Estimates of the quality of experimental maps are important in many stages of structure determination of macromolecules. Map quality is defined here as the correlation between a map and the map calculated based on a final refined model. Here we examine 10 different measures of experimental map quality using a set of 1359 maps calculated by reanalysis of 246 solved MAD, SAD, and MIR datasets. A simple Bayesian approach to estimation of map quality from one or more measures is presented. We find that a Bayesian estimator based on the skew of histograms of electron density is the most accurate of the 10 individual Bayesian estimators of map quality examined, with a correlation between estimated and actual map quality of 0.90. A combination of the skew of electron density with the local correlation of rms density gives a further improvement in estimating map quality, with an overall correlation coefficient of 0.92. The PHENIX AutoSol Wizard carries out automated structure solution based on any combination of SAD, MAD, SIR, or MIR datasets. The Wizard is based on tools from the PHENIX package and uses the Bayesian estimates of map quality described here to choose the highest-quality solutions after experimental phasing.

The incongruous"unexpected inapplicability of the [Crook's fluctuation theorem]" is due to an inexplicable, inappropriate use of inconsistent expressions. The girding is secure.

This work summarizes a two-year study by the U.S. Federal Methane Hydrate Advisory Committee recommending the future needs for federally-supported hydrate research. The Report was submitted to the US Congress on August 14, 2007 and includes four recommendations regarding (a) permafrost hydrate production testing, (b) marine hydrate viability assessment (c) climate effect of hydrates, and (d) international cooperation. A secure supply of natural gas is a vital goal of the U.S. national energy policy because natural gas is the cleanest and most widely used of all fossil fuels. The inherent cleanliness of natural gas, with the lowest CO2 emission per unit of heat energy of any fossil fuel, means substituting gas for coal and fuel oil will reduce emissions that can exacerbate the greenhouse effect. Both a fuel and a feedstock, a secure and reasonably priced supply of natural gas is important to industry, electric power generators, large and small commercial enterprises, and homeowners. Because each volume of solid gas hydrate contains as much as 164 standard volumes of methane, hydrates can be viewed as a concentrated form of natural gas equivalent to compressed gas but less concentrated than liquefied natural gas (LNG). Natural hydrate accumulations worldwide are estimated to …

In this paper, we report on studies of ion back bombardment in high average current dc and rf photoinjectors using a particle-in-cell/Monte Carlo method. Using H{sub 2} ion as an example, we observed that the ion density and energy deposition on the photocathode in rf guns are order of magnitude lower than that in a dc gun. A higher rf frequency helps mitigate the ion back bombardment of the cathode in rf guns.

The bacterial diversity associated with citrus leaf midribs was characterized 1 from citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rDNA microarray and 16S rDNA clone library sequencing to determine the microbial community composition of symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria from 15 phyla were present in the citrus leaf midribs while 20 orders from phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs compared to asymptomatic midribs. Candidatus Liberibacter asiaticus (Las) was detected at a very low level in asymptomatic plants, but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis was further verified by sequencing 16S rDNA clone libraries, which indicated the dominance of Las in symptomatic leaves. These data implicate Las as the pathogen responsible for HLB disease. Citrus is the most important commercial fruit crop in Florida. In recent years, citrus Huanglongbing (HLB), also called citrus greening, has severely affected Florida's citrus production and …

We have successfully built and operated a source deployment system for the KamLAND detector. This system was used to position radioactive sources throughout the delicate 1-kton liquid scintillator volume, while meeting stringent material cleanliness, material compatibility, and safety requirements. The calibration data obtained with this device were used to fully characterize detector position and energy reconstruction biases. As a result, the uncertainty in the size of the detector fiducial volume was reduced by a factor of two. Prior to calibration with this system, the fiducial volume was the largest source of systematic uncertainty in measuring the number of antineutrinos detected by KamLAND. This paper describes the design, operation and performance of this unique calibration system.

