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Progress on the Design and Fabrication of the MICE Focusing Magnets

Description: The Muon Ionization Cooling Experiment (MICE) focusing solenoid magnets focus the muon beam within the MICE cooling channel on a liquid or solid absorber that is within the warm bore of solenoid. The focusing magnet has a warm bore of 470 mm. his magnet consists of two coils 210-mm long that is separated by an aluminum mandrel that is 200 mm long. Each of the coils has its own leads. The coils may be operated in either the non-flip mode (solenoid mode with both coils at the same polarity) or the lip mode (quadrupole focusing mode where both coils are at opposite polarity). This report describes the focusing solenoid magnet design that will be built by the vendor. The progress on the construction of the first of the focusing magnets will also be discussed in this report. Ultimately three of these magnets will be built. These magnets will be cooled using a pair 1.5 W (at 4.2 K) pulse tube coolers.
Date: October 19, 2009
Creator: Green, Michael A; Baynham, D. Elwyn; Bradshaw, Thomas W.; Cobb, John H.; Lau, Wing W. & Yang, Stephanie Q.

HER2 signaling pathway activation and response of breast cancer cells to HER2-targeting agents is dependent strongly on the 3D microenvironment

Description: Development of effective and durable breast cancer treatment strategies requires a mechanistic understanding of the influence of the microenvironment on response. Previous work has shown that cellular signaling pathways and cell morphology are dramatically influenced by three-dimensional (3D) cultures as opposed to traditional two-dimensional (2D) monolayers. Here, we compared 2D and 3D culture models to determine the impact of 3D architecture and extracellular matrix (ECM) on HER2 signaling and on the response of HER2-amplified breast cancer cell lines to the HER2-targeting agents Trastuzumab, Pertuzumab and Lapatinib. We show that the response of the HER2-amplified AU565, SKBR3 and HCC1569 cells to these anti-HER2 agents was highly dependent on whether the cells were cultured in 2D monolayer or 3D laminin-rich ECM gels. Inhibition of {beta}1 integrin, a major cell-ECM receptor subunit, significantly increased the sensitivity of the HER2-amplified breast cancer cell lines to the humanized monoclonal antibodies Trastuzumab and Pertuzumab when grown in a 3D environment. Finally, in the absence of inhibitors, 3D cultures had substantial impact on HER2 downstream signaling and induced a switch between PI3K-AKT- and RAS-MAPKpathway activation in all cell lines studied, including cells lacking HER2 amplification and overexpression. Our data provide direct evidence that breast cancer cells are able to rapidly adapt to different environments and signaling cues by activating alternative pathways that regulate proliferation and cell survival, events that may play a significant role in the acquisition of resistance to targeted therapies.
Date: July 27, 2009
Creator: Weigelt, Britta; Lo, Alvin T; Park, Catherine C; Gray, Joe W & Bissell, Mina J

Ultrafast gigantic photo-response in charge-ordered organic salt (EDO-TTF)2PF6 on 10-fs time scales

Description: The initial dynamics of photo-induced phase transition in charge-ordered organic salt (EDO-TTF){sub 2}PF{sub 6} was investigated using 10-fs near-infrared laser pulses. We observed sub-20-fs gigantic photo-responses (|{Delta}R/R|>100%) due to intra-molecular vibration and a clear signature of a structural bottleneck ({approx}50 fs) for the first time.
Date: August 1, 2008
Creator: Itatani, J.; Rini, M.; Cavalleri, A.; Onda, K.; Ishikawa, T.; Ogihara, S. et al.

Elements of an environmental decision support system for seasonal wetland salt management in a river basin subjected to water quality regulation

Description: Seasonally managed wetlands in the Grasslands Basin on the west-side of California's San Joaquin Valley provide food and shelter for migratory wildfowl during winter months and sport for waterfowl hunters during the annual duck season. Surface water supply to these wetlands contain salt which, when drained to the San Joaquin River during the annual drawdown period, can negatively impact water quality and cause concern to downstream agricultural riparian water diverters. Recent environmental regulation, limiting discharges salinity to the San Joaquin River and primarily targeting agricultural non-point sources, now also targets return flows from seasonally managed wetlands. Real-time water quality management has been advocated as a means of continuously matching salt loads discharged from agricultural, wetland and municipal operations to the assimilative capacity of the San Joaquin River. Past attempts to build environmental monitoring and decision support systems (EDSS's) to implement this concept have enjoyed limited success for reasons that are discussed in this paper. These reasons are discussed in the context of more general challenges facing the successful implementation of a comprehensive environmental monitoring, modelling and decision support system for the San Joaquin River Basin.
Date: June 1, 2009
Creator: Quinn, N.W.T.

