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Showing papers by "Lawrence Berkeley National Laboratory published in 2009"


Journal ArticleDOI
TL;DR: A series of improvements to the spectroscopic reductions are described, including better flat fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities.
Abstract: This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11,663 deg^2 of imaging data, with most of the ~2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry on a 120° long, 2°.5 wide stripe along the celestial equator in the Southern Galactic Cap, with some regions covered by as many as 90 individual imaging runs. We include a co-addition of the best of these data, going roughly 2 mag fainter than the main survey over 250 deg^2. The survey has completed spectroscopy over 9380 deg^2; the spectroscopy is now complete over a large contiguous area of the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog, reducing the rms statistical errors at the bright end to 45 milliarcseconds per coordinate. We further quantify a systematic error in bright galaxy photometry due to poor sky determination; this problem is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities.

5,665 citations


Journal ArticleDOI
30 Oct 2009-Cell
TL;DR: The authors showed that colonisation of mice with a segmented filamentous bacterium (SFB) is sufficient to induce the appearance of CD4+ T helper cells that produce IL-17 and IL-22 (Th17 cells) in the lamina propria.

3,860 citations


Journal ArticleDOI
TL;DR: FastTree is a method for constructing large phylogenies and for estimating their reliability, instead of storing a distance matrix, that uses sequence profiles of internal nodes in the tree to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins.
Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N2) space and O(N2L) time, but FastTree requires just O(NLa + N) memory and O(Nlog (N)La) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 h and 2.4 GB of memory. Just computing pairwise Jukes–Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 h and 50 GB of memory. In simulations, FastTree was slightly more accurate than Neighbor-Joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

3,500 citations


Journal ArticleDOI
11 Jun 2009-Nature
TL;DR: This work demonstrates a gate-controlled, continuously tunable bandgap of up to 250 meV and suggests novel nanoelectronic and nanophotonic device applications based on graphene that have eluded previous attempts.
Abstract: The electronic bandgap is an intrinsic property of semiconductors and insulators that largely determines their transport and optical properties. As such, it has a central role in modern device physics and technology and governs the operation of semiconductor devices such as p-n junctions, transistors, photodiodes and lasers. A tunable bandgap would be highly desirable because it would allow great flexibility in design and optimization of such devices, in particular if it could be tuned by applying a variable external electric field. However, in conventional materials, the bandgap is fixed by their crystalline structure, preventing such bandgap control. Here we demonstrate the realization of a widely tunable electronic bandgap in electrically gated bilayer graphene. Using a dual-gate bilayer graphene field-effect transistor (FET) and infrared microspectroscopy, we demonstrate a gate-controlled, continuously tunable bandgap of up to 250 meV. Our technique avoids uncontrolled chemical doping and provides direct evidence of a widely tunable bandgap-spanning a spectral range from zero to mid-infrared-that has eluded previous attempts. Combined with the remarkable electrical transport properties of such systems, this electrostatic bandgap control suggests novel nanoelectronic and nanophotonic device applications based on graphene.

3,268 citations


Journal ArticleDOI
10 Jul 2009-Science
TL;DR: The results establish that Bi2Te3 is a simple model system for the three-dimensional topological insulator with a single Dirac cone on the surface, and points to promising potential for high-temperature spintronics applications.
Abstract: Three-dimensional topological insulators are a new state of quantum matter with a bulk gap and odd number of relativistic Dirac fermions on the surface. By investigating the surface state of Bi2Te3 with angle-resolved photoemission spectroscopy, we demonstrate that the surface state consists of a single nondegenerate Dirac cone. Furthermore, with appropriate hole doping, the Fermi level can be tuned to intersect only the surface states, indicating a full energy gap for the bulk states. Our results establish that Bi2Te3 is a simple model system for the three-dimensional topological insulator with a single Dirac cone on the surface. The large bulk gap of Bi2Te3 also points to promising potential for high-temperature spintronics applications.

