At the Advanced Light Source at Lawrence Berkeley National Laboratory, we are investigating how to increase both the speed and resolution of synchrotron infrared imaging. Synchrotron infrared beamlines have diffraction-limited spot sizes and high signal to noise, however spectral images must be obtained one point at a time and the spatial resolution is limited by the effects of diffraction. One technique to assist in speeding up spectral image acquisition is described here and uses compressive imaging algorithms. Compressive imaging can potentially attain resolutions higher than allowed by diffraction and/or can acquire spectral images without having to measure every spatial point individually thus increasing the speed of such maps. Here we present and discuss initial tests of compressive imaging techniques performed with ALS Beamline 1.4.3?s Nic-Plan infrared microscope, Beamline 1.4.4 Continuum XL IR microscope, and also with a stand-alone Nicolet Nexus 470 FTIR spectrometer.

Detailed spatial resolution tests were performed on beamline 1.4.4 at the Advanced Light Source synchrotron facility in Berkeley, CA. The high-brightness synchrotron source is coupled at this beamline to a Thermo-Electron Continumum XL infrared microscope. Two types of resolution tests in both the mid-IR (using a KBr beamsplitter and an MCT-A* detector) and in the near-IR (using a CaF2 beamsplitter and an InGaAS detector) were performed and compared to a simple diffraction-limited spot size model. At the shorter wavelengths in the near-IR the experimental results begin to deviate from only diffraction-limited. The entire data set is fit using a combined diffraction-limit and demagnified electron beam source size model. This description experimentally verifies how the physical electron beam size of the synchrotron source demagnified to the sample stage on the endstation begins to dominate the focussed spot size and therefore spatial resolution at higher energies. We discuss how different facilities, beamlines, and microscopes will affect the achievable spatial resolution.

Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.

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We report the detection of single ion impacts throughmonitoring of changes in the source-drain currents of field effecttransistors (FET) at room temperature. Implant apertures are formed inthe interlayer dielectrics and gate electrodes of planar, micro-scaleFETs by electron beam assisted etching. FET currents increase due to thegeneration of positively charged defects in gate oxides when ions(121Sb12+, 14+, Xe6+; 50 to 70 keV) impinge into channel regions. Implantdamage is repaired by rapid thermal annealing, enabling iterative cyclesof device doping and electrical characterization for development ofsingle atom devices and studies of dopant fluctuationeffects.

In this paper we discuss the pivotal role played by Sir John Pendry in the development of Low Energy Electron Diffraction (LEED) during the past three decades; the earliest understanding on the physics of LEED to the development of sophisticated methods for the structural solution of complex surfaces.

The National Ignition Facility (NIF), a 192-beam fusion laser, is presently under construction at the Lawrence Livermore National Laboratory with an expected completion in 2008. The facility contains 7,456 meter-scale optics for amplification, beam steering, vacuum barriers, focusing, polarization rotation, and wavelength conversion. A multiphase program was put in place to increase the monthly optical manufacturing rate by up to 20x while simultaneously reducing cost by up to 3x through a sub-scale development, full-scale facilitization, and a pilot production phase. Currently 80% of the optics are complete with over 50% installed. In order to manufacture the high quality optics at desired manufacturing rate of over 100 precision optics per month, new more deterministic advanced fabrication technologies had to be employed over those used to manufacture previous fusion lasers.

Photocatalytic lithography is an emerging technique that couples light with coated mask materials in order to pattern surface chemistry. We excite porphyrins to create radical species that photocatalytically oxidize, and thereby pattern, chemistries in the local vicinity. The technique advantageously does not necessitate mass transport or specified substrates, it is fast and robust and the wavelength of light does not limit the resolution of patterned features. We have patterned proteins and cells in order to demonstrate the utility of photocatalytic lithography in life science applications.

