We present a new linearly scaling three-dimensional fragment (LS3DF) method for large scale ab initio electronic structure calculations. LS3DF is based on a divide-and-conquer approach, which incorporates a novel patching scheme that effectively cancels out the artificial boundary effects due to the subdivision of the system. As a consequence, the LS3DF program yields essentially the same results as direct density functional theory (DFT) calculations. The fragments of the LS3DF algorithm can be calculated separately with different groups of processors. This leads to almost perfect parallelization on tens of thousands of processors. After code optimization, we were able to achieve 35.1 Tflop/s, which is 39% of the theoretical speed on 17,280 Cray XT4 processor cores. Our 13,824-atom ZnTeO alloy calculation runs 400 times faster than a direct DFT calculation, even presuming that the direct DFT calculation can scale well up to 17,280 processor cores. These results demonstrate the applicability of the LS3DF method to material simulations, the advantage of using linearly scaling algorithms over conventional O(N{sup 3}) methods, and the potential for petascale computation using the LS3DF method.

The electron beam ion trap (EBIT) facility at the Lawrence Livermore National Laboratory is being used to absolutely calibrate the transmission efficiency of X-ray filters employed by diodes and spectrometers used to diagnose laser-produced plasmas. EBIT emits strong, discrete monoenergetic lines at appropriately chosen X-ray energies. X-rays are detected using the high-resolution EBIT calorimeter spectrometer (ECS), developed for LLNL at the NASA/Goddard Space Flight Center. X-ray filter transmission efficiency is determined by dividing the X-ray counts detected when the filter is in the line of sight by those detected when out of the line of sight. Verification of filter thickness can be completed in only a few hours, and absolute efficiencies can be calibrated in a single day over a broad range from about 0.1 to 15 keV. The EBIT calibration lab has been used to field diagnostics (e.g., the OZSPEC instrument) with fully calibrated X-ray filters at the OMEGA laser. Extensions to use the capability for calibrating filter transmission for the DANTE instrument on the National Ignition Facility are discussed.

The theory of the strong nuclear force, Quantum Chromodynamics (QCD), can be numerically simulated from first principles on massively-parallel supercomputers using the method of Lattice Gauge Theory. We describe the special programming requirements of lattice QCD (LQCD) as well as the optimal supercomputer hardware architectures that it suggests. We demonstrate these methods on the BlueGene massively-parallel supercomputer and argue that LQCD and the BlueGene architecture are a natural match. This can be traced to the simple fact that LQCD is a regular lattice discretization of space into lattice sites while the BlueGene supercomputer is a discretization of space into compute nodes, and that both are constrained by requirements of locality. This simple relation is both technologically important and theoretically intriguing. The main result of this paper is the speedup of LQCD using up to 131,072 CPUs on the largest BlueGene/L supercomputer. The speedup is perfect with sustained performance of about 20% of peak. This corresponds to a maximum of 70.5 sustained TFlop/s. At these speeds LQCD and BlueGene are poised to produce the next generation of strong interaction physics theoretical results.

At the Savannah River Site (SRS), near Aiken South Carolina, there is a crucial need to remove residual quantities of highly radioactive iron-based sludge from large select underground storage tanks (e.g., 19,000 liters of sludge per tank), in order to support tank closure. The use of oxalic acid is planned to dissolve the residual sludge, hence, helping in the removal. Based on rigorous testing, primarily using 4 and 8 wt% oxalic acid solutions, it was concluded that the more concentrated the acid, the greater the amount of residual sludge that would be dissolved; hence, a baseline technology on using 8 wt% oxalic acid was developed. In stark contrast to the baseline technology, reports from other industries suggest that the dissolution will most effectively occur at 1 wt% oxalic acid (i.e., maintaining the pH near 2). The driver for using less oxalic acid is that less (i.e., moles) would decrease the severity of the downstream impacts (i.e., required oxalate solids removal efforts). To determine the initial feasibility of using 1 wt% acid to dissolve > 90% of the sludge solids, about 19,000 liters of representative sludge was modeled using about 530,000 liters of 0 to 8 wt% oxalic acid solutions. With …

We present a new linear scaling ab initio total energy electronic structure calculation method based on the divide-and-conquer strategy. This method is simple to implement, easily to parallelize, and produces very accurate results when compared with the direct ab initio method. The method has been tested using up to 8,000 processors, and has been used to calculate nanosystems up to 15,000 atoms.