2,823 citations


Journal ArticleDOI
TL;DR: In this article, a quantum field theory of gravity with dynamical critical exponent equal to $z = 3$ in the UV is presented. But this theory is restricted to satisfy the condition of detailed balance.
Abstract: We present a candidate quantum field theory of gravity with dynamical critical exponent equal to $z=3$ in the UV. (As in condensed-matter systems, $z$ measures the degree of anisotropy between space and time.) This theory, which at short distances describes interacting nonrelativistic gravitons, is power-counting renormalizable in $3+1$ dimensions. When restricted to satisfy the condition of detailed balance, this theory is intimately related to topologically massive gravity in three dimensions, and the geometry of the Cotton tensor. At long distances, this theory flows naturally to the relativistic value $z=1$, and could therefore serve as a possible candidate for a UV completion of Einstein's general relativity or an infrared modification thereof. The effective speed of light, the Newton constant and the cosmological constant all emerge from relevant deformations of the deeply nonrelativistic $z=3$ theory at short distances.

2,816 citations


Journal ArticleDOI
TL;DR: It is demonstrated how to use the computational environment R to integrate and jointly analyze experimental datasets, employing BioMart web services to provide the molecule mappings.
Abstract: Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

2,719 citations


Journal ArticleDOI
TL;DR: The bioorthogonal chemical reactions developed to date are described and how they can be used to study biomolecules.
Abstract: The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.

2,537 citations


Journal ArticleDOI
TL;DR: The new growth process introduced here establishes a method for the synthesis of graphene films on a technologically viable basis and produces monolayer graphene films with much larger domain sizes than previously attainable.
Abstract: Graphene, a single monolayer of graphite, has recently attracted considerable interest owing to its novel magneto-transport properties, high carrier mobility and ballistic transport up to room temperature. It has the potential for technological applications as a successor of silicon in the post Moore's law era, as a single-molecule gas sensor, in spintronics, in quantum computing or as a terahertz oscillator. For such applications, uniform ordered growth of graphene on an insulating substrate is necessary. The growth of graphene on insulating silicon carbide (SiC) surfaces by high-temperature annealing in vacuum was previously proposed to open a route for large-scale production of graphene-based devices. However, vacuum decomposition of SiC yields graphene layers with small grains (30-200 nm; refs 14-16). Here, we show that the ex situ graphitization of Si-terminated SiC(0001) in an argon atmosphere of about 1 bar produces monolayer graphene films with much larger domain sizes than previously attainable. Raman spectroscopy and Hall measurements confirm the improved quality of the films thus obtained. High electronic mobilities were found, which reach mu=2,000 cm (2) V(-1) s(-1) at T=27 K. The new growth process introduced here establishes a method for the synthesis of graphene films on a technologically viable basis.

2,493 citations


Journal ArticleDOI
TL;DR: The Roofline model offers insight on how to improve the performance of software and hardware in the rapidly changing world of connected devices.
Abstract: The Roofline model offers insight on how to improve the performance of software and hardware.

2,181 citations


Journal ArticleDOI
TL;DR: In this paper, the basic physics of laser pulse evolution in underdense plasmas is also reviewed, including the propagation, self-focusing, and guiding of laser pulses in uniform density channels and with preformed density channels.
Abstract: Laser-driven plasma-based accelerators, which are capable of supporting fields in excess of 100 GV/m, are reviewed. This includes the laser wakefield accelerator, the plasma beat wave accelerator, the self-modulated laser wakefield accelerator, plasma waves driven by multiple laser pulses, and highly nonlinear regimes. The properties of linear and nonlinear plasma waves are discussed, as well as electron acceleration in plasma waves. Methods for injecting and trapping plasma electrons in plasma waves are also discussed. Limits to the electron energy gain are summarized, including laser pulse diffraction, electron dephasing, laser pulse energy depletion, and beam loading limitations. The basic physics of laser pulse evolution in underdense plasmas is also reviewed. This includes the propagation, self-focusing, and guiding of laser pulses in uniform plasmas and with preformed density channels. Instabilities relevant to intense short-pulse laser-plasma interactions, such as Raman, self-modulation, and hose instabilities, are discussed. Experiments demonstrating key physics, such as the production of high-quality electron bunches at energies of 0.1-1 GeV, are summarized.