We present a combined theoretical and experimental study of water adsorption on Ru(0001) pre-covered with 0.25 monolayers (ML) of oxygen forming a (2 x 2) structure. Several structures were analyzed by means of Density Functional Theory calculations for which STM simulations were performed and compared with experimental data. Up to 0.25 monolayers the molecules bind to the exposed Ru atoms of the 2 x 2 unit cell via the lone pair orbitals. The molecular plane is almost parallel to the surface with its H atoms pointing towards the chemisorbed O atoms of the 2 x 2 unit cell forming hydrogen bonds. The existence of these additional hydrogen bonds increases the adsorption energy of the water molecule to approximately 616 meV, which is {approx}220 meV more stable than on the clean Ru(0001) surface with a similar configuration. The binding energy shows only a weak dependence on water coverage, with a shallow minimum for a row structure at 0.125 ML. This is consistent with the STM experiments that show a tendency of the molecules to form linear rows at intermediate coverage. Our calculations also suggest the possible formation of water dimers near 0.25 ML.

The three-dimensional particle-in-cell (3-D PIC) simulation code WARP is used to study positron confinement in antihydrogen traps. The magnetic geometry is close to that of a UC Berkeley experiment conducted, with electrons, as part of the ALPHA collaboration (W. Bertsche et al., AIP Conf. Proc. 796, 301 (2005)). In order to trap antihydrogen atoms, multipole magnetic fields are added to a conventional Malmberg-Penning trap. These multipole fields must be strong enough to confine the antihydrogen, leading to multipole field strengths at the trap wall comparable to those of the axial magnetic field. Numerical simulations reported here confirm recent experimental measurements of reduced particle confinement when a quadrupole field is added to a Malmberg-Penning trap. It is shown that, for parameters relevant to various antihydrogen experiments, the use of an octupole field significantly reducesthe positron losses seen with a quadrupole field. A unique method for obtaining a 3-D equilibrium of the positrons in the trap with a collisionless PIC code was developed especially for the study of the antihydrogen trap; however, it is of practical use for other traps as well.

The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

CO{sub 2} and heat fluxes were measured over a six-week period (09/08/2006 to 10/24/2006) by the eddy covariance (EC) technique at the Horseshoe Lake tree kill (HLTK), Mammoth Mountain, CA, a site with complex terrain and high, spatially heterogeneous CO{sub 2} emission rates. EC CO{sub 2} fluxes ranged from 218 to 3500 g m{sup -2} d{sup -1} (mean = 1346 g m{sup -2} d{sup -1}). Using footprint modeling, EC CO{sub 2} fluxes were compared to CO{sub 2} fluxes measured by the chamber method on a grid repeatedly over a 10-day period. Half-hour EC CO{sub 2} fluxes were moderately correlated (R{sup 2} = 0.42) with chamber fluxes, whereas average-daily EC CO{sub 2} fluxes were well correlated (R{sup 2} = 0.70) with chamber measurements. Average daily EC CO{sub 2} fluxes were correlated with both average daily wind speed and atmospheric pressure; relationships were similar to those observed between chamber CO{sub 2} fluxes and the atmospheric parameters over a comparable time period. Energy balance closure was assessed by statistical regression of EC energy fluxes (sensible and latent heat) against available energy (net radiation, less soil heat flux). While incomplete (R{sup 2} = 0.77 for 1:1 line), the degree of energy balance closure fell …

This paper describes models and methods for estimating theacoustic reflectivity of the welded interfaces between spot-welded sheetsfrom normal-incidence pulse-echo ultrasound signals. The simple geometryof the problem allows an abstraction that does not resort to complex waveequations. Instead, a reflectivity model predicts the timing andamplitude of the echoes arriving at the probe. This reflectivity model isnested in a signal processing model; recovering reflectivity firstrequires deconvolution to recover discrete impulses from the probesignal, then processing these with the reflectivity model. Reflectivitymaps of spot welds generated with this model show promise for predictingweld quality.

