Showing papers by "Lawrence Berkeley National Laboratory published in 2002"

Initial sequencing and comparative analysis of the mouse genome.

Abstract: The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.

Hybrid Nanorod-Polymer Solar Cells

Abstract: We demonstrate that semiconductor nanorods can be used to fabricate readily processed and efficient hybrid solar cells together with polymers. By controlling nanorod length, we can change the distance on which electrons are transported directly through the thin film device. Tuning the band gap by altering the nanorod radius enabled us to optimize the overlap between the absorption spectrum of the cell and the solar emission spectrum. A photovoltaic device consisting of 7-nanometer by 60-nanometer CdSe nanorods and the conjugated polymer poly-3(hexylthiophene) was assembled from solution with an external quantum efficiency of over 54% and a monochromatic power conversion efficiency of 6.9% under 0.1 milliwatt per square centimeter illumination at 515 nanometers. Under Air Mass (A.M.) 1.5 Global solar conditions, we obtained a power conversion efficiency of 1.7%.

PHENIX: building new software for automated crystallographic structure determination

Abstract: Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.

Direct evidence for neutrino flavor transformation from neutral current interactions in the Sudbury Neutrino Observatory

Abstract: Observations of neutral-current nu interactions on deuterium in the Sudbury Neutrino Observatory are reported. Using the neutral current (NC), elastic scattering, and charged current reactions and assuming the standard 8B shape, the nu(e) component of the 8B solar flux is phis(e) = 1.76(+0.05)(-0.05)(stat)(+0.09)(-0.09)(syst) x 10(6) cm(-2) s(-1) for a kinetic energy threshold of 5 MeV. The non-nu(e) component is phi(mu)(tau) = 3.41(+0.45)(-0.45)(stat)(+0.48)(-0.45)(syst) x 10(6) cm(-2) s(-1), 5.3sigma greater than zero, providing strong evidence for solar nu(e) flavor transformation. The total flux measured with the NC reaction is phi(NC) = 5.09(+0.44)(-0.43)(stat)(+0.46)(-0.43)(syst) x 10(6) cm(-2) s(-1), consistent with solar models.

Nanowire ultraviolet photodetectors and optical switches

Abstract: no attention has been given to the photoconducting properties of nanowires despite the exciting possibilities for use in optoelectronic circuits. Here, we show the possibility of creating highly sensitive nanowire switches by exploring the photoconducting properties of individual semiconductor nanowires. The conductivity of the ZnO nanowires is extremely sensitive to ultraviolet light exposure. The light-induced conductivity increase allows us to reversibly switch the nanowires between “OFF” and “ON” states, an optical gating phenomenon analogous to the commonly used electrical gating. [2,3,10]

Controlled growth of ZnO nanowires and their optical properties

Abstract: This article surveys recent developments in the rational synthesis of single-crystalline zinc oxide nanowires and their unique optical properties. The growth of ZnO nanowires was carried out in a simple chemical vapor transport and condensation (CVTC) system. Based on our fundamental understanding of the vapor–liquid–solid (VLS) nanowire growth mechanism, different levels of growth controls (including positional, orientational, diameter, and density control) have been achieved. Power-dependent emission has been examined and lasing action was observed in these ZnO nanowires when the excitation intensity exceeds a threshold (∼40 kW cm–2). These short-wavelength nanolasers operate at room temperature and the areal density of these nanolasers on substrate readily reaches 1 × 1010 cm–2. The observation of lasing action in these nanowire arrays without any fabricated mirrors indicates these single-crystalline, well-facetted nanowires can function as self-contained optical resonance cavities. This argument is further supported by our recent near-field scanning optical microscopy (NSOM) studies on single nanowires.

Handbook of Optical Materials

Abstract: CRYSTALLINE MATERIALS Introduction Physical Properties Optical Properties Mechanical Properties Thermal Properties Magnetooptic Properties Electrooptic Properties Elastooptic Properties Nonlinear Optical Properties GLASSES Introduction Commercial Optical Glasses Specialty Optical Glasses Fused Silica Fluoride Glasses Chalcogenide Glasses Magnetooptic Properties Electrooptic Properties Elastooptic Properties Nonlinear Optical Properties Special Glasses POLYMERIC MATERIALS Optical Plastics Index of Refraction Nonlinear Optical Properties Thermal Properties Engineering Data METALS Physical Properties of Selected Metals Optical Properties Mechanical Properties Thermal Properties Mirror Substrate Materials LIQUIDS Introduction Water Physical Properties of Selected Liquids Index of Refraction Nonlinear Optical Properties Magnetooptic Properties Commercial Optical Liquids GASES Introduction Physical Properties of Selected Gases Index of Refraction Nonlinear Optical Properties Magnetooptic Properties Atomic Resonance Filters APPENDICES Safe Handling of Optical Materials Abbreviations, Acronyms, and Mineralogical or Common Names for Optical Materials Abbreviations for Methods of Preparing Optical Materials and Thin Films Fundamental Physical Constants Units and Conversion Factors

