Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.

A gated spectrometer has been designed for real-time, pulsed infrared (IR) studies at the National Synchrotron Light ource at the Brookhaven National Laboratory. A pair of 90-degree, off-axis parabolic mirrors are used to relay the light from an entrance slit to an output IR recording camera. With an initial wavelength range of 1500–4500 nm required, gratings could not be used in the spectrometer because grating orders would overlap. A magnesium oxide prism, placed between these parabolic mirrors, serves as the dispersion element. The spectrometer is doubly telecentric. With proper choice of the air spacing between the prism and the second parabolic mirror, any spectral region of interest within the InSb camera array’s sensitivity region can be recorded. The wavelengths leaving the second parabolic mirror are collimated, thereby relaxing the camera positioning tolerance. To set up the instrument, two different wavelength (visible) lasers are introduced at the entrance slit and made collinear with the optical axis via flip mirrors. After dispersion by the prism, these two laser beams are directed to tick marks located on the outside housing of the gated IR camera. This provides first-order wavelength calibration for the instrument. Light that is reflected off the front prism face is …

Microfield exposure tools (METs) continue to play a dominant role in the development of extreme ultraviolet (EUV) resists. One of these tools is the 0.3 numerical aperture SEMATECH Berkeley MET operating as a resist and mask test center. Here they present an update on the tool summarizing some of the latest test and characterization results. they provide an update on the long-term aberration stability of the tool and present line-space imaging in chemically amplified photoresist down to the 20-nm half-pitch level. Although resist development has shown substantial progress in the area of resolution, line-edge-roughness (LER) remains a significant concern. Here we present a summary of recent LER performance results and consider the effect of mask contributors to the LER observed from the SEMATECH Berkeley microfield tool.

The authors estimate the energy fluence (energy per unit area) at the focal plane of a beam undergoing neutralized drift compression and neutralized solenoidal final focus, as is being carried out in the Neutralized Drift Compression Experiment (NDCX) at LBNL. In these experiments, in order to reach high beam intensity, the beam is compressed longitudinally by ramping the beam velocity (i.e. introducing a velocity tilt) over the course of the pulse, and the beam is transversely focused in a high field solenoid just before the target. To remove the effects of space charge, the beam drifts in a plasma. The tilt introduces chromatic aberrations, with different slices of the original beam having different radii at the focal plane. The fluence can be calculated by summing the contribution from the various slices. They develop analytic formulae for the energy fluence for beams that have current profiles that are initially constant in time. They compare with envelope and particle-in-cell calculations. The expressions derived are useful for predicting how the fluence scales with accelerator and beam parameters.

We use the radiative transfer code \phx\ to study the line formation of the wavelength region 5000-7000 Angstrom. This is the region where the SNe Ia defining Si II feature occurs. This region is important since the ratio of the two nearby silicon lines has been shown to correlate with the absolute blue magnitude. We use a grid of LTE synthetic spectral models to investigate the formation of line features in the spectra of SNe Ia. By isolating the main contributors to the spectral formation we show that the ions that drive the spectral ratio are FeIII, FeII, SiII and SII. While the first two strongly dominate the flux transfer, the latter two form in the same physical region inside of the supernova. We also show that the naive blackbody that one would derive from a fit to the observed spectrum is far different than the true underlying continuum.

Computer simulations using the 2D code"POSINST" were used to study the formation of the electron cloud in the wiggler section of the positron damping ring of the International Linear Collider. In order to simulate an x-y slice of the wiggler (i.e., a slice perpendicular to the beam velocity), each simulation assumed a constant vertical magnetic field. At values of the magnetic field where the cyclotron frequency was an integral multiple of the bunch frequency, and where the field strength was less than approximately 0.6 T, equilibrium average electron densities were up to three times the density found at other neighboring field values. Effects of this resonance between the bunch and cyclotron frequency are expected to be non-negligible when the beam bunch length is much less than the product of the electron cyclotron period and the beam velocity, for a beam moving at v~;;c. Details of the dynamics of the resonance are described.