Journal ArticleDOI
TL;DR: In addition to orchestrating cell-cycle checkpoints and DNA repair, a new and important role of the DDR is to allow damaged cells to communicate their compromised state to the surrounding tissue.
Abstract: Cellular senescence suppresses cancer by stably arresting the proliferation of damaged cells. Paradoxically, senescent cells also secrete factors that alter tissue microenvironments. The pathways regulating this secretion are unknown. We show that damaged human cells develop persistent chromatin lesions bearing hallmarks of DNA double-strand breaks (DSBs), which initiate increased secretion of inflammatory cytokines such as interleukin-6 (IL-6). Cytokine secretion occurred only after establishment of persistent DNA damage signalling, usually associated with senescence, not after transient DNA damage responses (DDRs). Initiation and maintenance of this cytokine response required the DDR proteins ATM, NBS1 and CHK2, but not the cell-cycle arrest enforcers p53 and pRb. ATM was also essential for IL-6 secretion during oncogene-induced senescence and by damaged cells that bypass senescence. Furthermore, DDR activity and IL-6 were elevated in human cancers, and ATM-depletion suppressed the ability of senescent cells to stimulate IL-6-dependent cancer cell invasiveness. Thus, in addition to orchestrating cell-cycle checkpoints and DNA repair, a new and important role of the DDR is to allow damaged cells to communicate their compromised state to the surrounding tissue.

Journal ArticleDOI

Journal ArticleDOI
27 Aug 2009-Nature
TL;DR: The results reveal a spin-momentum locked Dirac cone carrying a non-trivial Berry’s phase that is nearly 100 per cent spin-polarized, which exhibits a tunable topological fermion density in the vicinity of the Kramers point and can be driven to the long-sought topological spin transport regime.
Abstract: Helical Dirac fermions—charge carriers that behave as massless relativistic particles with an intrinsic angular momentum (spin) locked to its translational momentum—are proposed to be the key to realizing fundamentally new phenomena in condensed matter physics. Prominent examples include the anomalous quantization of magneto-electric coupling, half-fermion states that are their own antiparticle, and charge fractionalization in a Bose– Einstein condensate, all of which are not possible with conventional Dirac fermions of the graphene variety. Helical Dirac fermions have so far remained elusive owing to the lack of necessary spin-sensitive measurements and because such fermions are forbidden to exist in conventional materials harbouring relativistic electrons, such as graphene or bismuth. It has recently been proposed that helical Dirac fermions may exist at the edges of certain types of topologically ordered insulators—materials with a bulk insulating gap of spin–orbit origin and surface states protected against scattering by time-reversal symmetry—and that their peculiar properties may be accessed provided the insulator is tuned into the so-called topological transport regime. However, helical Dirac fermions have not been observed in existing topological insulators. Here we report the realization and characterization of a tunable topological insulator in a bismuthbased class of material by combining spin-imaging and momentum-resolved spectroscopies, bulk charge compensation, Hall transport measurements and surface quantum control. Our results reveal a spin-momentum locked Dirac cone carrying a nontrivial Berry’s phase that is nearly 100 per cent spin-polarized, which exhibits a tunable topological fermion density in the vicinity of the Kramers point and can be driven to the long-sought topological spin transport regime. The observed topological nodal state is shown to be protected even up to 300 K. Our demonstration of room-temperature topological order and non-trivial spintexture in stoichiometric Bi_2Se_3.M_x (M_x indicates surface doping or gating control) paves the way for future graphene-like studies of topological insulators, and applications of the observed spinpolarized edge channels in spintronic and computing technologies possibly at room temperature.

Journal ArticleDOI
TL;DR: AmiGO is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data.
Abstract: AmiGO is a web application that allows users to query, browse, and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium; it can also be downloaded and installed to browse local ontologies and annotations. AmiGO is free open source software developed and maintained by the GO Consortium.

Journal ArticleDOI
12 Feb 2009-Nature
TL;DR: In this paper, the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue.
Abstract: A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