Using density-functional theory they found that, depending on coverage, coadsorbed oxygen can act both as a promoter and as an inhibitor of the dissociation of water on Ru(0001), the transition between these two behaviors occurring at (0.2 M). The key factor that determines this transition is the adsorption energy of the reaction products, OH in particular. The chemistry of this coadsorbed system is dictated by the effective coordination of the Ru atoms that participate in the bonding of the different species. In particular, they observed that a low coverage of oxygen increases the adsorption energy of the OH fraction on the Ru surface. This surprising extra stabilization of the OH with the coadsorption of oxygen can be understood in the context of the metallic bonding and could well correspond to a general trend for the coadsorption of electronegative species on metallic surfaces.

As part of the Low Level RF (LLRF) upgrade project at Brookhaven National Laboratory's Collider-Accelerator Department (BNL C-AD), we have recently developed and tested a prototype high performance embedded controller. This controller is a custom designed PMC module employing a Xilinx V4FX60 FPGA with a PowerPC405 embedded processor, and a wide variety of on board peripherals (DDR2 SDRAM, FLASH, Ethernet, PCI, multi-gigabit serial transceivers, etc.). The controller is capable of running either an embedded version of LINUX or VxWorks, the standard operating system for RHIC front end computers (FECs). We have successfully demonstrated functionality of this controller as a standard RHIC FEC and tested all on board peripherals. We now have the ability to develop complex, custom digital controllers within the framework of the standard RHIC control system infrastructure. This paper will describe various aspects of this development effort, including the basic hardware, functional capabilities, the development environment, kernel and system integration, and plans for further development.

The National Ignition Facility (NIF) requires that pulses from each of the 192 laser beams be positioned on target with an accuracy of 50 {micro}m rms. Beam quality must be sufficient to focus a total of 1.8 MJ of 0.351-{micro}m light into a 600-{micro}m-diameter volume. An optimally flat beam wavefront can achieve this pointing and focusing accuracy. The control system corrects wavefront aberrations by performing closed-loop compensation during laser alignment to correct for gas density variations. Static compensation of flashlamp-induced thermal distortion is established just prior to the laser shot. The control system compensates each laser beam at 10 Hz by measuring the wavefront with a 77-lenslet Hartmann sensor and applying corrections with a 39-actuator deformable mirror. The distributed architecture utilizes SPARC AXi computers running Solaris to perform real-time image processing of sensor data and PowerPC-based computers running VxWorks to compute mirror commands. A single pair of SPARC and PowerPC processors accomplishes wavefront control for a group of eight beams. The software design uses proven adaptive optic control algorithms that are implemented in a multi-tasking environment to economically control the beam wavefronts in parallel. Prototype tests have achieved a closed-loop residual error of 0.03 waves rms. aberrations, the spot size …

We have conducted experiments on both the Vulcan and Titan laser facilities to study hot electron generation and transport in the context of fast ignition. Cu wires attached to Al cones were used to investigate the effect on coupling efficiency of plasma surround and the pre-formed plasma inside the cone. We found that with thin cones 15% of laser energy is coupled to the 40{micro}m diameter wire emulating a 40{micro}m fast ignition spot. Thick cone walls, simulating plasma in fast ignition, reduce coupling by x4. An increase of prepulse level inside the cone by a factor of 50 reduces coupling by a factor of 3.

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Recent studies demonstrated that Zn-phyllosilicate- and Zn-layered double hydroxide-type (Zn-LDH) precipitates may form in contaminated soils. However, the influence of soil properties and Zn content on the quantity and type of precipitate forming has not been studied in detail so far. In this work, we determined the speciation of Zn in six carbonate-rich surface soils (pH 6.2 to 7.5) contaminated by aqueous Zn in the runoff from galvanized power line towers (1322 to 30090 mg/kg Zn). Based on 12 bulk and 23 microfocused extended X-ray absorption fine structure (EXAFS) spectra, the number, type and proportion of Zn species were derived using principal component analysis, target testing, and linear combination fitting. Nearly pure Zn-rich phyllosilicate and Zn-LDH were identified at different locations within a single soil horizon, suggesting that the local availabilities of Al and Si controlled the type of precipitate forming. Hydrozincite was identified on the surfaces of limestone particles that were not in direct contact with the soil clay matrix. With increasing Zn loading of the soils, the percentage of precipitated Zn increased from {approx}20% to {approx}80%, while the precipitate type shifted from Zn-phyllosilicate and/or Zn-LDH at the lowest studied soil Zn contents over predominantly Zn-LDH at intermediate loadings …