The Lawrence Berkeley National Laboratory (Berkeley Lab) andthe Center for Sustainable Development in the Americas (CSDA) conductedtechnical studies and organized two training workshops to developcapacity in Central America for the evaluation of climate changeprojects. This paper describes the results of two baseline case studiesconducted for these workshops, one for the power sector and one for thecement industry, that were devised to illustrate certain approaches tobaseline setting. Multiproject baseline emission rates (BERs) for themain Guatemalan electricity grid were calculated from 2001 data. Inrecent years, the Guatemalan power sector has experienced rapid growth;thus, a sufficient number of new plants have been built to estimateviable BERs. We found that BERs for baseload plants offsetting additionalbaseload capacity ranged from 0.702 kgCO2/kWh (using a weighted averagestringency) to 0.507 kgCO2/kWh (using a 10th percentile stringency),while the baseline for plants offsetting load-followingcapacity is lowerat 0.567 kgCO2/kWh. For power displaced from existing load-followingplants, the rate is higher, 0.735 kgCO2/kWh, as a result of the age ofsome plants used for meeting peak loads and the infrequency of their use.The approved consolidated methodology for the Clean Development Mechanismyields a single rate of 0.753 kgCO2/kWh. Due to the relatively smallnumber of cement plants in the region and the regional nature of …

We report on atomic layer deposition of an {approx} 2-nm-thick ZnO layer on the inner surface of ultralow-density ({approx} 0.5% of the full density) nanoporous silica aerogel monoliths with an extremely large effective aspect ratio of {approx} 10{sup 5} (defined as the ratio of the monolith thickness to the average pore size). The resultant monoliths are formed by amorphous-SiO{sub 2}/wurtzite-ZnO nanoparticles which are randomly oriented and interconnected into an open-cell network with an apparent density of {approx} 3% and a surface area of {approx} 100 m{sup 2} g{sup -1}. Secondary ion mass spectrometry and high-resolution transmission electron microscopy imaging reveal excellent uniformity and crystallinity of ZnO coating. Oxygen K-edge and Zn L{sub 3}-edge soft x-ray absorption near-edge structure spectroscopy shows broadened O 2p- as well as Zn 4s-, 5s-, and 3d-projected densities of states in the conduction band.

Slurries of inorganic solids, containing both stable and radioactive elements, were produced during the cold war as by-products of the production of plutonium and enriched uranium and stored in large tanks at the Savannah River Site. Some of this high level waste is being processed into a stable glass waste form today. Waste processing involves various large scale operations such as tank mixing, inter-tank transfers, washing, gravity settling and decanting, chemical adjustment, and vitrification. The rheological properties of waste slurries are of particular interest. Methods for modeling flow curve data and predicting the properties of slurry blends are particularly important during certain operational phases. Several methods have been evaluated to predict the rheological properties of sludge slurry blends from the data on the individual slurries. These have been relatively successful.

Aqueous radioactive high-level waste slurries are combined during processing steps that ultimately produce a stable borosilicate glass waste form. Chemically treated waste slurries are combined with each other and with glass frit-water slurries to produce the melter feed. Understanding the evolution of the rheological properties of the slurries is an important aspect of removing and treating the stored waste. To a first approximation, combinations of colloidal waste slurry with {approx}0.1-mm mean diameter glass frit or glass beads act in an analogous matter to slurries of spherical beads in Newtonian liquids. The non-Newtonian rheological properties of the waste slurries without frit, however, add complexity to the hydrodynamic analysis. The use of shear rate dependent apparent viscosities with the modified Einstein equation was used to model the rheological properties of aqueous frit-waste slurries.

Conversion of legacy radioactive high-level waste at the Savannah River Site into a stable glass waste form involves a chemical pretreatment process to prepare the waste for vitrification. Waste slurry is treated with nitric and formic acids to achieve certain goals. The total quantity of acid added to a batch of waste slurry is constrained by the catalytic activity of trace noble metal fission products in the waste that can convert formic acid into hydrogen gas at many hundreds of times the radiolytic hydrogen generation rate. A large block of experimental process simulations were performed to characterize the chemical reactions that consume acid prior to hydrogen generation. The analysis led to a new equation for predicting the quantity of acid required to process a given volume of waste slurry.