Journal ArticleDOI
TL;DR: The design of a high-temperature-stable model catalytic system that consists of a Pt metal core coated with a mesoporous silica shell and the design concept used in the Pt@mSiO(2) core-shell catalyst can be extended to other metal/metal oxide compositions.
Abstract: Recent advances in colloidal synthesis enabled the precise control of the size, shape and composition of catalytic metal nanoparticles, enabling their use as model catalysts for systematic investigations of the atomic-scale properties affecting catalytic activity and selectivity. The organic capping agents stabilizing colloidal nanoparticles, however, often limit their application in high-temperature catalytic reactions. Here, we report the design of a high-temperature-stable model catalytic system that consists of a Pt metal core coated with a mesoporous silica shell (Pt@mSiO2). Inorganic silica shells encaged the Pt cores up to 750 ∘C in air and the mesopores providing direct access to the Pt core made the Pt@mSiO2 nanoparticles as catalytically active as bare Pt metal for ethylene hydrogenation and CO oxidation. The high thermal stability of Pt@mSiO2 nanoparticles enabled high-temperature CO oxidation studies, including ignition behaviour, which was not possible for bare Pt nanoparticles because of their deformation or aggregation. The results suggest that the Pt@mSiO2 nanoparticles are excellent nanocatalytic systems for high-temperature catalytic reactions or surface chemical processes, and the design concept used in the Pt@mSiO2 core–shell catalyst can be extended to other metal/metal oxide compositions. Colloidal synthesis can help to precisely control the shape and composition of catalytic metal nanoparticles, but it has so far proved difficult to use these particles in high-temperature reactions. Core–shell structures capable of isolating Pt-mesoporous silica nanoparticles have now been shown to be catalytically active for ethylene hydrogenation and CO oxidation at high temperature.

Journal ArticleDOI
TL;DR: The optical 'carpet' cloak is designed using quasi-conformal mapping to conceal an object that is placed under a curved reflecting surface by imitating the reflection of a flat surface and enables broadband and low-loss invisibility at a wavelength range of 1,400-1,800 nm.
Abstract: Invisibility devices have captured the human imagination for many years. Recent theories have proposed schemes for cloaking devices using transformation optics and conformal mapping. Metamaterials, with spatially tailored properties, have provided the necessary medium by enabling precise control over the flow of electromagnetic waves. Using metamaterials, the first microwave cloaking has been achieved but the realization of cloaking at optical frequencies, a key step towards achieving actual invisibility, has remained elusive. Here, we report the first experimental demonstration of optical cloaking. The optical 'carpet' cloak is designed using quasi-conformal mapping to conceal an object that is placed under a curved reflecting surface by imitating the reflection of a flat surface. The cloak consists only of isotropic dielectric materials, which enables broadband and low-loss invisibility at a wavelength range of 1,400-1,800 nm.

Journal ArticleDOI
TL;DR: The Palomar Transient Factory (PTF) as mentioned in this paper is a fully-automated, wide-field survey aimed at a systematic exploration of the optical transient sky.
Abstract: The Palomar Transient Factory (PTF) is a fully-automated, wide-field survey aimed at a systematic exploration of the optical transient sky. The transient survey is performed using a new 8.1 square degree camera installed on the 48 inch Samuel Oschin telescope at Palomar Observatory; colors and light curves for detected transients are obtained with the automated Palomar 60 inch telescope. PTF uses 80% of the 1.2 m and 50% of the 1.5 m telescope time. With an exposure of 60 s the survey reaches a depth of m_(g′) ≈ 21.3 and m_R ≈ 20.6 (5σ, median seeing). Four major experiments are planned for the five-year project: (1) a 5 day cadence supernova search; (2) a rapid transient search with cadences between 90 s and 1 day; (3) a search for eclipsing binaries and transiting planets in Orion; and (4) a 3π sr deep H-alpha survey. PTF provides automatic, real-time transient classification and follow-up, as well as a database including every source detected in each frame. This paper summarizes the PTF project, including several months of on-sky performance tests of the new survey camera, the observing plans, and the data reduction strategy. We conclude by detailing the first 51 PTF optical transient detections, found in commissioning data.

Journal ArticleDOI
TL;DR: A cytochemical protocol suitable for the histochemical detection of individual senescent cells both in culture and tissue biopsies is described and the fluorescence-based methods have the advantages of being more quantitative and sensitive.
Abstract: Normal cells can permanently lose the ability to proliferate when challenged by potentially oncogenic stress, a process termed cellular senescence. Senescence-associated beta-galactosidase (SA-betagal) activity, detectable at pH 6.0, permits the identification of senescent cells in culture and mammalian tissues. Here we describe first a cytochemical protocol suitable for the histochemical detection of individual senescent cells both in culture and tissue biopsies. The second method is based on the alkalinization of lysosomes, followed by the use of 5-dodecanoylaminofluorescein di-beta-D-galactopyranoside (C12FDG), a fluorogenic substrate for betagal activity. The cytochemical method takes about 30 min to execute, and several hours to a day to develop and score. The fluorescence methods take between 4 and 8 h to execute and can be scored in a single day. The cytochemical method is applicable to tissue sections and requires simple reagents and equipment. The fluorescence-based methods have the advantages of being more quantitative and sensitive.