Multi-Modality Phantom Development

Description: Multi-modality imaging has an increasing role in the diagnosis and treatment of a large number of diseases, particularly if both functional and anatomical information are acquired and accurately co-registered. Hence, there is a resulting need for multi modality phantoms in order to validate image co-registration and calibrate the imaging systems. We present our PET-ultrasound phantom development, including PET and ultrasound images of a simple prostate phantom. We use agar and gelatin mixed with a radioactive solution. We also present our development of custom multi-modality phantoms that are compatible with PET, transrectal ultrasound (TRUS), MRI and CT imaging. We describe both our selection of tissue mimicking materials and phantom construction procedures. These custom PET-TRUS-CT-MRI prostate phantoms use agargelatin radioactive mixtures with additional contrast agents and preservatives. We show multi-modality images of these custom prostate phantoms, as well as discuss phantom construction alternatives. Although we are currently focused on prostate imaging, this phantom development is applicable to many multi-modality imaging applications.
Date: March 20, 2009
Creator: Huber, Jennifer S.; Peng, Qiyu & Moses, William W.

Combined U-Th/He and 40Ar/39Ar geochronology of post-shield lavas from the Mauna Kea and Kohala volcanoes, Hawaii

Description: Late Quaternary, post-shield lavas from the Mauna Kea and Kohala volcanoes on the Big Island of Hawaii have been dated using the {sup 40}Ar/{sup 39}Ar and U-Th/He methods. The objective of the study is to compare the recently demonstrated U-Th/He age method, which uses basaltic olivine phenocrysts, with {sup 40}Ar/{sup 39}Ar ages measured on groundmass from the same samples. As a corollary, the age data also increase the precision of the chronology of volcanism on the Big Island. For the U-Th/He ages, U, Th and He concentrations and isotopes were measured to account for U-series disequilibrium and initial He. Single analyses U-Th/He ages for Hamakua lavas from Mauna Kea are 87 {+-} 40 ka to 119 {+-} 23 ka (2{sigma} uncertainties), which are in general equal to or younger than {sup 40}Ar/{sup 39}Ar ages. Basalt from the Polulu sequence on Kohala gives a U-Th/He age of 354 {+-} 54 ka and a {sup 40}Ar/{sup 39}Ar age of 450 {+-} 40 ka. All of the U-Th/He ages, and all but one spurious {sup 40}Ar/{sup 39}Ar ages conform to the previously proposed stratigraphy and published {sup 14}C and K-Ar ages. The ages also compare favorably to U-Th whole rock-olivine ages calculated from {sup 238}U - {sup 230}Th disequilibria. The U-Th/He and {sup 40}Ar/{sup 39}Ar results agree best where there is a relatively large amount of radiogenic {sup 40}Ar (>10%), and where the {sup 40}Ar/{sup 36}Ar intercept calculated from the Ar isochron diagram is close to the atmospheric value. In two cases, it is not clear why U-Th/He and {sup 40}Ar/{sup 39}Ar ages do not agree within uncertainty. U-Th/He and {sup 40}Ar/{sup 39}Ar results diverge the most on a low-K transitional tholeiitic basalt with abundant olivine. For the most alkalic basalts with negligible olivine phenocrysts, U-Th/He ages were unattainable while {sup 40}Ar/{sup 39}Ar ...
Date: October 1, 2009
Creator: Aciego, S.M.; Jourdan, F.; DePaolo, D.J.; Kennedy, B.M.; Renne, P.R. & Sims, K.W.W.