Chemical pre-treatment of radioactive waste at the Savannah River Site is performed to prepare the waste for vitrification into a stable waste glass form. During pre-treatment, compounds in the waste become catalytically active. Mercury, rhodium, and palladium become active for nitrite destruction by formic acid, while rhodium and ruthenium become active for catalytic conversion of formic acid into hydrogen and carbon dioxide. Nitrite ion is present during the maximum activity of rhodium, but is consumed prior to the activation of ruthenium. Catalytic hydrogen generation during pre-treatment can exceed radiolytic hydrogen generation by several orders of magnitude. Palladium and mercury impact the maximum catalytic hydrogen generation rates of rhodium and ruthenium by altering the kinetics of nitrite ion decomposition. New data are presented that illustrate the interactions of these various species.

A combined theoretical and experimental study of the ionized dimers of thymine and adenine, TT, AA, and AT, is presented. Adiabatic and vertical ionization energies(IEs) for monomers and dimers as well as thresholds for the appearance of the protonated species are reported and analyzed. Non-covalent interactions stronglyaffect the observed IEs. The magnitude and the nature of the effect is different for different isomers of the dimers. The computations reveal that for TT, the largestchanges in vertical IEs (0.4 eV) occur in asymmetric h-bonded and symmetric pi- stacked isomers, whereas in the lowest-energy symmetric h-bonded dimer the shiftin IEs is much smaller (0.1 eV). The origin of the shift and the character of the ionized states is different in asymmetric h-bonded and symmetric stacked isomers. Inthe former, the initial hole is localized on one of the fragments, and the shift is due to the electrostatic stabilization of the positive charge of the ionized fragment by thedipole moment of the neutral fragment. In the latter, the hole is delocalized, and the change in IE is proportional to the overlap of the fragments' MOs. The shifts in AAare much smaller due to a less effcient overlap and a smaller dipole moment. The ionization …

This report addresses the high-level overview of the WMA C performance assessment.

The experimental reaction between [1,2,4-(Me3C)3C5H2]2CeCH2Ph and CH3X, X = F, Cl, Br, and I, yields the metathetical exchange products, [1,2,4-(Me3C)3C5H2]2CeX and CH3CH2Ph. The reaction is complicated by the equilibrium between the benzyl derivative and the metallacycle [[1,2,4-(Me3C)3C5H2] [(Me3C)2C5H2C(CH3)2CH2]Ce, plus toluene since the metallacycle reacts with CH3X. Labelling studies show that the methyl group of the methylhalide is transferred intact to the benzyl group. The mechanism, as revealed by DFT calculations on (C5H5)2CeCH2Ph and CH3F, does not proceed by way of a four-center mechanism, (sigma-bond metathesis) but a lower barrier process involves a haptotropic shift of the Cp2Ce fragment so that at the transition state the para-carbon of the benzene ring is attached to the Cp2Ce fragment while the CH2 fragment of the benzyl group attacks CH3F that is activated by coordination to the metal ion. As a result the mechanism is classified as an associative interchange process.

To augment steady-state design calculations, dynamic models of three offgas systems that will be used in the Waste Treatment Plant now under construction at the Hanford Site were developed using Aspen Custom Modeler{trademark}. The offgas systems modeled were those for the High Level Waste (HLW) melters, Low Activity Waste (LAW) melters and HLW Pulse Jet Ventilation (PJV) system. The models do not include offgas chemistry but only consider the two major species in the offgas stream which are air and water vapor. This is sufficient to perform material and energy balance calculations that accurately show the dynamic behavior of gas pressure, temperature, humidity and flow throughout the systems. The models are structured to perform pressure drop calculations across the various unit operations using a combination of standard engineering calculations and empirical data based correlations for specific pieces of equipment. The models include process controllers, gas ducting, control valves, exhaust fans and the offgas treatment equipment. The models were successfully used to analyze a large number of operating scenarios including both normal and off-normal conditions.

For this after dinner talk I intersperse images of real lattices with a discussion of the motivations for lattice gauge theory and some current unresolved issues.