Journal ArticleDOI
TL;DR: The observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO(3) shows that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall.
Abstract: Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO3. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features. Domain walls may be important in future electronic devices, given their small size as well as the fact that their location can be controlled. In the case of insulating multiferroic oxides, domain walls are now discovered to be electrically conductive, suggesting their possible use in logic and memory applications.

Journal ArticleDOI
K. Aamodt1, N. Abel2, A. Abrahantes Quintana, A. Acero  +989 moreInstitutions (76)
TL;DR: In this paper, the production of mesons containing strange quarks (KS, φ) and both singly and doubly strange baryons (,, and − + +) are measured at mid-rapidity in pp collisions at √ s = 0.9 TeV with the ALICE experiment at the LHC.

Journal ArticleDOI
27 Mar 2009-Science
TL;DR: This study of an ideal low-dimensional interface, a hole in graphene, exhibits the complex behavior of atoms at a boundary with the mechanism of edge reconstruction investigated and the stability of the “zigzag” edge configuration demonstrated.
Abstract: Although the physics of materials at surfaces and edges has been extensively studied, the movement of individual atoms at an isolated edge has not been directly observed in real time. With a transmission electron aberration-corrected microscope capable of simultaneous atomic spatial resolution and 1-second temporal resolution, we produced movies of the dynamics of carbon atoms at the edge of a hole in a suspended, single atomic layer of graphene. The rearrangement of bonds and beam-induced ejection of carbon atoms are recorded as the hole grows. We investigated the mechanism of edge reconstruction and demonstrated the stability of the "zigzag" edge configuration. This study of an ideal low-dimensional interface, a hole in graphene, exhibits the complex behavior of atoms at a boundary.

Journal ArticleDOI
Brian Yanny1, Constance M. Rockosi2, Heidi Jo Newberg3, Gillian R. Knapp4, Jennifer K. Adelman-McCarthy1, Bonnie Alcorn1, S. Allam1, Carlos Allende Prieto5, Carlos Allende Prieto6, Deokkeun An7, K. S. J. Anderson8, K. S. J. Anderson9, Scott F. Anderson10, Coryn A. L. Bailer-Jones11, Steve Bastian1, Timothy C. Beers12, Eric F. Bell11, Vasily Belokurov13, Dmitry Bizyaev8, Norm Blythe8, John J. Bochanski10, William N. Boroski1, Jarle Brinchmann14, J. Brinkmann8, Howard Brewington8, Larry N. Carey10, Kyle M. Cudworth15, Michael L. Evans10, Nick Evans13, Evalyn Gates15, Boris T. Gänsicke16, Bruce Gillespie8, G. F. Gilmore13, Ada Nebot Gomez-Moran, Eva K. Grebel17, Jim Greenwell10, James E. Gunn4, Cathy Jordan8, Wendell Jordan8, Paul Harding18, Hugh C. Harris, John S. Hendry1, Diana Holder8, Inese I. Ivans4, Željko Ivezić10, Sebastian Jester11, Jennifer A. Johnson7, Stephen M. Kent1, S. J. Kleinman8, Alexei Y. Kniazev11, Jurek Krzesinski8, Richard G. Kron15, Nikolay Kuropatkin1, Svetlana Lebedeva1, Young Sun Lee12, R. French Leger1, Sébastien Lépine19, Steve Levine, Huan Lin1, Dan Long8, Craig P. Loomis4, Robert H. Lupton4, O. Malanushenko8, Viktor Malanushenko8, Bruce Margon2, David Martínez-Delgado11, P. M. McGehee20, Dave Monet, Heather L. Morrison18, Jeffrey A. Munn, Eric H. Neilsen1, Atsuko Nitta8, John E. Norris21, Daniel Oravetz8, Russell Owen10, Nikhil Padmanabhan22, Kaike Pan8, R. S. Peterson1, Jeffrey R. Pier, Jared Platson1, Paola Re Fiorentin11, Paola Re Fiorentin23, Gordon T. Richards24, Hans-Walter Rix11, David J. Schlegel22, Donald P. Schneider25, Matthias R. Schreiber26, Axel Schwope, Valena C. Sibley1, Audrey Simmons8, Stephanie A. Snedden8, J. Allyn Smith27, Larry Stark10, Fritz Stauffer8, Matthias Steinmetz, Christopher Stoughton1, Mark SubbaRao28, Mark SubbaRao15, Alexander S. Szalay29, Paula Szkody10, Aniruddha R. Thakar29, Sivarani Thirupathi12, Douglas L. Tucker1, A. Uomoto30, Daniel E. Vanden Berk25, S. Vidrih17, Yogesh Wadadekar31, Yogesh Wadadekar4, S. Watters8, R. Wilhelm32, Rosemary F. G. Wyse29, Jean Yarger8, Daniel B. Zucker13 
TL;DR: The Sloan Extension for Galactic Understanding and Exploration (SEGUE) Survey as mentioned in this paper obtained approximately 240,000 moderate-resolution spectra from 3900 to 9000 of fainter Milky Way stars (14.0 10 per resolution element).
Abstract: The Sloan Extension for Galactic Understanding and Exploration (SEGUE) Survey obtained {approx}240,000 moderate-resolution (R {approx} 1800) spectra from 3900 {angstrom} to 9000 {angstrom} of fainter Milky Way stars (14.0 10 per resolution element, stellar atmospheric parameters are estimated, including metallicity, surface gravity, and effective temperature. SEGUE obtained 3500 deg{sup 2} of additional ugriz imaging (primarily at low Galactic latitudes) providing precise multicolor photometry ({sigma}(g, r, i) {approx} 2%), ({sigma}(u, z) {approx} 3%) and astrometry ({approx}0.1) for spectroscopic target selection. The stellar spectra, imaging data, and derived parameter catalogs for this survey are publicly available as part of Sloan Digital Sky Survey Data Release 7.