The cleaning of Si{sub 0.85}Ge{sub 0.15} surfaces using HCl and HF solutions is studied using synchrotron radiation photoelectron spectroscopy. The HF solution is found to be effective in removing both the Si oxide and the Ge oxide while the HCl solution can only remove part of the Ge oxide. For samples treated with HF, four spectral components are needed to fit the Ge 3d photoemission spectra. One is the bulk component and the other three are attributed to the surface Ge atoms with mono-hydride, di-hydride and tri-hydride terminations, respectively.

National Synchrotron Light Source II (NSLS II) will be a 3-GeV, 792-meter circumference, 3rd generation synchrotron radiation facility, with ultra low emittance and extremely high brightness. the storage ring has 30 Double-Bend-Achromatic (DBA) cells. in each cell, there are five magnets and chamber girders, and one straight section for insertion devices or Radio Frequency (RF) cavities or injection. Most vacuum chambers are made from extruded aluminum with two different cross sections: one fitted in the dipole magnets, and the other surrounded by multipole magnets. They discuss the layout of the DBA cells, the detailed design of the cell's vacuum chambers, the mounting of the Beam-Position-Monitor (BPM) buttons, discrete absorbers, lumped pumps and the distributed Non-Evaporable Getter (NEG) strips, and describe the fabrication and testing of these prototype cell chambers. The account also details the development of the chamber bakeout process, the NEG stri's supports, and the RF shielded bellows.

A comprehensive matrix of 60 tests was designed to explore the effect of calcium chloride vs. sodium chloride and the ratio R of nitrate concentration over chloride concentration on the repassivation potential of Alloy 22. Tests were conducted using the cyclic potentiodynamic polarization (CPP) technique at 75 C and at 90 C. Results show that at a ratio R of 0.18 and higher nitrate was able to inhibit the crevice corrosion in Alloy 22 induced by chloride. Current results fail to show in a consistent way a different effect on the repassivation potential of Alloy 22 for calcium chloride solutions than for sodium chloride solutions.

Generally, mechanical polishing is performed to diminish the cutting damage followed by chemical etching to remove the remaining damage on crystal surfaces. In this paper, we detail the findings from our study of the effects of various chemical treatments on the roughness of crystal surfaces. We prepared several CdZnTe (CZT) and CdMnTe (CMT) crystals by mechanical polishing with 5 {micro}m and/or lower grits of Al{sub 2}O{sub 3} abrasive papers including final polishing with 0.05-{micro}m particle size alumina powder and then etched them for different periods with a 2%, 5% Bromine-Methanol (B-M) solution, and also with an E-solution (HNO{sub 3}:H{sub 2}O:Cr{sub 2}O{sub 7}). The material removal rate (etching rate) from the crystals was found to be 10 {micro}m, 30 {micro}m, and 15 {micro}m per minute, respectively. The roughness of the resulting surfaces was determined by the Atomic Force Microscopy (AFM) to identify the most efficient surface processing method by combining mechanical and chemical polishing.

Two significant seismic events were analyzed using the crustal velocity model developed under this contract. The M{sub W} = 4.55 Korea earthquake of January 20, 2007 occurred in the Republic of Korea on land and within the dense digital seismic network. Using P-wave arrivals from 60 broadband, short-period and acceleration stations, the event occurred at 37.68N, 128.58E at a depth of 7.5 km at 20070120115653.8. Source inversion was performed using the accelerometer recordings in the 0.05-0.20 Hz band the broadband data in the 0.02-0.10 Hz band, with identical focal mechanisms and source depths of 9 and 11 km, respectively. This is the largest event on land in South Korea since the M{sub W} 4.7 event on December 13, 1996. Forward modeling of the waveforms at INCN and MDJ indicates the ability of the current model to match observations on the Korean Peninsula and the effect of significant pulse shape modification for paths that partially cross the Sea of Japan. The results of using the local network data provide a ground truth point for other studies analyzing seismic events on the peninsula. The isotropic seismic moment of the October 9, 2006 North Korea explosion was estimated from the Rayleigh-wave spectral amplitudes …

We demonstrate the feasibility of generating thousands of transgenic Drosophila melanogaster lines in which the expression of an exogenous gene is reproducibly directed to distinct small subsets of cells in the adult brain. We expect the expression patterns produced by the collection of 5,000 lines that we are currently generating to encompass all neurons in the brain in a variety of intersecting patterns. Overlapping 3-kb DNA fragments from the flanking noncoding and intronic regions of genes thought to have patterned expression in the adult brain were inserted into a defined genomic location by site-specific recombination. These fragments were then assayed for their ability to function as transcriptional enhancers in conjunction with a synthetic core promoter designed to work with a wide variety of enhancer types. An analysis of 44 fragments from four genes found that >80% drive expression patterns in the brain; the observed patterns were, on average, comprised of <100 cells. Our results suggest that the D. melanogaster genome contains >50,000 enhancers and that multiple enhancers drive distinct subsets of expression of a gene in each tissue and developmental stage. We expect that these lines will be valuable tools for neuroanatomy as well as for the elucidation of neuronal …

