Working at Lawrence Livermore National Laboratory (LLNL) this summer has provided a very unique and special experience for me. I feel that the research opportunities given to me have allowed me to significantly benefit my research group, the laboratory, the Department of Homeland Security, and the Department of Energy. The researchers in the Single Particle Aerosol Mass Spectrometry (SPAMS) group were very welcoming and clearly wanted me to get the most out of my time in Livermore. I feel that my research partner, Veena Venkatachalam of MIT, and I have been extremely productive in meeting our research goals throughout this summer, and have learned much about working in research at a national laboratory such as Lawrence Livermore. I have learned much about the technical aspects of research while working at LLNL, however I have also gained important experience and insight into how research groups at national laboratories function. I believe that this internship has given me valuable knowledge and experience which will certainly help my transition to graduate study and a career in engineering. My work with Veena Venkatachalam in the SPAMS group this summer has focused on two major projects. Initially, we were tasked with an analysis of data …

Magnetic resonance imaging (MRI) has developed into a powerful clinical tool for imaging the human body (1). This technique is based on nuclear magnetic resonance (NMR) of protons (2, 3) in a static magnetic field B{sub 0}. An applied radiofrequency pulse causes the protons to precess about B{sub 0} at their Larmor frequency {nu}{sub 0} = ({gamma}/2{pi})B{sub 0}, where {gamma} is the gyromagnetic ratio; {gamma}/2{pi} = 42.58 MHz/tesla. The precessing protons generate an oscillating magnetic field and hence a voltage in a nearby coil that is amplified and recorded. The application of three-dimensional magnetic field gradients specifies a unique magnetic field and thus an NMR frequency in each voxel of the subject, so that with appropriate encoding of the signals one can acquire a complete image (4). Most clinical MRI systems involve magnetic fields generated by superconducting magnets, and the current trend is to higher magnetic fields than the widely used 1.5-T systems (5). Nonetheless, there is ongoing interest in the development of less expensive imagers operating at lower fields. Commercially available 0.2-T systems based on permanent magnets offer both lower cost and a more open access than their higher-field counterparts, at the expense of signal-to-noise-ratio (SNR) and spatial resolution. …

As the development of extreme ultraviolet (EUV) lithography progresses, interest grows in the extension of traditional optical components to the EUV regime. The strong absorption of EUV by most materials and its extremely short wavelength, however, makes it very difficult to implement many components that are commonplace in the longer wavelength regimes. One such component is the diffractive optical element used, for example, in illumination systems to efficiently generate modified pupil fills. Here we demonstrate the fabrication and characterization of EUV binary phase-only computer-generated holograms allowing arbitrary far-field diffraction patterns to be generated.

The National Ignition Facility (NIF) is a 192-beam Nd:glass laser facility being constructed at the Lawrence Livermore National Laboratory (LLNL) to conduct research in inertial confinement fusion (ICF) and high energy density (HED) science. When completed, NIF will produce 1.8 MJ, 500 TW of ultraviolet light, making it the world's largest and highest-energy laser system. The NIF is poised to become the world's preeminent facility for conducting ICF and fusion energy research and for studying matter at extreme densities and temperatures.

High-contrast adaptive optics systems, such as those needed to image extrasolar planets, are known to require excellent wavefront control and diffraction suppression. At the Laboratory for Adaptive Optics on the Extreme Adaptive Optics testbed, we have already demonstrated wavefront control of better than 1 nm rms within controllable spatial frequencies. Corresponding contrast measurements, however, are limited by amplitude variations, including those introduced by the micro-electrical-mechanical-systems (MEMS) deformable mirror. Results from experimental measurements and wave optic simulations of amplitude variations on the ExAO testbed are presented. We find systematic intensity variations of about 2% rms, and intensity variations with the MEMS to be 6%. Some errors are introduced by phase and amplitude mixing because the MEMS is not conjugate to the pupil, but independent measurements of MEMS reflectivity suggest that some error is introduced by small non-uniformities in the reflectivity.

In 1949-1951 the University of California was traumatized and seriously damaged by a Loyalty Oath controversy. Wolfgang K. H. Panofsky, a young and promising physics professor and researcher at Lawrence's Radiation Laboratory, was caught up in the turmoil.