A comparison of global optimization algorithms with standard benchmark functions and real-world applications using Energy Plus

Description: There is an increasing interest in the use of computer algorithms to identify combinations of parameters which optimise the energy performance of buildings. For such problems, the objective function can be multi-modal and needs to be approximated numerically using building energy simulation programs. As these programs contain iterative solution algorithms, they introduce discontinuities in the numerical approximation to the objective function. Metaheuristics often work well for such problems, but their convergence to a global optimum cannot be established formally. Moreover, different algorithms tend to be suited to particular classes of optimization problems. To shed light on this issue we compared the performance of two metaheuristics, the hybrid CMA-ES/HDE and the hybrid PSO/HJ, in minimizing standard benchmark functions and real-world building energy optimization problems of varying complexity. From this we find that the CMA-ES/HDE performs well on more complex objective functions, but that the PSO/HJ more consistently identifies the global minimum for simpler objective functions. Both identified similar values in the objective functions arising from energy simulations, but with different combinations of model parameters. This may suggest that the objective function is multi-modal. The algorithms also correctly identified some non-intuitive parameter combinations that were caused by a simplified control sequence of the building energy system that does not represent actual practice, further reinforcing their utility.
Date: September 1, 2009
Creator: Kamph, Jerome Henri; Robinson, Darren & Wetter, Michael

Building Commissioning: A Golden Opportunity for Reducing Energy Costs and Greenhouse-gas Emissions

Description: The aim of commissioning new buildings is to ensure that they deliver, if not exceed, the performance and energy savings promised by their design. When applied to existing buildings, commissioning identifies the almost inevitable 'drift' from where things should be and puts the building back on course. In both contexts, commissioning is a systematic, forensic approach to quality assurance, rather than a technology per se. Although commissioning has earned increased recognition in recent years - even a toehold in Wikipedia - it remains an enigmatic practice whose visibility severely lags its potential. Over the past decade, Lawrence Berkeley National Laboratory has built the world's largest compilation and meta-analysis of commissioning experience in commercial buildings. Since our last report (Mills et al. 2004) the database has grown from 224 to 643 buildings (all located in the United States, and spanning 26 states), from 30 to 100 million square feet of floorspace, and from $17 million to $43 million in commissioning expenditures. The recorded cases of new-construction commissioning took place in buildings representing $2.2 billion in total construction costs (up from 1.5 billion). The work of many more commissioning providers (18 versus 37) is represented in this study, as is more evidence of energy and peak-power savings as well as cost-effectiveness. We now translate these impacts into avoided greenhouse gases and provide new indicators of cost-effectiveness. We also draw attention to the specific challenges and opportunities for high-tech facilities such as labs, cleanrooms, data centers, and healthcare facilities. The results are compelling. We developed an array of benchmarks for characterizing project performance and cost-effectiveness. The median normalized cost to deliver commissioning was $0.30/ft2 for existing buildings and $1.16/ft2 for new construction (or 0.4% of the overall construction cost). The commissioning projects for which data are available revealed over 10,000 energy-related problems, resulting ...
Date: July 16, 2009
Creator: Mills, Evan

Global Cooling: Policies to Cool the World and Offset Global Warming from CO2 Using Reflective Roofs and Pavements

Description: Increasing the solar reflectance of the urban surface reduce its solar heat gain, lowers its temperatures, and decreases its outflow of thermal infrared radiation into the atmosphere. This process of 'negative radiative forcing' can help counter the effects of global warming. In addition, cool roofs reduce cooling-energy use in air conditioned buildings and increase comfort in unconditioned buildings; and cool roofs and cool pavements mitigate summer urban heat islands, improving outdoor air quality and comfort. Installing cool roofs and cool pavements in cities worldwide is a compelling win-win-win activity that can be undertaken immediately, outside of international negotiations to cap CO{sub 2} emissions. We propose an international campaign to use solar reflective materials when roofs and pavements are built or resurfaced in temperate and tropical regions.
Date: August 28, 2009
Creator: Akbari, Hashem; Levinson, Ronnen; Rosenfeld, Arthur & Elliot, Matthew

Normal and tumor-derived myoepithelial cells differ in their ability to interact with luminal breast epithelial cells for polarity and basement membrane deposition