Beam instability caused by the electron cloud has been observed in positron and proton storage rings, and it is expected to be a limiting factor in the performance of future colliders [1-3]. The effect is expected to be particularly severe in magnetic field regions. To test possible mitigation methods in magnetic fields, we have installed a new 4-dipole chicane experiment in the PEP-II Low Energy Ring (LER) at SLAC with both bare and TiN-coated aluminum chambers. In particular, we have observed a large variation of the electron flux at the chamber wall as a function of the chicane dipole field. We infer this is a new high order resonance effect where the energy gained by the electrons in the positron beam depends on the phase of the electron cyclotron motion with respect to the bunch crossing, leading to a modulation of the secondary electron production. Presumably the cloud density is modulated as well and this resonance effect could be used to reduce its magnitude in future colliders. We present the experimental results obtained during January 2008 until the April final shut-down of the PEP-II machine.

Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.

Electron clouds and gas pressure rise limit the performance of many major accelerators. A multi-laboratory effort to understand the underlying physics via the combined application of experiment, theory, and simulation is underway. We present here the status of the simulation capability development, based on a merge of the three-dimensional parallel Particle-In-Cell (PIC) accelerator code WARP and the electron cloud code POSINST, with additional functionalities. The development of the new capability follows a ''roadmap'' describing the different functional modules, and their inter-relationships, that are ultimately needed to reach self-consistency. Newly developed functionalities include a novel particle mover bridging the time scales between electron and ion motion, a module to generate neutrals desorbed by beam ion impacts at the wall, and a module to track impact ionization of the gas by beam ions or electrons. Example applications of the new capability to the modeling of electron effects in the High Current Experiment (HCX) are given.

Using 385 fb{sup -1} of e{sup +}e{sup -} collision data collected at center-of-mass energies around 10.6 GeV, we search for time-integrated CP violation in the Cabibbo-suppressed decays D{sup 0}/{bar D}{sup 0} {yields} {pi}{sup -}{pi}{sup +}{pi}{sup 0} and D{sup 0}/{bar D}{sup 0} {yields} K{sup -}K{sup +}{pi}{sup 0} with both model-independent and model-dependent methods. Measurements of the asymmetries in amplitudes of flavor states and CP eigenstates provide constraints on theories beyond the Standard Model, some of which predict CP violation in amplitudes at the 1% level or higher. We find no evidence of CP violation and hence no conflict with the Standard Model.

Fiber optic grating sensors have been used to measure multi-dimensional strain, pressure, temperature, corrosion and moisture. This paper presents a method of using fiber grating sensors to measure the position and velocity of a very fast event associated with a blast wave. A chirped fiber grating of 50 mm length is placed in a highly energetic material. The action of the shock wave is to destroy the fiber grating as it propagates along it. By using a spectral filter such as a chirped fiber grating in combination with high speed detectors the position and velocity of the shock wave may be determined. A layout of a system used to experimentally verify this technique is described and results presented for two different highly energetic materials.

Two and a quarter centuries ago, a heavy mineral ore was found which was thought to contain a new chemical element called heavy stone (or tungsten in Swedish). A few years later, the metal was separated from its oxide and the new element (Z=74) was called wolfram. Over the years since that time, both the names wolfram and tungsten were attached to this element in various countries. Sixty years ago, IUPAC chose wolfram as the official name for the element. A few years later, under pressure from the press in the USA, the alternative name tungsten was also allowed by IUPAC. Now the original, official name 'wolfram' has been deleted by IUPAC as one of the two alternate names for the element. The history of this controversy is described here.

Quiescent double barrier (QDB) conditions often form when an internal transport barrier is created with high-power neutral-beam injection into a quiescent H-mode (QH) plasma. These QH-modes offer an attractive, high-performance operating scenario for burning plasma experiments due to their quasi-stationarity and lack of edge localized modes (ELMs). Our initial experiments and modeling using ECH/ECCD in QDB shots were designed to control the current profile and, indeed, we have observed a strong dependence on the q-profile when EC-power is used inside the core transport barrier region. While strong electron heating is observed with EC power injection, we also observe a drop in the other core parameters; ion temperature and rotation, electron density and impurity concentration. These dynamically changing conditions provide a rapid evolution of T{sub e} T{sub i} profiles accessible with 0.3 < (T{sub e} T{sub i}){sub axis} < 0.8 observed in QDB discharges. We are exploring the correlation and effects of observed density profile changes with respect to these time-dependent variations in the temperature ratio. Thermal and particle diffusivity calculations over this temperature ratio range indicate a consistency between the rise in temperature ratio and an increase in transport corresponding to the observed change in density.