Extreme ultraviolet (EUV) microscopy is an important tool for the investigation of the performance of EUV masks, for detecting the presence and the characteristics of defects, and for evaluating the effectiveness of defect repair techniques. Aerial image measurement bypasses the difficulties inherent to photoresist imaging and enables high data collection speed and flexibility. It provides reliable and quick feedback for the development of masks and lithography system modeling methods. We operate the SEMATECH Berkeley Actinic Inspection Tool (AIT), a EUV microscope installed at the Advanced Light Source at Lawrence Berkeley National Laboratory. The AIT is equipped with several high-magnification Fresnel zoneplate lenses, with various numerical aperture values, that enable it image the reflective mask surface with various resolution and magnification settings. Although the AIT has undergone significant recent improvements in terms of imaging resolution and illumination uniformity, there is still room for improvement. In the AIT, an off-axis zoneplate lens collects the light coming from the sample and an image of the sample is projected onto an EUV-sensitive CCD camera. The simplicity of the optical system is particularly helpful considering that the AIT alignment has to be performed every time that a sample or a zoneplate is replaced. The alignment …

Platinum nanocubes and nanopolyhedra with tunable size from 5 to 9 nm were synthesized by controlling the reducing rate of metal precursor ions in a one-pot polyol synthesis. A two-stage process is proposed for the simultaneous control of size and shape. In the first stage, the oxidation state of the metal ion precursors determined the nucleation rate and consequently the number of nuclei. The reaction temperature controlled the shape in the second stage by regulation of the growth kinetics. These well-defined nanocrystals were loaded into MCF-17 mesoporous silica for examination of catalytic properties. Pt loadings and dispersions of the supported catalysts were determined by elemental analysis (ICP-MS) and H2 chemisorption isotherms, respectively. Ethylene hydrogenation rates over the Pt nanocrystals were independent of both size and shape and comparable to Pt single crystals. For pyrrole hydrogenation, the nanocubes enhanced ring-opening ability and thus showed a higher selectivity to n-butylamine as compared to nanopolyhedra.

High-average-power free-electron lasers often rely on energy-recovering linacs. In a high-efficiency free electron laser, the main limitation to high average power stems from the fractional energy spread induced by the free-electron laser process. Managing beams with large fractional energy spread while simultaneously avoiding beam losses is extremely challenging and relies on intricate longitudinal phase space manipulations. In this paper we discuss a possible alternative technique that makes use of an emittance exchange between one of the transverse and the longitudinal phase spaces.

The IRT 2000 research reactor, operated by the Bulgarian Institute for Nuclear Research and Nuclear Energy (INRNE), safely shipped all of their Russian-origin nuclear fuel from the Republic of Bulgaria to the Russian Federation beginning in 2003 and completing in 2008. These fresh and spent fuel shipments removed all highly enriched uranium (HEU) from Bulgaria. The fresh fuel was shipped by air in December 2003 using trucks and a commercial cargo aircraft. One combined spent fuel shipment of HEU and low enriched uranium (LEU) was completed in July 2008 using high capacity VPVR/M casks transported by truck, barge, and rail. The HEU shipments were assisted by the Russian Research Reactor Fuel Return Program (RRRFR) and the LEU spent fuel shipment was funded by Bulgaria. This report describes the work, approvals, organizations, equipment, and agreements required to complete these shipments and concludes with several major lessons learned.

The CMS software stack currently consists of more than 2 Million lines of code developed by over 250 authors with a new version being released every week. CMS has setup a release validation process for quality assurance which enables the developers to compare to previous releases and references. This process provides the developers with reconstructed datasets of real data and MC samples. The samples span the whole range of detector effects and important physics signatures to benchmark the performance of the software. They are used to investigate interdependency effects of software packages and to find and fix bugs. The samples have to be available in a very short time after a release is published to fit into the streamlined CMS development cycle. The standard CMS processing infrastructure and dedicated resources at CERN and FNAL are used to achieve a very short turnaround of 24 hours. The here described release validation process is an integral part of CMS software development and contributes significantly to ensure stable production and analysis. It's success emphasizes the importance of a streamlined release validation process for projects with a large code basis and significant number of developers and can function as an example for future projects.

Current proton exchange membrane (PEM) technologies are inadequate to address the projected needs for fuel cell performance above 80 ºC. Continuing research into traditional ion carriers in novel membrane materials offers the promise of marginal improvement, representing only an evolutionary increase in performance. This conclusion is supported by the role of water in conduction. Thus, the key to better PEMs is not to eliminate water, but to change the role of water by developing ion carriers that will bind water more tightly than traditional sulfur or phosphorus based carriers resulting in materials that will conduct at higher temperatures. This change entails having a carrier structure that interacts more intimately with water and by increasing the ion carrier anionic charge to result in more tightly held inner shell protonated waters of hydration. Both of these factors synergistically act to maintain a critical water concentration at the carrier necessary for conduction. In this work, polyoxometalate (POM) clusters were selected to serve as these different proton carriers.

