A linear scaling approach for general and accurate pseudopotential Density Functional Theory calculations is presented. It is based on a Finite Difference discretization. Effective O(N) scaling is achieved by confining the orbitals in spherical localization regions. To improve accuracy and flexibility while computing the smallest possible number of orbitals, we propose an algorithm to adapt localization regions during computation. Numerical results for a polyacethylene chain and a magnesium oxide ring are presented.

Antisense oligodeoxynucleotide (ODN) inhibition emerges as an effective means for probing gene function in plant cells. Employing this method we have established the importance of the SUSIBA2 transcription factor for regulation of starch synthesis in barley endosperm, and arrived at a model for the role of the SUSIBAs in sugar signaling and source-sink commutation during cereal endosperm development. In this addendum we provide additional data demonstrating the suitability of the antisense ODN technology in studies on starch branching enzyme activities in barley leaves. We also comment on the mechanism for ODN uptake in plant cells. Antisense ODNs are short (12-25 nt-long) stretches of single-stranded ODNs that hybridize to the cognate mRNA in a sequence-specific manner, thereby inhibiting gene expression. They are naturally occurring in both prokaryotes and eukaryotes where they partake in gene regulation and defense against viral infection. The mechanisms for antisense ODN inhibition are not fully understood but it is generally considered that the ODN either sterically interferes with translation or promotes transcript degradation by RNase H activation. The earliest indication of the usefulness of antisense ODN technology for the purposes of molecular biology and medical therapy was the demonstration in 1978 that synthetic ODNs complementary to Raos …

Here we show that labile particulate iron and manganese concentrations in the upper 500m of the Western Subarctic Pacific, an iron-limited High Nutrient Low Chlorophyll (HNLC) region, have prominent subsurface maxima between 100-200 m, reaching 3 nM and 600 pM, respectively. The subsurface concentration maxima in particulate Fe are characterized by a more reduced oxidation state, suggesting a source from primary volcagenic minerals such as from the Kuril/Kamchatka margin. The systematics of these profiles suggest a consistently strong lateral advection of labile Mn and Fe from redox-mobilized labile sources at the continental shelf supplemented by a more variable source of Fe from the upper continental slope. This subsurface supply of iron from the continental margin is shallow enough to be accessible to the surface through winter upwelling and vertical mixing, and is likely a key source of bioavailable Fe to the HNLC North Pacific.

High level radioactive liquid waste generated as a result of the production of nuclear material for the United States defense program at the Savannah River Site has been stored as 36 million gallons in underground tanks. About ten percent of the waste volume is sludge, composed of insoluble metal hydroxides primarily hydroxides of Mn, Fe, Al, Hg, and most radionuclides including fission products. The remaining ninety percent of the waste volume is saltcake, composed of primarily sodium (nitrites, nitrates, and aluminates) and hydroxides. Saltcakes account for 30% of the radioactivity while the sludge accounts for 70% of the radioactivity. A pilot plant salt disposition processing system has been designed at the Savannah River Site for interim processing of salt solution and is composed of two facilities: the Actinide Removal Process Facility (ARPF) and the Modular Caustic Side Solvent Extraction Unit (MCU). Data from the pilot plant salt processing system will be used for future processing salt at a much higher rate in a new salt processing facility. Saltcake contains significant amounts of actinides, and other long-lived radioactive nuclides such as strontium and cesium that must be extracted prior to disposal as low level waste. The extracted radioactive nuclides will be …

Sr3(Ru1-xMnx)2O7, in which 4d-Ru is substituted by the more localized 3d-Mn, is studied by x-ray dichroism and spin-resolved density functional theory. We find that Mn impurities do not exhibit the same 4+ valence of Ru, but act as 3+ acceptors; the extra eg electron occupies the in-plane 3dx2-y2 orbital instead of the expected out-of-plane 3d3z2-r2. We propose that the 3d-4d interplay, via the ligand oxygen orbitals, is responsible for this crystal-field level inversion and the material's transition to an antiferromagnetic, possibly orbitally ordered, low-temperature state.