Description: The signals that determine the correct polarity of breast epithelial structures in vivo are not understood. We have shown previously that luminal epithelial cells can be polarized when cultured within a reconstituted basement membrane gel. We reasoned that such cues in vivo may be given by myoepithelial cells. Accordingly, we used an assay where luminal epithelial cells are incorrectly polarized to test this hypothesis. We show that culturing human primary luminal epithelial cells within collagen-I gels leads to formation of structures with no lumina and with reverse polarity as judged by dual stainings for sialomucin, epithelial specific antigen or occludin. No basement membrane is deposited, and {beta}4-integrin staining is negative. Addition of purified human myoepithelial cells isolated from normal glands corrects the inverse polarity, and leads to formation of double-layered acini with central lumina. Among the laminins present in the human breast basement membrane (laminin-1, -5 and -10/11), laminin-1 was unique in its ability to substitute for myoepithelial cells in polarity reversal. Myoepithelial cells were purified also from four different breast cancer sources including a biphasic cell line. Three out of four samples either totally lacked the ability to interact with luminal epithelial cells, or conveyed only correction of polarity in a fraction of acini. This behavior was directly related to the ability of the tumor myoepithelial cells to produce {alpha}-1 chain of laminin. In vivo, breast carcinomas were either negative for laminin-1 (7/12 biopsies) or showed a focal, fragmented deposition of a less intensely stained basement membrane (5/12 biopsies). Dual staining with myoepithelial markers revealed that tumorassociated myoepithelial cells were either negative or weakly positive for expression of laminin-1, establishing a strong correlation between loss of laminin-1 and breast cancer. We conclude that the double-layered breast acinus may be recapitulated in culture and that one reason for the ability ...
Date: October 4, 2001
Creator: Gudjonsson, Thorarinn; Ronnov-Jessen, Lone; Villadsen, Rene; Rank, Fritz; Bissell, Mina J. & Petersen, Ole William

Biomass Energy Data Book: Edition 2

Description: The Biomass Energy Data Book is a statistical compendium prepared and published by Oak Ridge National Laboratory (ORNL) under contract with the Biomass Program in the Energy Efficiency and Renewable Energy (EERE) program of the Department of Energy (DOE). Designed for use as a convenient reference, the book represents an assembly and display of statistics and information that characterize the biomass industry, from the production of biomass feedstocks to their end use, including discussions on sustainability. This is the second edition of the Biomass Energy Data Book which is only available online in electronic format. There are five main sections to this book. The first section is an introduction which provides an overview of biomass resources and consumption. Following the introduction to biomass, is a section on biofuels which covers ethanol, biodiesel and bio-oil. The biopower section focuses on the use of biomass for electrical power generation and heating. The fourth section is on the developing area of biorefineries, and the fifth section covers feedstocks that are produced and used in the biomass industry. The sources used represent the latest available data. There are also four appendices which include frequently needed conversion factors, a table of selected biomass feedstock characteristics, assumptions for selected tables and figures, and discussions on sustainability. A glossary of terms and a list of acronyms are also included for the reader's convenience.
Date: December 1, 2009
Creator: Wright, Lynn L; Boundy, Robert Gary; Badger, Philip C; Perlack, Robert D & Davis, Stacy Cagle

Environmental Baseline Survey Report for the Title Transfer of Land Parcel ED-4 at the East Tennessee Technology Park, Oak Ridge, Tennessee