We have recently implemented polarization smoothing (PS) on one quad of the NIF laser. Specially cut KDP and DKDP crystals at 420 x 420 mm sizes were used to scramble the incident 351 nm laser polarization over the beam aperture. The intensity contrast deduced from the measured focal spot images for one of the NIF beams is in very good agreement with the expected contrast. KDP and DKDP crystals are known to produce considerable amount of transverse stimulated Raman scattering (SRS) when irradiated with large beams at {approx}1-2 GW/cm2. In order to measure the transverse SRS, we attached optical fibers on the side of one of the PS crystals. The KDP PS crystal showed > 1 J/cm2 side scattered SRS at irradiances of 1.2 GW/cm2. The DKDP (70% deuteration level) PS crystal showed significantly less SRS. Detailed analysis of the SRS scattering in the PS crystal is in progress.

A laser ablation/ionization mass spectrometer system is described for the direct chemical analysis of solids. An Nd:YAG laser is used for ablation and ionization of the sample in a quadrupole ion trap operated in an ion-storage (IS) mode that is coupled with a reflectron time-of-flight mass spectrometer (TOF-MS). Single pulse experiments have demonstrated simultaneous detection of up to 14 elements present in glasses in the ppm range. However, detection of the components has produced non-stoichiometric results due to difference in ionization potentials and fractionation effects. Time-of-flight secondary ionization mass spectrometry (TOF-SIMS) was used to spatially map elemental species on the surface and provide further evidence of fractionation effects. Resolution (m/Dm) of 1500 and detection limits of approximately 10 pg have been achieved with a single laser pulse. The system configuration and related operating principles for accurately measuring low concentrations of isotopes are described.

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We present the first large-acceptance measurement of event-wise <p{sub t}> fluctuations in Au-Au collisions at {radical}s{sub NN} = 130 GeV. Significant nonstatistical fluctuations are observed. The measured fractional r.m.s. width excess of the event-wise <p{sub t}> distribution for the 15% most-central events for charged hadrons within |{eta}| < 1 and 0.15 {le} p{sub t} {le} 2 GeV/c is 13.7 {+-} 0.1(stat) {+-}1.3(syst)% relative to a statistical reference. The variation of charge-independent fluctuation excess with centrality is non-monotonic but smooth. Charge-dependent nonstatistical fluctuations are also observed.

A variety of electron emission processes have been studied in detail for both atomic and molecular systems, using a highly efficient experimental system comprising two time-of-flight (TOF) rotatable electron energy analyzers and a 3rd generation synchrotron light source. Two examples are used here to illustrate the obtained results. Firstly, electron emissions in the HCL molecule have been mapped over a 14 eV wide photon energy range over the Cl 2p ionization threshold. Particular attention is paid to the dissociative core-excited states, for which the Auger electron emission shows photon energy dependent features. Also, the evolution of resonant Auger to the normal Auger decay distorted by post-collision interaction has been observed and the resonating behavior of the valence photoelectron lines studied. Secondly, an atomic system, neon, in which excitation of doubly excited states and their subsequent decay to various accessible ionic states has been studied. Since these processes only occurs via inter-electron correlations, the many body dynamics of an atom can be probed, revealing relativistic effects, surprising in such a light atom. Angular distribution of the decay of the resonances to the parity unfavored continuum exhibits significant deviation from the LS coupling predictions.

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Energy Information Systems (EIS), which can monitor and analyze building energy consumption and related data throughout the Internet, have been increasing in use over the last decade. Though EIS developers describe the capabilities, costs, and benefits of EIS, many of these descriptions are idealized and often insufficient for potential users to evaluate cost, benefit and operational usefulness. LBNL has conducted a series of case studies of existing EIS and related technology installations. This study explored the following questions: (1) How is the EIS used in day-to-day operation? (2) What are the costs and benefits of an EIS? (3) Where do the energy savings come from? This paper reviews the process of these technologies from installation through energy management practice. The study is based on interviews with operators and energy managers who use EIS. Analysis of energy data trended by EIS and utility bills was also conducted to measure the benefit. This paper explores common uses and findings to identify energy savings attributable to EIS, and discusses non-energy benefits as well. This paper also addresses technologies related to EIS that have been demonstrated and evaluated by LBNL.