The beam delivery system for the linear collider focuses beams to nanometer sizes at its interaction point, collimates the beam halo to provide acceptable background in the detector and has a provision for state-of-the art beam instrumentation in order to reach the ILCs physics goals. This paper describes the design details and status of the baseline configuration considered for the reference design and also lists alternatives.

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A robust multivariate time series method has been established for the Monte Carlo calculation of neutron multiplication problems. The method is termed Coarse Mesh Projection Method (CMPM) and can be implemented using the coarse statistical bins for acquisition of nuclear fission source data. A novel aspect of CMPM is the combination of the general technical principle of projection pursuit in the signal processing discipline and the neutron multiplication eigenvalue problem in the nuclear engineering discipline. CMPM enables reactor physicists to accurately evaluate major eigenvalue separations of nuclear reactors with continuous energy Monte Carlo calculation. CMPM was incorporated in the MCNP Monte Carlo particle transport code of Los Alamos National Laboratory. The great advantage of CMPM over the traditional Fission Matrix method is demonstrated for the three space-dimensional modeling of the initial core of a pressurized water reactor.

Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least …

Mineral carbonation is a promising concept for permanent CO{sub 2} sequestration due to the vast natural abundance of the raw materials and the permanent storage of CO{sub 2} in solid form as carbonates. The sequestration of CO{sub 2} through the employment of magnesium silicates--olivine and serpentine--is beyond the proof of concept stage. For the work done in this project, serpentine was chosen as the feedstock mineral due to its abundance and availability. Although the reactivity of olivine is greater than that of serpentine, physical and chemical treatments have been shown to increase greatly the reactivity of serpentine. The primary drawback to mineral carbonation is reaction kinetics. To accelerate the carbonation, aqueous processes are preferred, where the minerals are first dissolved in solution. In aqueous carbonation, the key step is the dissolution rate of the mineral, where the mineral dissolution reaction is likely to be surface-controlled. The relatively low reactivity of serpentine has warranted research into physical and chemical treatments that have been shown to greatly increase its reactivity. The use of sulfuric acid as an accelerating medium for the removal of magnesium from serpentine has been investigated. To accelerate the dissolution process, the mineral can be ground to very fine …

Cross sections that cannot be measured in the laboratory, e.g. because the target lifetime is too short, can be inferred indirectly from a different reaction forming the same compound system, but with a more accessible beam/target combination (the ''surrogate-reaction'' technique). The reactions share the same compound system and a common decay mechanism, but they involve different formation processes. Therefore, an implicit constraint is imposed on the inferred cross section deduced from the measured surrogate-reaction data, through the common decay mechanism. In this paper, the mathematical consequences of this implicit constraint are investigated. General formulas are derived from upper and lower bounds on the inferred cross section, estimated from surrogate data in a procedure which does not require any modeling of the common decay process. As an example, the formulas developed here are applied to the case of the {sup 235}U(n,f) cross section, deduced from {sup 234}U(t,pf) surrogate data. The calculated bounds are not very tight in this particular case. However, by introducing a few qualitative assumptions about the physics of the fission process, meaningful bounds on the deduced cross section are obtained. Upper and lower limits for the cross-section ratio of the (n,f) reaction on the {sup 235}U isomer at …

Simulations of the x-ray free-electron laser (FEL) oscillator are presented that include transverse effects and realistic Bragg crystal properties with the two-dimensional code GINGER. In the present cases considered the radiation divergence is much narrower than the crystal acceptance, and the numerical algorithm can be simplified by ignoring the finite angular bandwidth of the crystal. In this regime GINGER shows that the saturated x-ray pulses have 109 photons and are nearly Fourier-limited with peak powers in excess of 1 MW. Wealso include preliminary results for a four-mirror cavity that can be tuned in wavelength over a few percent, with future plans to incorporate the full transverse response of the Bragg crystals into GINGER to more accurately model this tunable source.