Description: This environmental baseline survey (EBS) report documents the baseline environmental conditions of a land parcel referred to as 'ED-4' (ED-4) at the U. S. Department of Energy's (DOE's) East Tennessee Technology Park (ETTP). DOE is proposing to transfer the title of this land to the Heritage Center, LLC. Parcel ED-4 is a land parcel that consists of two noncontiguous areas comprising a total of approximately 18 acres located east of the ETTP. The western tract of ED-4 encompasses approximately 8.5 acres in the northeastern quadrant of the intersection of Boulevard Road and Highway 58. The eastern tract encompasses an area of approximately 9.5 acres in the northwestern quadrant of the intersection of Blair Road and Highway 58 (the Oak Ridge Turnpike). Aerial photographs and site maps from throughout the history of the ETTP, going back to its initial development in the 1940s as the Oak Ridge Gaseous Diffusion Plant (ORGDP), indicate that this area has been undeveloped woodland with the exception of three support facilities for workers constructing the ORGDP since federal acquisition in 1943. These three support facilities, which were located in the western tract of ED-4, included a recreation hall, the Town Hall Camp Operations Building, and the Property Warehouse. A railroad spur also formerly occupied a portion of Parcel ED-4. These former facilities only occupied approximately 5 percent of the total area of Parcel ED-4. This report provides supporting information for the transfer of this government-owned property at ETTP to a non-federal entity. This EBS is based upon the requirements of Sect. 120(h) of the Comprehensive Environmental Response, Compensation, and Liability Act of 1980 (CERCLA). In order to support a Clean Parcel Determination (CPD) in accordance with CERCLA Sect. 120(h)(4)(d), groundwater and sediment samples were collected within, and adjacent to, the Parcel ED-4 study area. The potential ...
Date: May 1, 2008
Creator: SAIC

Electrodic voltages in the presence of dissolved sulfide: Implications for monitoring natural microbial activity

Description: There is growing interest in the development of new monitoring strategies for obtaining spatially extensive data diagnostic of microbial processes occurring in the earth. Open-circuit potentials arising from variable redox conditions in the fluid local-to-electrode surfaces (electrodic potentials) were recorded for a pair of silver-silver chloride electrodes in a column experiment, whereby a natural wetland soil containing a known community of sulfate reducers was continuously fed with a sulfate-rich nutrient medium. Measurements were made between five electrodes equally spaced along the column and a reference electrode placed on the column inflow. The presence of a sulfate reducing microbial population, coupled with observations of decreasing sulfate levels, formation of black precipitate (likely iron sulfide),elevated solid phase sulfide, and a characteristic sulfurous smell, suggest microbial-driven sulfate reduction (sulfide generation) in our column. Based on the known sensitivity of a silver electrode to dissolved sulfide concentration, we interpret the electrodic potentials approaching 700 mV recorded in this experiment as an indicator of the bisulfide (HS-) concentration gradients in the column. The measurement of the spatial and temporal variation in these electrodic potentials provides a simple and rapid method for monitoring patterns of relative HS- concentration that are indicative of the activity of sulfate-reducing bacteria. Our measurements have implications both for the autonomous monitoring of anaerobic microbial processes in the subsurface and the performance of self-potential electrodes, where it is critical to isolate, and perhaps quantify, electrochemical interfaces contributing to observed potentials.
Date: October 1, 2008
Creator: Slater, L.; Ntarlagiannis, D.; Yee, N.; O'Brien, M.; Zhang, C. & Williams, K. H.

Comparison of Complementary Reactions in the Production of Mt

Description: The new reaction 208Pb(59Co,n)266Mt was studied using the Berkeley Gas-filled Separator at the Lawrence Berkeley National Laboratory 88-Inch Cyclotron. A cross section of 7.7+5.2-3.3 pb was measured at a compound nucleus excitation energy of 14.9 MeV. The measured decay properties of 266Mt and its daughters correspond well with existing data. We compare this experimental result to transactinide compound nucleus formation model predictions, and the previously studied 209Bi(58Fe,n)266Mt reaction.
Date: January 21, 2009
Creator: Nelson, Sarah; Gregorich, Kenneth; Dragojevic, Irena; Ellison, Paul; Garcia, Mitch Andre; Gates, Jacklyn et al.

A novel technique for the production of cool colored concrete tile and asphalt shingle roofing products

