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.

The attached report contains the final technical report for the above-mentioned project.

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.

The purpose of this report is to provide a concise but comprehensive overview of Atmospheric Radiation Measurement Climate Research Facility instrumentation status. The report is divided into the following five sections: (1) new instrumentation in the process of being acquired and deployed, (2) field campaigns, (3) existing instrumentation and progress on improvements or upgrades, (4) proposed future instrumentation, and (5) Small Business Innovation Research instrument development.

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.

JET has performed two dedicated carbon migration experiments on the final run day of separate campaigns (2001 and 2004) using {sup 13}CH{sub 4} methane injected into repeated discharges. The EDGE2D/NIMBUS code modelled the carbon migration in both experiments. This paper describes this modelling and identifies a number of important migration pathways: (1) deposition and erosion near the injection location, (2) migration through the main chamber SOL, (3) migration through the private flux region aided by E x B drifts, and (4) neutral migration originating near the strike points. In H-Mode, type I ELMs are calculated to influence the migration by enhancing erosion during the ELM peak and increasing the long-range migration immediately following the ELM. The erosion/re-deposition cycle along the outer target leads to a multistep migration of {sup 13}C towards the separatrix which is called 'walking'. This walking created carbon neutrals at the outer strike point and led to {sup 13}C deposition in the private flux region. Although several migration pathways have been identified, quantitative analyses are hindered by experimental uncertainty in divertor leakage, and the lack of measurements at locations such as gaps and shadowed regions.

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Structural Health Monitoring (SHM) promises to deliver great benefits to many industries. Primarily among them is a potential for large cost savings in maintenance of complex structures such as aircraft and civil infrastructure. However, several large obstacles remain before widespread use on structures can be accomplished. The development of three components would address many of these obstacles: a robust sensor validation procedure, a low-cost active-sensing hardware and an integrated software package for transition to field deployment. The research performed in this thesis directly addresses these three needs and facilitates the adoption of SHM on a larger scale, particularly in the realm of SHM based on piezoelectric (PZT) materials. The first obstacle addressed in this thesis is the validation of the SHM sensor network. PZT materials are used for sensor/actuators because of their unique properties, but their functionality also needs to be validated for meaningful measurements to be recorded. To allow for a robust sensor validation algorithm, the effect of temperature change on sensor diagnostics and the effect of sensor failure on SHM measurements were classified. This classification allowed for the development of a sensor diagnostic algorithm that is temperature invariant and can indicate the amount and type of sensor failure. …

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.

In response to DOE's Solicitation for Grant Applications DE-PS36-03GO93007, 'Hydrogen Production and Delivery Research', SRI International (SRI) proposed to conduct work under Technical Topic Area 5, Advanced Electrolysis Systems; Sub-Topic 5B, High-Temperature Steam Electrolysis. We proposed to develop a prototype of a modular industrial system for low-cost generation of H{sub 2} (<$2/kg) by steam electrolysis with anodic depolarization by CO. Water will be decomposed electrochemically into H{sub 2} and O{sub 2} on the cathode side of a high-temperature electrolyzer. Oxygen ions will migrate through an oxygen-ion-conductive solid oxide electrolyte. Gas mixtures on the cathode side (H{sub 2} + H{sub 2}O) and on the anode side (CO + CO{sub 2}) will be reliably separated by the solid electrolyte. Depolarization of the anodic process will decrease the electrolysis voltage, and thus the electricity required for H{sub 2} generation and the cost of produced H{sub 2}. The process is expected to be at least 10 times more energy-efficient than low-temperature electrolysis and will generate H{sub 2} at a cost of approximately $1-$1.5/kg. The operating economics of the system can be made even more attractive by deploying it at locations where waste heat is available; using waste heat would reduce the electricity required for …

The U.S. Department of Energy (DOE) and the U.S. Council for Automotive Research (composed of automakers Ford, General Motors, and Chrysler) announced in January 2002 a new cooperative research effort. Known as FreedomCAR (derived from 'Freedom' and 'Cooperative Automotive Research'), it represents DOE's commitment to developing public/private partnerships to fund high-risk, high-payoff research into advanced automotive technologies. Efficient fuel cell technology, which uses hydrogen to power automobiles without air pollution, is a very promising pathway to achieve the ultimate vision. The new partnership replaces and builds upon the Partnership for a New Generation of Vehicles initiative that ran from 1993 through 2001. The Advanced Power Electronics and Electric Machines (APEEM) subprogram within the Vehicle Technologies Program provides support and guidance for many cutting-edge automotive technologies now under development. Research is focused on understanding and improving the way the various new components of tomorrow's automobiles will function as a unified system to improve fuel efficiency. In supporting the development of hybrid propulsion systems, the APEEM effort has enabled the development of technologies that will significantly improve advanced vehicle efficiency, costs, and fuel economy. The APEEM subprogram supports the efforts of the FreedomCAR and Fuel Partnership through a three-phase approach intended to: …

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.

