprocessing. Simple raw materials, including Al{sub 2}O{sub 3} and TiO{sub 2} were combined with simulated waste components to produce multiphase ceramics containing hollandite-type phases, perovskites (particularly BaTiO{sub 3}), pyrochlores and other minor metal titanate phases. Three fabrication methodologies were used, including melting and crystallizing, pressing and sintering, and Spark Plasma Sintering (SPS), with the intent of studying phase evolution under various sintering conditions. X-Ray Diffraction (XRD) and Scanning Electron Microscopy coupled with Energy Dispersive Spectroscopy (SEM/EDS) results showed that the partitioning of the waste elements in the sintered materials was very similar, despite varying stoichiometry of the phases formed. Identification of excess Al{sub 2}O{sub 3} via XRD and SEM/EDS in the first series of compositions led to a Phase II study, with significantly reduced Al{sub 2}O{sub 3} concentrations and increased waste loadings. The Phase II compositions generally contained a reduced amount of unreacted Al{sub 2}O{sub 3} as identified by XRD. Chemical composition measurements showed no significant issues with meeting the target compositions. However, volatilization of Cs and Mo was identified, particularly during melting, since sintering …

Space-charge neutralization is required to compress and focus a pulsed, high-current ion beam on a target for warm dense matter physics or heavy ion fusion experiments. We described approaches to produce dense plasma in and near the final focusing solenoid through which the ion beam travels, thereby providing an opportunity for the beam to acquire the necessary space-charge compensating electrons. Among the options are plasma injection from pulsed vacuum arc sources located outside the solenoid, and using a high current (> 4 kA) pulsed vacuum arc plasma from a ring cathode near the edge of the solenoid. The plasma distribution is characterized by photographic means, by an array of movable Langmuir probes, by a small single probe, and by evaluating Stark broadening of the Balmer H beta spectral line. In the main approach described here, the plasma is produced at several cathode spots distributed azimuthally on the ring cathode. It is shown that the plasma is essentially hollow, as determined by the structure of the magnetic field, though the plasma density exceeds 1014 cm-3 in practically all zones of the solenoid volume if the ring electrode is placed a few centimeters off the center of the solenoid. The plasma is …

We study the initial and final state interaction effects in the transverse momentum dependent parton distributions in the small-x saturation region. In particular, we discuss the quark distributions in the semi-inclusive deep inelastic scattering, Drell-Yan lepton pair production and dijet-correlation processes in pA collisions. We calculate the quark distributions in the scalar-QED model and then extend to the color glass condensate formalism in QCD. The quark distributions are found universal between the DIS and Drell-Yan processes. On the other hand, the quark distribution from the qq'-->qq' channel contribution to the dijet-correlation process is not universal. However, we find that it can be related to the quark distribution in DIS process by a convolution with the normalized unintegrated gluon distribution in the CGC formalism in the large Nc limit.

The Morse-Smale (MS) complex has proven to be a useful tool in extracting and visualizing features from scalar-valued data. However, existing algorithms to compute the MS complex are restricted to either piecewise linear or discrete scalar fields. This paper presents a new combinatorial algorithm to compute MS complexes for two dimensional piecewise bilinear functions defined on quadrilateral meshes. We derive a new invariant of the gradient flow within a bilinear cell and use it to develop a provably correct computation which is unaffected by numerical instabilities. This includes a combinatorial algorithm to detect and classify critical points as well as a way to determine the asymptotes of cell-based saddles and their intersection with cell edges. Finally, we introduce a simple data structure to compute and store integral lines on quadrilateral meshes which by construction prevents intersections and enables us to enforce constraints on the gradient flow to preserve known invariants.

The sudden release of toxic contaminants that reach indoor spaces can be hazardous to building occupants. For an acutely toxic contaminant, the speed of the emergency response strongly influences the consequences to occupants. The design of a real time sensor system is made challenging both by the urgency and complex nature of the event, and by the imperfect sensors and models available to describe it. In this research, we use Bayesian modeling to combine information from multiple types of sensors to improve the characterization of a release. We discuss conceptual and algorithmic considerations for selecting and fusing information from disparate sensors. To explore system performance, we use both real tracer gas data from experiments in a three story building, along with synthetic data, including information from door position sensors. The added information from door position sensors is found to be useful for many scenarios, but not always. We discuss the physical conditions and design factors that affect these results, such as the influence of the door positions on contaminant transport. We highlight potential benefits of multisensor data fusion, challenges in realizing those benefits, and opportunities for further improvement.

A ring cathode for a pulsed, high-current, multi-spot cathodic arc discharge was placed inside a pulsed magnetic solenoid. Photography is used to evaluate the plasma distribution. The plasma appears hollow for cathode positions close the center of the solenoid, and it is guided closer to the axis when the cathode is away from the center.