Description: The widespread use of solar-reflective roofing materials can save energy, mitigate urban heat islands and slow global warming by cooling the roughly 20% of the urban surface that is roofed. In this study we created prototype solar-reflective nonwhite concrete tile and asphalt shingle roofing materials using a two-layer spray coating process intended to maximize both solar reflectance and factory-line throughput. Each layer is a thin, quick-drying, pigmented latex paint based on either acrylic or a poly(vinylidene fluoride)/acrylic blend. The first layer is a titanium dioxide rutile white basecoat that increases the solar reflectance of a gray-cement concrete tile from 0.18 to 0.79, and that of a shingle surfaced with bare granules from 0.06 to 0.62. The second layer is a 'cool' color topcoat with weak near-infrared (NIR) absorption and/or strong NIR backscattering. Each layer dries within seconds, potentially allowing a factory line to pass first under the white spray, then under the color spray. We combined a white basecoat with monocolor topcoats in various shades of red, brown, green and blue to prepare 24 cool color prototype tiles and 24 cool color prototypes shingles. The solar reflectances of the tiles ranged from 0.26 (dark brown; CIELAB lightness value L* = 29) to 0.57 (light green; L* = 76); those of the shingles ranged from 0.18 (dark brown; L* = 26) to 0.34 (light green; L* = 68). Over half of the tiles had a solar reflectance of at least 0.40, and over half of the shingles had a solar reflectance of at least 0.25.
Date: November 20, 2009
Creator: Levinson, Ronnen; Akbari, Hashem; Berdahl, Paul; Wood, Kurt; Skilton, Wayne & Petersheim, Jerry

Improved Spatial Resolution for Reflection Mode Infrared Microscopy

Description: Standard commercial infrared microscopes operating in reflection mode use a mirror to direct the reflected light from the sample to the detector. This mirror blocks about half of the incident light, however, and thus degrades the spatial resolution by reducing the umerical aperture of the objective. Here, we replace the mirror with a 50% beamsplitter to allow full illumination of the objective and retain a way to direct the reflected light to the detector. The improved spatial resolution is demonstrated using two different microscopes apable of diffraction-limited resolution: the first microscope is coupled to a synchrotron source and utilizes a single point detector, whereas the second microscope has a standard blackbody source and uses a focal planetarray (FPA) detector.
Date: October 9, 2009
Creator: Bechtel, Hans A.; Martin, Michael C.; May, T.E. & Lerch, Philippe

Improved Spatial Resolution For Reflection Mode Infrared Spectromicroscopy

Description: Standard commercial infrared microscopes operating in reflection mode use a mirror to direct the reflected light from the sample to the detector. This mirror blocks about half of the incident light, however, and thus degrades the spatial resolution by reducing the numerical aperture of the objective. Here, we replace the mirror with a 50% beamsplitter to allow full illumination of the objective and retain a way to direct the reflected light to the detector. The improved spatial resolution is demonstrated using a microscope coupled to a synchrotron source.
Date: August 13, 2009
Creator: Bechtel, Hans A; Martin, Michael C.; May, T. E. & Lerch, Philippe

The U-tube: A new paradigm in borehole fluid sampling

Description: Fluid samples from deep boreholes can provide insights into subsurface physical, chemical, and biological conditions. Recovery of intact, minimally altered aliquots of subsurface fluids is required for analysis of aqueous chemistry, isotopic composition, and dissolved gases, and for microbial community characterization. Unfortunately, for many reasons, collecting geofluids poses a number of challenges, from formation contamination by drilling to maintaining integrity during recovery from depths. Not only are there substantial engineering issues in retrieval of a representative sample, but there is often the practical reality that fluid sampling is just one of many activities planned for deep boreholes. The U-tube geochemical sampling system presents a new paradigm for deep borehole fluid sampling. Because the system is small, its ability to integrate with other measurement systems and technologies opens up numerous possibilities for multifunctional integrated wellbore completions. To date, the U-tube has been successfully deployed at four different field sites, each with a different deployment modality, at depths from 260 m to 2 km. While the U-tube has proven to be highly versatile, these installations have resulted in data that provide additional insights for improving future U-tube deployments.
Date: October 1, 2009
Creator: Freifeld, B. M.

2006/07 Field Testing of Cellulose Fiber Insulation Enhanced with Phase Change Material