This research project falls in the domain of response surface methodology, which seeks cost-effective ways to accurately fit an approximate function to experimental data. Modeling and computer simulation are essential tools in modern science and engineering. A computer simulation can be viewed as a function that receives input from a given parameter space and produces an output. Running the simulation repeatedly amounts to an equivalent number of function evaluations, and for complex models, such function evaluations can be very time-consuming. It is then of paramount importance to intelligently choose a relatively small set of sample points in the parameter space at which to evaluate the given function, and then use this information to construct a surrogate function that is close to the original function and takes little time to evaluate. This study was divided into two parts. The first part consisted of comparing four sampling methods and two function approximation methods in terms of efficiency and accuracy for simple test functions. The sampling methods used were Monte Carlo, Quasi-Random LP{sub {tau}}, Maximin Latin Hypercubes, and Orthogonal-Array-Based Latin Hypercubes. The function approximation methods utilized were Multivariate Adaptive Regression Splines (MARS) and Support Vector Machines (SVM). The second part of the study …

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.

Most prokaryotes of interest to DOE are poorly understood. Even when full genomic sequences are available, the function of only a small number of gene products are clear. The critical question is how to best infer the most probable network architectures in cells that are poorly characterized. The project goal is to create a computational hypothesis testing (CHT) framework that combines large-scale dynamical simulation, a database of bioinformatics-derived probable interactions, and numerical parallel architecture data-fitting routines to explore many “what if ?” hypotheses about the functions of genes and proteins within pathways and their downstream effects on molecular concentration profiles and corresponding phenotypes. From this framework we expect to infer signal transduction pathways and gene expression networks in prokaryotes. Detailed mechanistic models of E. Coli have been developed that directly incorporate DNA sequence information. The CHT framework is implemented in the NIEngine network inference software. NIEngine has been applied to recover gene regulatory networks in E. coli to assess performance. Application to Shewanel la oneidensi and other organism of interest DOE will be conducted in partnership with Jim Collin's Lab at Boston University and other academic partners. The CHT framework has also found broad application in the automated learning of …

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.

This report summarizes the methodology and results of a user perspectives study conducted by the Community Driven Improvement of Globus Software (CDIGS) project. The purpose of the study was to document the work-related goals and challenges facing today's scientific technology users, to record their perspectives on Globus software and the distributed-computing ecosystem, and to provide recommendations to the Globus community based on the observations. Globus is a set of open source software components intended to provide a framework for collaborative computational science activities. Rather than attempting to characterize all users or potential users of Globus software, our strategy has been to speak in detail with a small group of individuals in the scientific community whose work appears to be the kind that could benefit from Globus software, learn as much as possible about their work goals and the challenges they face, and describe what we found. The result is a set of statements about specific individuals experiences. We do not claim that these are representative of a potential user community, but we do claim to have found commonalities and differences among the interviewees that may be reflected in the user community as a whole. We present these as a series …

During two years of SciDAC PERC-2, our activities had centered largely on development of new performance analysis techniques to enable efficient use on systems containing thousands or tens of thousands of processors. In addition, we continued our application engagement efforts and utilized our tools to study the performance of various SciDAC applications on a variety of HPC platforms.

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 …

Global sensitivity analysis (GSA) measures the variation of a model output as a function of the variations of the model inputs given their ranges. In this paper we consider variance-based GSA methods that do not rely on certain assumptions about the model structure such as linearity or monotonicity. These variance-based methods decompose the output variance into terms of increasing dimensionality called 'sensitivity indices', first introduced by Sobol' [25]. Sobol' developed a method of estimating these sensitivity indices using Monte Carlo simulations. McKay [13] proposed an efficient method using replicated Latin hypercube sampling to compute the 'correlation ratios' or 'main effects', which have been shown to be equivalent to Sobol's first-order sensitivity indices. Practical issues with using these variance estimators are how to choose adequate sample sizes and how to assess the accuracy of the results. This paper proposes a modified McKay main effect method featuring an adaptive procedure for accuracy assessment and improvement. We also extend our adaptive technique to the computation of second-order sensitivity indices. Details of the proposed adaptive procedure as wells as numerical results are included in this paper.

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.