Pacific Northwest National Laboratory (PNNL) has been tasked by Bechtel National Inc. (BNI) on the River Protection Project-Hanford Tank Waste Treatment and Immobilization Plant (RPP-WTP) project to perform research and development activities to resolve technical issues identified for the Pretreatment Facility (PTF). The Pretreatment Engineering Platform (PEP) was designed and constructed and is to be operated as part of a plan to respond to issue M12, “Undemonstrated Leaching Processes.” The PEP is a 1/4.5-scale test platform designed to simulate the WTP pretreatment caustic leaching, oxidative leaching, ultrafiltration solids concentration, and slurry washing processes. The PEP replicates the WTP leaching processes using prototypic equipment and control strategies. The PEP also includes non-prototypic ancillary equipment to support the core processing. Two operating scenarios are currently being evaluated for the ultrafiltration process (UFP) and leaching operations. The first scenario has caustic leaching performed in the UFP-2 ultrafiltration feed vessels (i.e., vessel UFP-VSL-T02A in the PEP; and vessels UFP-VSL-00002A and B in the WTP PTF). The second scenario has caustic leaching conducted in the UFP-1 ultrafiltration feed preparation vessels (i.e., vessels UFP-VSL-T01A and B in the PEP; vessels UFP-VSL-00001A and B in the WTP PTF). In both scenarios, 19-M sodium hydroxide solution (NaOH, caustic) …

We present experimental studies of the gain length and saturation power level from 1.5 nm to 1.5 Angstroms at the Linac Coherent Light Source (LCLS). By disrupting theFEL process with an orbit kick, we are able to measure the X-ray intensity as a function of undulator length. This kick method is cross-checked with the method of removing undulator sections. We also study the FEL-induced electron energy loss after saturation to determine the optimal taper of the undulator K values. The experimental results are compared to theory and simulations.

Pacific Northwest National Laboratory (PNNL) has been tasked by Bechtel National Inc. (BNI) on the River Protection Project-Hanford Tank Waste Treatment and Immobilization Plant (RPP-WTP) project to perform research and development activities to resolve technical issues identified for the Pretreatment Facility (PTF). The Pretreatment Engineering Platform (PEP) was designed, constructed, and operated as part of a plan to respond to issue M12, “Undemonstrated Leaching Processes.” The PEP is a 1/4.5-scale test platform designed to simulate the WTP pretreatment caustic leaching, oxidative leaching, ultrafiltration solids concentration, and slurry washing processes. The PEP replicates the WTP leaching processes using prototypic equipment and control strategies. Two operating scenarios were evaluated for the ultrafiltration process (UFP) and leaching operations. The first scenario has caustic leaching performed in the UFP-VSL-T01A/B ultrafiltration feed vessels, identified as Integrated Test A. The second scenario has caustic leaching conducted in the UFP-VSL-T02A ultrafiltration feed preparation vessel, identified as Integrated Test B. Washing operations in PEP Integrated Tests A and B were conducted successfully as per the approved run sheets. However, various minor instrumental problems occurred, and some of the process conditions specified in the run sheet were not met during the wash operations, such as filter-loop flow-rate targets not …

The second stage of the FERMI FEL, named FEL-2, is based on the principle of high-gain harmonic generation and relies on a double-seeded cascade. Recent developments stimulated a revision of the original setup, which was designed to cover the spectral range between 40 and 10 nm. The numerical simulations we present here show that the nominal (expected) electron-beam performance allows extension of the FEL spectral range down to 4 nm. A significant amount of third harmonic power can be also expected. We also show that the proposed setup is flexible enough for exploiting future developments of new seed sources, e.g., high harmonic generation in gases.

Bright ?eld imaging of biological samples stained with antibodies and/or special stains provides a rapid protocol for visualizing various macromolecules. However, this method of sample staining and imaging is rarely employed for direct quantitative analysis due to variations in sample fixations, ambiguities introduced by color composition, and the limited dynamic range of imaging instruments. We demonstrate that, through the decomposition of color signals, staining can be scored on a cell-by-cell basis. We have applied our method to Flbroblasts grown from histologically normal breast tissue biopsies obtained from two distinct populations. Initially, nuclear regions are segmented through conversion of color images into gray scale, and detection of dark elliptic features. Subsequently, the strength of staining is quanti?ed by a color decomposition model that is optimized by a graph cut algorithm. In rare cases where nuclear signal is significantly altered as a result of samplepreparation, nuclear segmentation can be validated and corrected. Finally, segmented stained patterns are associated with each nuclear region following region-based tessellation. Compared to classical non-negative matrix factorization, proposed method (i) improves color decomposition, (ii) has a better noise immunity, (iii) is more invariant to initial conditions, and (iv) has a superior computing performance