Description: Most recent improvements in building envelope technologies suggest that in the near future, residences will be routinely constructed to operate with very low heating and cooling loads. In that light, the application of novel building materials containing active thermal components (e.g., phase change materials [PCMs,] sub-venting, radiant barriers, and integrated hydronic systems) is like a final step in achieving relatively significant heating and cooling energy savings from technological improvements in the building envelope. It is expected that optimized building envelope designs using PCMs for energy storage can effectively bring notable savings in energy consumption and reductions in peak hour power loads. During 2006/07, a research team at Oak Ridge National Laboratory (ORNL) performed a series of laboratory and field tests of several wall and roof assemblies using PCM-enhanced cellulose insulation. This report summarizes the test results from the perspective of energy performance. The ORNL team is working on both inorganic and organic PCMs; this report discusses only paraffinic PCMs. A limited economical analysis also is presented. PCMs have been tested as a thermal mass component in buildings for at least 40 years. Most of the research studies found that PCMs enhanced building energy performance. In the case of the application of organic PCMs, problems such as high initial cost and PCM leaking (surface sweating) have hampered widespread adoption. Paraffinic hydrocarbon PCMs generally performed well, with the exception that they increased the flammability of the building envelope.
Date: December 1, 2008
Creator: Kosny, Jan; Yarbrough, David W; Miller, William A; Petrie, Thomas; Childs, Phillip W & Syed, Azam M

Highly mismatched crystalline and amorphous GaN(1-x)As(x) alloys in the whole composition range

Description: Alloying is a commonly accepted method to tailor properties of semiconductor materials for specific applications. Only a limited number of semiconductor alloys can be easily synthesized in the full composition range. Such alloys are, in general, formed of component elements that are well matched in terms of ionicity, atom size, and electronegativity. In contrast there is a broad class of potential semiconductor alloys formed of component materials with distinctly different properties. In most instances these mismatched alloys are immiscible under standard growth conditions. Here we report on the properties of GaN1-xAsx, a highly mismatched, immiscible alloy system that was successfully synthesized in the whole composition range using a nonequilibrium low temperature molecular beam epitaxy technique. The alloys are amorphous in the composition range of 0.17<x<0.75 and crystalline outside this region. The amorphous films have smooth morphology, homogeneous composition, and sharp, well defined optical absorption edges. The band gap energy varies in a broad energy range from ~;;3.4 eV in GaN to ~;;0.8 eV at x~;;0.85. The reduction in the band gap can be attributed primarily to the downward movement of the conduction band for alloys with x>0.2, and to the upward movement of the valence band for alloys with x<0.2. The unique features of the band structure offer an opportunity of using GaN1-xAsx alloys for various types of solar power conversion devices.
Date: August 29, 2009
Creator: Yu, K. M.; Novikov, S. V.; Broesler, R.; Demchenko, I. N.; Denlinger, J. D.; Liliental-Weber, Z. et al.

Direct Photonic-Plasmonic Coupling and Routing in Single Nanowires

Description: Metallic nanoscale structures are capable of supporting surface plasmon polaritons (SPPs), propagating collective electron oscillations with tight spatial confinement at the metal surface. SPPs represent one of the most promising structures to beat the diffraction limit imposed by conventional dielectric optics. Ag nano wires have drawn increasing research attention due to 2D sub-100 nm mode confinement and lower losses as compared with fabricated metal structures. However, rational and versatile integration of Ag nanowires with other active and passive optical components, as well as Ag nanowire based optical routing networks, has yet to be achieved. Here, we demonstrate that SPPs can be excited simply by contacting a silver nanowire with a SnO2 nanoribbon that serves both as an unpolarized light source and a dielectric waveguide. The efficient coupling makes it possible to measure the propagation-distance-dependent waveguide spectra and frequency-dependent propagation length on a single Ag nanowire. Furthermore, we have demonstrated prototypical photonic-plasmonic routing devices, which are essential for incorporating low-loss Ag nanowire waveguides as practical components into high-capacity photonic circuits.
Date: October 20, 2009
Creator: Yan, Rouxue; Pausauskie, Peter; Huang, Jiaxing & Yang, Piedong

High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays

Description: A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small ({approx}40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue. Using an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE. MIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
Date: February 24, 2009
Creator: Wang, Yuker; Carlton, Victoria E.H.; Karlin-Neumann, George; Sapolsky, Ronald; Zhang, Li; Moorhead, Martin et al.

Gene expression profiling--Opening the black box of plant ecosystem responses to global change

Description: The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Since the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and non-model species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.
Date: November 1, 2009
Creator: Leakey, A.D.B.; Ainsworth, E.A.; Bernard, S.M.; Markelz, R.J.C.; Ort, D.R.; Placella, S.A.P. et al.