While window frames typically represent 20-30% of the overall window area, their impact on the total window heat transfer rates may be much larger. This effect is even greater in low-conductance (highly insulating) windows that incorporate very low-conductance glazing. Developing low-conductance window frames requires accurate simulation tools for product research and development. Based on a literature review and an evaluation of current methods of modeling heat transfer through window frames, we conclude that current procedures specified in ISO standards are not sufficiently adequate for accurately evaluating heat transfer through the low-conductance frames. We conclude that the near-term priorities for improving the modeling of heat transfer through low-conductance frames are: (1) Add 2D view-factor radiation to standard modeling and examine the current practice of averaging surface emissivity based on area weighting and the process of making an equivalent rectangular frame cavity. (2) Asses 3D radiation effects in frame cavities and develop recommendation for inclusion into the design fenestration tools. (3) Assess existing correlations for convection in vertical cavities using CFD. (4) Study 2D and 3D natural convection heat transfer in frame cavities for cavities that are proven to be deficient from item 3 above. Recommend improved correlations or full CFD modeling …

Mesh-based PDE simulation codes are becoming increasingly sophisticated and rely on advanced meshing and discretization tools. Unfortunately, it is still difficult to interchange or interoperate tools developed by different communities to experiment with various technologies or to develop new capabilities. To address these difficulties, we have developed component interfaces designed to support the information flow of mesh-based PDE simulations. We describe this information flow and discuss typical roles and services provided by the geometry, mesh, and field components of the simulation. Based on this delineation for the roles of each component, we give a high-level description of the abstract data model and set of interfaces developed by the Department of Energy's Interoperable Tools for Advanced Petascale Simulation (ITAPS) center. These common interfaces are critical to our interoperability goal, and we give examples of several services based upon these interfaces including mesh adaptation and mesh improvement.

The electronic structures of BiFeO{sub 3} (BF) and Mn-doped BiFeO{sub 3} (BF(Mn)) have been studied by X-ray absorption spectroscopy (XAS) and soft-X-ray emission spectroscopy (SXES). The BF and BF(Mn) have the mixed valence state of Fe{sup 2+} and Fe{sup 3+}. The valence band is mainly composed of O 2p state hybridized with the majority-spin t{sub 2g} and e{sub g} orbitals of Fe 3d state. The conduction band is composed of the minority-spin t{sub 2g} and e{sub g} orbitals of Fe 3d. The band gaps of BF and BF(Mn) are estimated to be 1.3 eV and 2.7 eV, respectively. The increase of band gap with Mn substitution contributes to the change of bandwidth of valence band.

In this talk, we present the first, numerically stable, results for the one-loop amplitudes needed for computing W; Z + 3 jet cross sections at the LHC to next-to-leading order in the QCD coupling. We implemented these processes in BlackHat, an automated program based on on-shell methods. These methods scale very well with increasing numbers of external partons, and are applicable to a wide variety of problems of phenomenological interest at the LHC.

The Department of Energy (DOE) has developed, modeled, and tested several different ion exchange media and column designs for cesium removal. One elutable resin and one non-elutable resin were considered for this salt processing application. Deployment of non-elutable Crystalline Silicotitanate and elutable Resorcinol Formaldehyde in several different column configurations were assessed in a formal Systems Engineering Evaluation (SEE). Salt solutions were selected that would allow a grouping of non-compliant tanks to be closed. Tests were run with the elutable resin to determine compatibility with the resin configuration required for an in-tank ion exchange system. Models were run to estimate the ion exchange cycles required with the two resins in several column configurations. Material balance calculations were performed to estimate the impact on the High Level Waste (HLW) system at the Savannah River Site (SRS). Conceptual process diagrams were used to support the hazard analysis. Data from the hazard analysis was used to determine the relative impact on safety. This report will discuss the technical inputs, SEE methods, results and path forward to complete the technical maturation of ion exchange.

Discrete DNA-gold nanoparticle conjugates with DNA lengths as short as 15 bases for both 5 nm and 20 nm gold particles have been purified by anion-exchange HPLC. Conjugates comprising short DNA (<40 bases) and large gold particles (>_ 20 nm) are difficult to purify by other means, and are potential substrates for plasmon coupling experiments. Conjugate purity is demonstrated by hybridizing complementary conjugates to form discrete structures, which are visualized by TEM.