The Department of Energy Livermore Site Office requested a technical review of remedial alternatives proposed for the Building 812 Operable Unit, Site 300 at the Lawrence Livermore National Laboratory. The team visited the site and reviewed the alternatives proposed for soil remediation in the draft RI/FS and made the following observations and recommendations. Based on the current information available for the site, the team did not identify a single technology that would be cost effective and/or ecologically sound to remediate DU contamination at Building 812 to current remedial goals. Soil washing is not a viable alternative and should not be considered at the site unless final remediation levels can be negotiated to significantly higher levels. This recommendation is based on the results of soil washing treatability studies at Fernald and Ashtabula that suggest that the technology would only be effective to address final remediation levels higher than 50 pCi/g. The technical review team identified four areas of technical uncertainty that should be resolved before the final selection of a preferred remedial strategy is made. Areas of significant technical uncertainty that should be addressed include: (1) Better delineation of the spatial distribution of surface contamination and the vertical distribution of subsurface …

Epigenetics refers to the study of heritable changes in genome function that occur without a change in primary DNA sequence. The 2009 Gordon Conference in Epigenetics will feature discussion of various epigenetic phenomena, emerging understanding of their underlying mechanisms, and the growing appreciation that human, animal, and plant health all depend on proper epigenetic control. Special emphasis will be placed on genome-environment interactions particularly as they relate to human disease. Towards improving knowledge of molecular mechanisms, the conference will feature international leaders studying the roles of higher order chromatin structure, noncoding RNA, repeat elements, nuclear organization, and morphogenic evolution. Traditional and new model organisms are selected from plants, fungi, and metazoans.

The Rare Isotope Science Assessment Committee (RISAC) was convened by the National Research Council in response to an informal request from the DOE’s Office of Nuclear Physics and the White House Office of Management and Budget. The charge to the committee is to examine and assess the broader scientific and international contexts of a U.S.-based rare-isotope facility. The committee met for the first time on December 16-17, 2005, in Washington, DC, and held three subsequent meetings. The committee’s final report was publicly released in unedited, prepublication form on Friday, December 8, 2006. The report was published in full-color by the National Academies Press in April 2007. Copies of the report were distributed to key decision makers and stakeholders around the world.

Simulations were completed to determine the energy deposition of an ILC bunch using FLUKA, Geant4 and EGS4 to a set of different spoiler designs. These shower simulations were used as inputs to thermal and mechanical studies using ANSYS. This paper presents a proposal to optimize the material choice and mechanical design of ILC spoilers jaws using ATF and benchmark the energy deposition simulations and the ANSYS studies giving the researchers valuable data which will help achieve a definitive ILC spoiler design.

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Pathogen identification is a crucial first defense against bioterrorism. A major emphasis of our national biodefense strategy is to establish fast, accurate and sensitive assays for diagnosis of infectious diseases agents. Such assays will ensure early and appropriate treatment of infected patients. Rapid diagnostics can also support infection control measures, which monitor and limit the spread of infectious diseases agents. Many select agents are highly transmissible in the early stages of disease, and it is critical to identify infected patients and limit the risk to the remainder of the population and to stem potential panic in the general population. Nucleic acid-based molecular approaches for identification overcome many of the deficiencies associated with conventional culture methods by exploiting both large- and small-scale genomic differences between organisms. PCR-based amplification of highly conserved ribosomal RNA (rRNA) genes, intergenic sequences, and specific toxin genes is currently the most reliable approach for bacterial, fungal and many viral pathogenic agents. When combined with fluorescence-based oligonucleotide detection systems, this approach provides real-time, quantitative, high fidelity analysis capable of single nucleotide allelic discrimination (4). These probe systems offer rapid turn around time (<2 h) and are suitable for high throughput, automated multiplex operations that are critical for clinical …