Various forms of general and localized corrosion represent principal threats to the integrity of DOE liquid waste storage tanks. These tanks, which are of a single wall or double wall design, depending upon their age, are fabricated from welded carbon steel and contain a complex waste-form comprised of NaOH and NaNO{sub 3}, along with trace amounts of phosphate, sulfate, carbonate, and chloride. Because waste leakage can have a profound environmental impact, considerable interest exists in predicting the accumulation of corrosion damage, so as to more effectively schedule maintenance and repair. The different tasks that are being carried out under the current program are as follows: (1) Theoretical and experimental assessment of general corrosion of iron/steel in borate buffer solutions by using electrochemical impedance spectroscopy (EIS), ellipsometry and XPS techniques; (2) Development of a damage function analysis (DFA) which would help in predicting the accumulation of damage due to pitting corrosion in an environment prototypical of DOE liquid waste systems; (3) Experimental measurement of crack growth rate, acoustic emission signals and coupling currents for fracture in carbon and low alloy steels as functions of mechanical (stress intensity), chemical (conductivity), electrochemical (corrosion potential, ECP), and microstructural (grain size, precipitate size, etc) variables …

We are studying the gamma ray and neutron multiplicity of various fission processes, beginning with the spontaneous fission of {sup 252}Cf, for a variety of basic and applied science purposes. The Livermore-Berkeley Array for Collaborative Experiments (LiBerACE) consists of six high-purity germanium Clover detectors (HPGe) each enclosed by an array of 16 bismuth-germanate (BGO) detectors. These detectors were arranged in a cubic pattern around a 1 {micro}Ci {sup 252}Cf source to attempt to cover as much solid angle of gamma ray emission as possible with a high level of segmentation. The single-gamma detector response function is determined at several energies by tagging in a HPGe detector on the photopeak of one of two gamma rays in two-gamma ray calibration sources and observing the multiplicity of the remainder of the array. Summing these single-gamma responses in groups yields the response function of the array to higher multiplicity events, which are convolved with multiplicity distributions from theoretical models and compared to the measured results to test the models validity.

The GGF Student Scholar program enabled GGF the opportunity to bring over sixty qualified graduate and under-graduate students with interests in grid technologies to its three annual events over the three-year program.

To meet the needs of a growing population and to provide us with a higher quality of life, increasing pressures are being placed on our environment through the development of agriculture, industry, and infrastructures. Soil erosion, groundwater depletion, salinization, and pollution have been recognized for decades as major threats to ecosystems and human health. More recently, the progressive substitution of fossil fuels by biofuels for energy production and climate change have been recognized as potential threats to our water resources and sustained agricultural productivity. The vadose zone mediates many of the processes that govern water resources and quality, such as the partition of precipitation into infiltration and runoff , groundwater recharge, contaminant transport, plant growth, evaporation, and energy exchanges between the Earth's surface and its atmosphere. It also determines soil organic carbon sequestration and carbon-cycle feedbacks, which could substantially impact climate change. The vadose zone's inherent spatial variability and inaccessibility precludes direct observation of the important subsurface processes. In a societal context where the development of sustainable and optimal environmental management strategies has become a priority, there is a strong prerequisite for the development of noninvasive characterization and monitoring techniques of the vadose zone. In particular, hydrogeophysical approaches applied at …

This report tabulates data generated by laboratory characterization and testing of three samples collected from tank C-103. The data presented here will form the basis for a release model that will be developed for tank C-103. These release models are being developed to support the tank risk assessments performed by CH2M HILL Hanford Group, Inc. for DOE.

The Savannah River Site F-Tank Farm Closure project has successfully performed Mechanical Sludge Removal (MSR) using the Waste on Wheels (WOW) system for the first time within one of its storage tanks. The WOW system is designed to be relatively mobile with the ability for many components to be redeployed to multiple waste tanks. It is primarily comprised of Submersible Mixer Pumps (SMPs), Submersible Transfer Pumps (STPs), and a mobile control room with a control panel and variable speed drives. In addition, the project is currently preparing another waste tank for MSR utilizing lessons learned from this previous operational activity. These tanks, designated as Tank 6 and Tank 5 respectively, are Type I waste tanks located in F-Tank Farm (FTF) with a capacity of 2,840 cubic meters (750,000 gallons) each. The construction of these tanks was completed in 1953, and they were placed into waste storage service in 1959. The tank's primary shell is 23 meters (75 feet) in diameter, and 7.5 meters (24.5 feet) in height. Type I tanks have 34 vertically oriented cooling coils and two horizontal cooling coil circuits along the tank floor. Both Tank 5 and Tank 6 received and stored F-PUREX waste during their operating …

The desire to improve and expand the scope of clinical magnetic resonance imaging (MRI) has prompted the search for contrast agents of higher efficiency. The development of better agents requires consideration of the fundamental coordination chemistry of the gadolinium(III) ion and the parameters that affect its efficacy as a proton relaxation agent. In optimizing each parameter, other practical issues such as solubility and in vivo toxicity must also be addressed, making the attainment of safe, high-relaxivity agents a challenging goal. Here we present recent advances in the field, with an emphasis on the hydroxypyridinone family of Gd{sup III} chelates.