The Savannah River Site's HB-Line Facility completed a campaign in which fifty (50) cans of neptunium oxide were produced and shipped to the Idaho National Laboratory in the 9975 shipping container. This shipping campaign involved the addition of neptunium oxide to the 9975 Safety Analysis Report for Packaging (SARP) as a new content and subsequently a Letter of Amendment to the SARP content table. This paper will address the proper steps which should be taken to add a new content table to a SARP. It will also address the importance of product sampling and understanding the material shipping requirements of a SARP.

Understanding heat transport on nanoscale dimensions is important for fundamental advances in nanoscience, as well as for practical applications such as thermal management in nano-electronics, thermoelectric devices, photovoltaics, nanomanufacturing, as well as nanoparticle thermal therapy. Here we report the first time-resolved measurements of heat transport across nanostructured interfaces. We observe the transition from a diffusive to a ballistic thermal transport regime, with a corresponding increase in the interface resistivity for line widths smaller than the phonon mean free path in the substrate. Resistivities more than three times higher than the bulk value are measured for the smallest line widths of 65 nm. Our findings are relevant to the modeling and design of heat transport in nanoscale engineered systems, including nanoelectronics, photovoltaics and thermoelectric devices.

Fast magnetization dynamics in the micro- and nanometer regime are an interesting field of research. On these length scales magnetic structures can be designed to contain a single vortex or a single domain wall. Both size and speed of these patterns are of great interest in todays research for prospective non-volatile data storage devices. Especially the possibility to move domain-walls by spin-polarized current gained a lot of interest. Magnetic configurations can be imaged by soft X-ray magnetic microscopy with a spatial resolution down to 15 nm. By a stroboscopic pump and probe measurement scheme a temporal resolution below 100 ps is achieved. This provides the opportunity to directly image changes in magnetic domains and domain-wall motion. We image oscillations of a single domain wall in a confining potential in time steps of 200 ps by time resolved X-ray microscopy at the full-field soft X-ray transmission microscope at the Advanced Light Source in Berkeley (beamline 6.1.2). Domain walls are prepared in permalloy nanostructures with a restoring potential. The oscillation of a 180{sup o} domain wall is triggered by nanosecond current pulses. The spin-polarized current and the accompanying Oersted field can contribute to the motion of the wall. By analysis of the …

MINOS is an accelerator neutrino oscillation experiment at Fermilab. An intense high energy neutrino beam is produced at Fermilab and sent to a near detector on the Fermilab site and also to a 5 kTon far detector 735 km away in the Soudan mine in northern Minnesota. The experiment has now had several years of running with millions of events in the near detector and hundreds of events recorded in the far detector. I will report on the recent results from this experiment which include precise measurement of |{Delta}m{sup 2}{sub 32}|, analysis of neutral current data to limit the component of sterile neutrinos and the search for {nu}{sub {mu}} {yields} {nu}{sub e} conversion. The focus will be on the analysis of data for {nu}{sub {mu}} {yields} {nu}{sub e} conversion. Using data from an exposure of 3.14 x 10{sup 20} protons on target, we have selected electron type events in both the near and the far detector. The near detector is used to measure the background which is extrapolated to the far detector. We have found 35 events in the signal region with a background expectation of 27 {+-} 5(stat) {+-} 2(syst). Using this observation we set a 90% C.L. limit …

Brief scientific notes on the relationship between coarse woody debris and arthropod abundance.

This report evaluates the relative performance of 12 global and four direct beam solar radiometers deployed at a single site over a 12-month period. Test radiometer irradiances were compared with a reference irradiance consisting of either an absolute cavity radiometer (during calibrations) or a low uncertainty thermopile pyrheliometer (during the evaluation period) for pyrheliometers; and for pyranometers a reference global irradiance computed from the reference pyrheliometer and diffuse irradiance from a shaded pyranometer.