Journal ArticleDOI
TL;DR: In this article, synthetic protein scaffolds bearing interaction domains from metazoan signaling proteins were used to spatially recruit metabolic enzymes in a designable manner, and the modularity of these domains enabled them to optimize the stoichiometry of three mevalonate biosynthetic enzymes recruited to a synthetic complex.
Abstract: Engineered metabolic pathways constructed from enzymes heterologous to the production host often suffer from flux imbalances, as they typically lack the regulatory mechanisms characteristic of natural metabolism. In an attempt to increase the effective concentration of each component of a pathway of interest, we built synthetic protein scaffolds that spatially recruit metabolic enzymes in a designable manner. Scaffolds bearing interaction domains from metazoan signaling proteins specifically accrue pathway enzymes tagged with their cognate peptide ligands. The natural modularity of these domains enabled us to optimize the stoichiometry of three mevalonate biosynthetic enzymes recruited to a synthetic complex and thereby achieve 77-fold improvement in product titer with low enzyme expression and reduced metabolic load. One of the same scaffolds was used to triple the yield of glucaric acid, despite high titers (0.5 g/l) without the synthetic complex. These strategies should prove generalizeable to other metabolic pathways and programmable for fine-tuning pathway flux.

Journal ArticleDOI
TL;DR: Putative oxygen positions obtained from a Xenon derivative indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII, and the chloride position suggests a role in proton-transfer reactions.
Abstract: Photosystem II (PSII) is a large homodimeric protein-cofactor complex located in the photosynthetic thylakoid membrane that acts as light-driven water:plastoquinone oxidoreductase. The crystal structure of PSII from Thermosynechococcus elongatus at 2.9-A resolution allowed the unambiguous assignment of all 20 protein subunits and complete modeling of all 35 chlorophyll a molecules and 12 carotenoid molecules, 25 integral lipids and 1 chloride ion per monomer. The presence of a third plastoquinone Q(C) and a second plastoquinone-transfer channel, which were not observed before, suggests mechanisms for plastoquinol-plastoquinone exchange, and we calculated other possible water or dioxygen and proton channels. Putative oxygen positions obtained from a Xenon derivative indicate a role for lipids in oxygen diffusion to the cytoplasmic side of PSII. The chloride position suggests a role in proton-transfer reactions because it is bound through a putative water molecule to the Mn(4)Ca cluster at a distance of 6.5 A and is close to two possible proton channels.