Using 226 million B{bar B} events recorded on the {Upsilon}(4S) resonance with the BABAR detector at the SLAC e{sup +}e{sup -} PEP-II storage rings, they reconstruct B{sup -} {yields} D*{sup 0}e{sup -}{bar {nu}}{sub e} decays using the decay chain D*{sup 0} {yields} D{sup 0}{pi}{sup 0} and D{sup 0} {yields} K{sup -} {pi}{sup +}. From the dependence of their differential rate on the w, the dot product of the four-velocities of B{sup -} and D*{sup 0}, and using the form factor description by Caprini et al. with the parameters F(1) and {rho}{sub 1{sub 1}}{sup 2}, they obtain the results {rho}{sub A{sub 1}}{sup 2} = 1.16 {+-} 0.06 {+-} 0.08, F(1) {center_dot} |V{sub cb}| = (35.9 {+-} 0.6 {+-} 1.4) {center_dot} 10{sup -3}, and {beta}(B{sup -} {yields} D*{sup 0} e{sup -}{bar {nu}}{sub e}) = (5.56 {+-} 0.08 {+-} 0.41)%.

The definition and delineation of microbial species are of great importance and challenge due to the extent of evolution and diversity. Whole-genome DNA-DNA hybridization is the cornerstone for defining procaryotic species relatedness, but obtaining pairwise DNA-DNA reassociation values for a comprehensive phylogenetic analysis of procaryotes is tedious and time consuming. A previously described microarray format containing whole-genomic DNA (the community genome array or CGA) was rigorously evaluated as a high-throughput alternative to the traditional DNA-DNA reassociation approach for delineating procaryotic species relationships. DNA similarities for multiple bacterial strains obtained with the CGA-based hybridization were comparable to those obtained with various traditional whole-genome hybridization methods (r=0.87, P<0.01). Significant linear relationships were also observed between the CGA-based genome similarities and those derived from small subunit (SSU) rRNA gene sequences (r=0.79, P<0.0001), gyrB sequences (r=0.95, P<0.0001) or REP- and BOX-PCR fingerprinting profiles (r=0.82, P<0.0001). The CGA hybridization-revealed species relationships in several representative genera, including Pseudomonas, Azoarcus and Shewanella, were largely congruent with previous classifications based on various conventional whole-genome DNA-DNA reassociation, SSU rRNA and/or gyrB analyses. These results suggest that CGA-based DNA-DNA hybridization could serve as a powerful, high-throughput format for determining species relatedness among microorganisms.

Fluor Hanford, Inc. (FH) is proud to submit the Plutonium Finishing Plant (PFP) 241-Z liquid Waste Treatment Facility Deactivation and Demolition (D&D) Project for consideration by the Project Management Institute as Project of the Year for 2008. The decommissioning of the 241-Z Facility presented numerous challenges, many of which were unique with in the Department of Energy (DOE) Complex. The majority of the project budget and schedule was allocated for cleaning out five below-grade tank vaults. These highly contaminated, confined spaces also presented significant industrial safety hazards that presented some of the most hazardous work environments on the Hanford Site. The 241-Z D&D Project encompassed diverse tasks: cleaning out and stabilizing five below-grade tank vaults (also called cells), manually size-reducing and removing over three tons of process piping from the vaults, permanently isolating service utilities, removing a large contaminated chemical supply tank, stabilizing and removing plutonium-contaminated ventilation ducts, demolishing three structures to grade, and installing an environmental barrier on the demolition site . All of this work was performed safely, on schedule, and under budget. During the deactivation phase of the project between November 2005 and February 2007, workers entered the highly contaminated confined-space tank vaults 428 times. Each entry …

First-principles generalized pseudopotential theory (GPT) provides a fundamental basis for bridging the quantum-atomistic gap from density-functional quantum mechanics to large scale atomistic simulation in metals and alloys. In directionally-bonded bcc transition metals, advanced generation model GPT or MGPT potentials based on canonical d bands have been developed for Ta, Mo and V and successfully applied to a wide range of thermodynamic and mechanical properties at both ambient and extreme conditions of pressure and temperature, including high-pressure phase transitions, multiphase equation of state; melting and solidification; thermoelasticity; and the atomistic simulation of point defects, dislocations and grain boundaries needed for the multiscale modeling of plasticity and strength. Recent algorithm improvements have also allowed an MGPT implementation beyond canonical bands to achieve increased accuracy, extension to f-electron actinide metals, and high computational speed. A further advance in progress is the development temperature-dependent MGPT potentials that subsume electron-thermal contributions to high-temperature properties.