Abstract. Many of the soils in the south-eastern US are characterized by an argillic, or clay horizon, that largely parallels the soil surface at depths ranging from a few centimeters to 100 cen-timeters. The degree to which these argillic horizons alter subsurface movement of infiltrated water is not well known. Interflow, or throughflow, is shallow lateral subsurface flow that moves over a horizon that restricts percolation. This research investigates how often and under what conditions a relatively deep (20-150+cm) argillic horizon on low slope (2-6%) hillsides causes interflow to oc-cur. Research is being conducted at the Savannah River Site, Aiken, South Carolina, on a small zero-order watershed. In the first phase of this research, a high resolution topographic map of the clay layer was developed. This map will be used to instrument designated “low” spots with max rise piezo-meters in order to determine if there is channelized subsurface flow. In situ conductivities of the clay layer and the surface horizons were measured using an Amoozegar meter, and bulk density samples were taken and measured. Along with soil topographic measurements, data-logging piezometers have been installed to measure the piezometric head above, in, and below the argillic horizon to further investigate interflow …

We propose a scheme that combines the echo-enabled harmonic generation technique with the bunch compression and allows to generate harmonic numbers of a few hundred in a microbunched beam through up-conversion of the frequency of an ultraviolet seed laser. Sending this beam through a short undulator results in an isolated sub-100 attoseconds pulse of x-ray radiation. Using a representative realistic set of parameters, we show that 1 nm x-ray pulse with peak power exceeding 100 MW and duration as short as 34 attoseconds (FWHM) can be generated from a 200 nm ultraviolet seed laser.

We report on a search for the supersymmetric partner of the bottom quark produced from gluino decays in data from 2.5 fb{sup -1} of integrated luminosity collected by the Collider Detector at Fermilab at {radical}s = 1.96 TeV. Candidate events are selected requiring two or more jets and large missing transverse energy. At least two of the jets are required to be tagged as originating from a b quark to enhance the sensitivity. The results are in good agreement with the prediction of the standard model processes, giving no evidence for gluino decay to sbottom quarks. This result constrains the gluino-pair-production cross section to be less than 40 fb at 95% credibility level for a gluino mass of 350 GeV/c{sup 2}.

The protonation reactions of oxalate (ox) and the complex formation of uranium(VI) with oxalate in 1.05 mol kg{sup -1} NaClO{sub 4} were studied at variable temperatures (10-70 C). Three U(VI)/ox complexes (UO{sub 2}ox{sub j}{sup (2-2j){sup +}} with j = 1, 2, 3) were identified in this temperature range. The formation constants and the molar enthalpies of complexation were determined by spectrophotometry and calorimetry. The complexation of uranium(VI) with oxalate ion is exothermic at lower temperatures (10-40 C) and becomes endothermic at higher temperatures (55-70 C). In spite of this, the free energy of complexation becomes more negative at higher temperatures due to increasingly more positive entropy of complexation that exceeds the increase of the enthalpy of complexation. The thermodynamic parameters at different temperatures, in conjunction with the literature data for other dicarboxylic acids, provide insight into the relative strength of U(VI) complexes with a series of dicarboxylic acids (oxalic, malonic and oxydiacetic) and rationalization for the highest stability of U(VI)/oxalate complexes in the series. The data reported in this study are of importance in predicting the migration of uranium(VI) in geological environments in the case of failure of the engineering barriers which protect waste repositories.

As energy prices skyrocket and interest in alternative, clean energy sources builds, interest in nuclear energy has increased. This increased interest in nuclear energy has been termed the “Nuclear Renaissance”. The performance of nuclear fuels, fuels and reactor materials and waste products are becoming a more important issue as the potential for designing new nuclear reactors is more immediate. The Idaho National Laboratory (INL) Materials and Fuels Complex (MFC) Analytical Laboratory Hot Cells (ALHC) are rising to the challenge of characterizing new reactor materials, byproducts and performance. The ALHC is a facility located near Idaho Falls, Idaho at the INL Site. It was built in 1958 as part of the former Argonne National Laboratory West Complex to support the operation of the second Experimental Breeder Reactor (EBR-II). It is part of a larger analytical laboratory structure that includes wet chemistry, instrumentation and radiochemistry laboratories. The purpose of the ALHC is to perform analytical chemistry work on highly radioactive materials. The primary work in the ALHC has traditionally been dissolution of nuclear materials so that less radioactive subsamples (aliquots) could be transferred to other sections of the laboratory for analysis. Over the last 50 years though, the capabilities within the ALHC …

Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EGFR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. We were interested in identifying subnetworks within the EGFR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EGFR-MEK signaling. This model was comprised of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype specific subnetworks, including one that suggested PAK1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that PAK1 overexpressing cell lines would have increased sensitivity to MEK inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three MEK inhibitors. We found that PAK1 over-expressing luminal breast cancer cell lines are significantly more sensitive to MEK inhibition as compared to those that express PAK1 at low levels. This indicates that …