Journal ArticleDOI
05 Jun 2009-Science
TL;DR: Using in situ transmission electron microscopy, it is shown that platinum nanocrystals can grow either by monomer attachment from solution or by particle coalescence, and it is suggested that colloidal nanocrystal take different pathways of growth based on their size- and morphology-dependent internal energies.
Abstract: Understanding of colloidal nanocrystal growth mechanisms is essential for the syntheses of nanocrystals with desired physical properties. The classical model for the growth of monodisperse nanocrystals assumes a discrete nucleation stage followed by growth via monomer attachment, but has overlooked particle-particle interactions. Recent studies have suggested that interactions between particles play an important role. Using in situ transmission electron microscopy, we show that platinum nanocrystals can grow either by monomer attachment from solution or by particle coalescence. Through the combination of these two processes, an initially broad size distribution can spontaneously narrow into a nearly monodisperse distribution. We suggest that colloidal nanocrystals take different pathways of growth based on their size- and morphology-dependent internal energies.

Journal ArticleDOI
TL;DR: A roadmap emphasizing low-cost alternatives that could become a dominant new approach for photovoltaics research and deployment is developed and it is found that devices performing below 10% power conversion efficiencies deliver the same lifetime energy output as those above 20% when a 3/4 material reduction is achieved.
Abstract: Solar photovoltaics have great promise for a low-carbon future but remain expensive relative to other technologies Greatly increased penetration of photovoltaics into global energy markets requires an expansion in attention from designs of high-performance to those that can deliver significantly lower cost per kilowatt-hour To evaluate a new set of technical and economic performance targets, we examine material extraction costs and supply constraints for 23 promising semiconducting materials Twelve composite materials systems were found to have the capacity to meet or exceed the annual worldwide electricity consumption of 17 000 TWh, of which nine have the potential for a significant cost reduction over crystalline silicon We identify a large material extraction cost (cents/watt) gap between leading thin film materials and a number of unconventional solar cell candidates including FeS2, CuO, and Zn3P2 We find that devices performing below 10% power conversion efficiencies deliver the same lifetime en

Journal ArticleDOI
TL;DR: The direct growth of highly regular, single-crystalline nanopillar arrays of optically active semiconductors on aluminium substrates that are then configured as solar-cell modules for enabling highly versatile solar modules on both rigid and flexible substrates with enhanced carrier collection efficiency arising from the geometric configuration of the nanopillars.
Abstract: Solar energy represents one of the most abundant and yet least harvested sources of renewable energy. In recent years, tremendous progress has been made in developing photovoltaics that can be potentially mass deployed. Of particular interest to cost-effective solar cells is to use novel device structures and materials processing for enabling acceptable efficiencies. In this regard, here, we report the direct growth of highly regular, single-crystalline nanopillar arrays of optically active semiconductors on aluminium substrates that are then configured as solar-cell modules. As an example, we demonstrate a photovoltaic structure that incorporates three-dimensional, single-crystalline n-CdS nanopillars, embedded in polycrystalline thin films of p-CdTe, to enable high absorption of light and efficient collection of the carriers. Through experiments and modelling, we demonstrate the potency of this approach for enabling highly versatile solar modules on both rigid and flexible substrates with enhanced carrier collection efficiency arising from the geometric configuration of the nanopillars.

Journal ArticleDOI
12 Jun 2009-Science
TL;DR: It is found that various molecular metal chalcogenide complexes can serve as convenient ligands for colloidal nanocrystals and nanowires and can be converted into semiconducting complexes.
Abstract: Similar to the way that atoms bond to form molecules and crystalline structures, colloidal nanocrystals can be combined together to form larger assemblies. The properties of these structures are determined by the properties of individual nanocrystals and by their interactions. The insulating nature of organic ligands typically used in nanocrystal synthesis results in very poor interparticle coupling. We found that various molecular metal chalcogenide complexes can serve as convenient ligands for colloidal nanocrystals and nanowires. These ligands can be converted into semiconducting phases upon gentle heat treatment, generating inorganic nanocrystal solids. The utility of the inorganic ligands is demonstrated for model systems, including highly conductive arrays of gold nanocrystals capped with Sn2S6(4-) ions and field-effect transistors on cadmium selenide nanocrystals.