The oxidation status of uranium in sediments is important because the solubility of this toxic and radioactive element is much greater for U(VI) than for U(IV) species. Thus, redox manipulation to promote precipitation of UO{sub 2} is receiving interest as a method to remediate U-contaminated sediments. Presence of Fe and Mn oxides in sediments at much higher concentrations than U requires understanding of their redox status as well. This study was conducted to determine changes in oxidation states of U, Fe, and Mn in U-contaminated sediments from Oak Ridge National Laboratory. Oxidation states of these elements were measured in real-time and nondestructively using X-ray absorption spectroscopy, on sediment columns supplied with synthetic groundwater containing organic carbon (OC, 0, 3, 10, 30 and 100 mM OC as lactate) for over 400 days. In sediments supplied with OC {ge} 30 mM, 80% of the U was reduced to U(IV), with transient reoxidation at about 150 days. Mn(III,IV) oxides were completely reduced to Mn(II) in sediments infused with OC {ge} 3 mM. However, Fe remained largely unreduced in all sediment columns, showing that Fe(III) can persist as an electron acceptor in reducing sediments over long times. This result in combination with the complete …

The Savannah River Site's (SRS) Defense Waste Processing Facility (DWPF) began stabilizing high level waste (HLW) in a glass matrix in 1996. Over the past few years, there have been several process and equipment improvements at the DWPF to increase the rate at which the high level waste can be stabilized. These improvements have either directly increased waste processing rates or have desensitized the process to upsets, thereby minimizing downtime and increasing production. Improvements due to optimization of waste throughput with increased HLW loading of the glass resulted in a 6% waste throughput increase based upon operational efficiencies. Improvements in canister production include the pour spout heated bellows liner (5%), glass surge (siphon) protection software (2%), melter feed pump software logic change to prevent spurious interlocks of the feed pump with subsequent dilution of feed stock (2%) and optimization of the steam atomized scrubber (SAS) operation to minimize downtime (3%) for a total increase in canister production of 12%. A number of process recovery efforts have allowed continued operation. These include the off gas system pluggage and restoration, slurry mix evaporator (SME) tank repair and replacement, remote cleaning of melter top head center nozzle, remote melter internal inspection, SAS pump …

This study addresses the issue of waste and cover subsidence caused by corrosion of the non-crushable waste containers defined as containers with significant void space that will not be stabilized by dynamic compaction of the Earea Slit Trenches at the Savannah River Site. Concentrations at the hypothetical 100-m well were evaluated for 1,000 years and compared with the base case value for compliance. To generalize the results, a hypothetical, no-decay radionuclide characterized by a Kd (5 ml/g) that would be most problematic was selected. Although the non-crushable containers will not be stabilized by dynamic compaction, these containers will gradually corrode, eventually collapse after placement of the final closure cap and cause the cap to subside resulting in an increase of the infiltration rates. The vadose zone model estimated the contaminant fluxes that were input to the aquifer model for prediction of concentrations at the 100-m well. To study the potential effect of trench subsidence on the well concentrations within the 1000-year time window, two high-impact cases were considered. In the first case, trenches subsided right after dynamic compaction (i.e., at 125 years). In the second case, trenches subsided at 419 years to make the peak concentrations from both the subsided …

Starch branching enzyme (SBE) activity in the cassava storage root exhibited a diurnal fluctuation, dictated by a transcriptional oscillation of the corresponding SBE genes. The peak of SBE activity coincided with the onset of sucrose accumulation in the storage, and we conclude that the oscillatory mechanism keeps the starch synthetic apparatus in the storage root sink in tune with the flux of sucrose from the photosynthetic source. When storage roots were uncoupled from the source, SBE expression could be effectively induced by exogenous sucrose. Turanose, a sucrose isomer that cannot be metabolized by plants, mimicked the effect of sucrose, demonstrating that downstream metabolism of sucrose was not necessary for signal transmission. Also glucose and glucose-1-P induced SBE expression. Interestingly, induction by sucrose, turanose and glucose but not glucose-1-P sustained an overt semidian (12-h) oscillation in SBE expression and was sensitive to the hexokinase (HXK) inhibitor glucosamine. These results suggest a pivotal regulatory role for HXK during starch synthesis. Abscisic acid (ABA) was another potent inducer of SBE expression. Induction by ABA was similar to that of glucose-1-P in that it bypassed the semidian oscillator. Both the sugar and ABA signaling cascades were disrupted by okadaic acid, a protein phosphatase inhibitor. …