Corrosion of steel canisters, stored in a repository for spent fuel and high-level nuclear wastes, leads to the generation and accumulation of hydrogen gas in the backfilled emplacement tunnels, which may significantly affect long-term repository safety. Previous studies used H{sub 2} generation rates based on the volume of the waste or canister material and the stoichiometry of the corrosion reaction. However, iron corrosion and H{sub 2} generation rates vary with time, depending on factors such as amount of iron, water availability, water contact area, and aqueous and solid chemistry. To account for these factors and feedback mechanisms, we developed a chemistry model related to iron corrosion, coupled with two-phase (liquid and gas) flow phenomena that are driven by gas-pressure buildup associated with H{sub 2} generation and water consumption. Results indicate that by dynamically calculating H{sub 2} generation rates based on a simple model of corrosion chemistry, and by coupling this corrosion reaction with two-phase flow processes, the degree and extent of gas pressure buildup could be much smaller compared to a model that neglects the coupling between flow and reactive transport mechanisms. By considering the feedback of corrosion chemistry, the gas pressure increases initially at the canister, but later decreases …

Amorphous titania (TiO{sub 2}) is an important precursor for synthesis of single-phase nanocrystalline anatase. We synthesized x-ray amorphous titania by hydrolysis of titanium ethoxide at the ice point. Transmission electron microscopy examination and nitrogen gas adsorption indicated the particle size of the synthesized titania is {approx} 2 nm. Synchrotron wide-angle x-ray scattering (WAXS) was used to probe the atomic correlations in this amorphous sample. Atomic pair-distribution function (PDF) derived from Fourier transform of the WAXS data was used for reverse Monte Carlo (RMC) simulations of the atomic structure of the amorphous TiO{sub 2} nanoparticles. Molecular dynamics simulations were used to generate input structures for the RMC. X-ray absorption spectroscopy (XAS) simulations were used to screen candidate structures obtained from the RMC by comparing with experimental XAS data. The structure model that best describes both the WAXS and XAS data shows that an amorphous TiO{sub 2} particle consists of a highly distorted shell and a small strained anatase-like crystalline core. The average coordination number of Ti is 5.3 and most Ti-O bonds are populated around 1.940 {angstrom}. Relative to bulk TiO{sub 2}, the reduction of the coordination number is primarily due to the truncation of the Ti-O octahedra at the amorphous …

Recent CO{sub 2} sequestration pilot projects have implemented novel approaches to well-based subsurface monitoring aimed at increasing the amount and quality of information available from boreholes. Some of the drivers for the establishment of new well-based technologies and methodologies arise from: (1) the need for data to assess physical and geochemical subsurface processes associated with CO{sub 2} emplacement; (2) the high cost of deep boreholes and need to maximize data yield from each; (3) need for increased temporal resolution to observe plume evolution; (4) a lack of established processes and technologies for integrated permanent sensors in the oil and gas industry; and (5) a lack of regulatory guidance concerning the amount, type, and duration of monitoring required for long-term performance confirmation of a CO{sub 2} storage site. In this paper we will examine some of the latest innovations in well-based monitoring and present examples of integrated monitoring programs.

During an incident of national significance involving radioactive materials protective action guides (PAGs) are established to protect workers and the public from harmful exposure levels of radioactive materials. The PAGs are stated in terms of dose and must be converted to measurable quantities in various media (DRLs). This workshop will present the current PAGs, methods for converting the PAGs to DRLs, and using the Data Quality Objectives process in the Multi-agency Radiological Laboratory Analytical Protocols Manual (MARLAP), derive measurement quality objectives (MQOs) for the laboratories. Examples from the Empire 09 exercise will be used in this presentation.

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