Isotopes of rutherfordium (258-261Rf) were produced in irradiations of 238U targets with 26Mg beams. Excitation functions were measured for the 4n, 5n and 6n exit channels. Production of 261Rf in the 3n exit channel with a cross section of 28+92-26 pb was observed. Alpha decay of 258Rf was observed for the first time with an alpha-particle energy of 9.05+-0.03 MeV and an alpha/total decay branching ratio of 0.31+-0.11. In 259Rf, the electron capture/total decay branching ratio was measured to be 0.15+-0.04. The measured half-lives for 258Rf, 259Rf and 260Rf were 14.7+1.2-1.0 ms, 2.5+0.4-0.3 s and 22.2+3.0-2.4 ms, respectively, in agreement with literature data. The systematics of the alpha decay Q values and of the partial spontaneous fission half-lives were evaluated for even-even nuclides in the region of the N = 152, Z = 100 deformed shell. The influence of the N = 152 shell on the alpha decay Q values for rutherfordium was observed to be similar to that of the lighter elements (96<_ Z<_ 102). However, the N = 152 shell does not stabilize the rutherfordium isotopes against spontaneous fission, as it does in the lighter elements (96<_ Z<_102).

Femtosecond time-resolved soft x-ray transient absorption spectroscopy based on a high-order harmonic generation source is used to investigate the dissociative ionization of CH{sub 2}Br{sub 2} induced by 800 nm strong-field irradiation. At moderate peak intensities (2.0 x 10{sup 14} W/cm{sup 2}), strong-field ionization is accompanied by ultrafast C-Br bond dissociation, producing both neutral Br ({sup 2}P{sub 3/2}) and Br* ({sup 2}P{sub 1/2}) atoms together with the CH{sub 2}Br{sup +} fragment ion. The measured rise times for Br and Br* are 130 {+-} 22 fs and 74 {+-} 10 fs, respectively. The atomic bromine quantum state distribution shows that the Br/Br* population ratio is 8.1 {+-} 3.8 and that the Br {sup 2}P{sub 3/2} state is not aligned. The observed product distribution and the timescales of the photofragment appearances suggest that multiple field-dressed potential energy surfaces are involved in the dissociative ionization process. In addition, the transient absorption spectrum of CH{sub 2}Br{sub 2}{sup +} suggests that the alignment of the molecule relative to the polarization axis of the strong-field ionizing pulse determines the electronic symmetry of the resulting ion; alignment of the Br-Br, H-H, and C{sub 2} axis of the molecule along the polarization axis results in the production of the …

Crosswell seismic acquisition provides an ideal geometry for monitoring travel time changes in the subsurface. Analysis of delay time in terms of a characteristic frequency allows us to estimate optimal acquisition parameters (frequency and distance). We have deployed standard data acquisition equipment for continuous monitoring of crosswell travel time in two separate field experiments, with well spacing of 3 and 30 m. The acquisition hardware used for the field experiments is described, along with environmental effects (such as temperature) that influence the measurements. Two field experiments are described that correlate changes in travel time (and therefore velocity) with changes in barometric pressure. The results from the two field sites show a pressure sensitivity for velocity of 10{sup -6}/Pa to 10{sup -8}/Pa.

Over the past half-century, the Applied Mathematics program in the U.S. Department of Energy's Office of Advanced Scientific Computing Research has made significant, enduring advances in applied mathematics that have been essential enablers of modern computational science. Motivated by the scientific needs of the Department of Energy and its predecessors, advances have been made in mathematical modeling, numerical analysis of differential equations, optimization theory, mesh generation for complex geometries, adaptive algorithms and other important mathematical areas. High-performance mathematical software libraries developed through this program have contributed as much or more to the performance of modern scientific computer codes as the high-performance computers on which these codes run. The combination of these mathematical advances and the resulting software has enabled high-performance computers to be used for scientific discovery in ways that could only be imagined at the program's inception. Our nation, and indeed our world, face great challenges that must be addressed in coming years, and many of these will be addressed through the development of scientific understanding and engineering advances yet to be discovered. The U.S. Department of Energy (DOE) will play an essential role in providing science-based solutions to many of these problems, particularly those that involve the energy, …