Single gallium nitride nanowire lasers

Abstract: There is much current interest in the optical properties of semiconductor nanowires, because the cylindrical geometry and strong two-dimensional confinement of electrons, holes and photons make them particularly attractive as potential building blocks for nanoscale electronics and optoelectronic devices, including lasersand nonlinear optical frequency converters. Gallium nitride (GaN) is a wide-bandgap semiconductor of much practical interest, because it is widely used in electrically pumped ultraviolet-blue light-emitting diodes, lasers and photodetectors. Recent progress in microfabrication techniques has allowed stimulated emission to be observed from a variety of GaN microstructures and films. Here we report the observation of ultraviolet-blue laser action in single monocrystalline GaN nanowires, using both near-field and far-field optical microscopy to characterize the waveguide mode structure and spectral properties of the radiation at room temperature. The optical microscope images reveal radiation patterns that correlate with axial Fabry-Perot modes (Q approximately 10(3)) observed in the laser spectrum, which result from the cylindrical cavity geometry of the monocrystalline nanowires. A redshift that is strongly dependent on pump power (45 meV microJ x cm(-2)) supports the idea that the electron-hole plasma mechanism is primarily responsible for the gain at room temperature. This study is a considerable advance towards the realization of electron-injected, nanowire-based ultraviolet-blue coherent light sources.

Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality.

Abstract: Recent advances in statistical mechanical theory can be used to solve a fundamental problem in experimental thermodynamics. In 1997, Jarzynski proved an equality relating the irreversible work to the equilibrium free energy difference, DeltaG. This remarkable theoretical result states that it is possible to obtain equilibrium thermodynamic parameters from processes carried out arbitrarily far from equilibrium. We test Jarzynski's equality by mechanically stretching a single molecule of RNA reversibly and irreversibly between two conformations. Application of this equality to the irreversible work trajectories recovers the DeltaG profile of the stretching process to within k(B)T/2 (half the thermal energy) of its best independent estimate, the mean work of reversible stretching. The implementation and test of Jarzynski's equality provides the first example of its use as a bridge between the statistical mechanics of equilibrium and nonequilibrium systems. This work also extends the thermodynamic analysis of single molecule manipulation data beyond the context of equilibrium experiments.

Block-by-Block Growth of Single-Crystalline Si/SiGe Superlattice Nanowires

Abstract: Heterojunction and superlattice formation is essential for many potential applications of semiconductor nanowires in nanoscale optoelectronics. We have developed a hybrid pulsed laser ablation/chemical capor deposition (PLA-CVD) process for the synthesis of semiconductor nanowires with longitudinal ordered heterostructures. The laser ablation process generates a programmable pulsed vapor source, which enables the nanowire growth in a block-by-block fashion with a well-defined compositional profile along the wire axis. Single-crystalline nanowires with longitudinal Si/SiGe superlattice structure have been successfully synthesized. This unique class of heterostructured one-dimensional nanostructures holds great potential in applications such as light emitting devices and thermoelectrics.

Control, exploitation and tolerance of intracellular noise

Abstract: Noise has many roles in biological function, including generation of errors in DNA replication leading to mutation and evolution, noise-driven divergence of cell fates, noise-induced amplification of signals, and maintenance of the quantitative individuality of cells. Yet there is order to the behaviour and development of cells. They operate within strict parameters and in many cases this behaviour seems robust, implying that noise is largely filtered by the system. How can we explain the use, rejection and sensitivity to noise that is found in biological systems? An exploration of the sources and consequences of noise calls for the use of stochastic models.

Photochemical synthesis of gold nanorods.

Abstract: Gold nanorods have been synthesized by photochemically reducing gold ions within a micellar solution. The aspect ratio of the rods can be controlled with the addition of silver ions. This process reported here is highly promising for producing uniform nanorods, and more importantly it will be useful in resolving the growth mechanism of anisotropic metal nanoparticles due to its simplicity and the relatively slow growth rate of the nanorods.

A measurement by BOOMERANG of multiple peaks in the angular power spectrum of the cosmic microwave background

Abstract: This paper presents a measurement of the angular power spectrum of the cosmic microwave background from l = 75 to l = 1025 (~10' to 24) from a combined analysis of four 150 GHz channels in the BOOMERANG experiment. The spectrum contains multiple peaks and minima, as predicted by standard adiabatic inflationary models in which the primordial plasma undergoes acoustic oscillations. These results, in concert with other types of cosmological measurements and theoretical models, significantly constrain the values of ?tot, ?bh2, ?ch2, and ns.

Measurement of Day and Night Neutrino Energy Spectra at SNO and Constraints on Neutrino Mixing Parameters

Abstract: The Sudbury Neutrino Observatory (SNO) has measured day and night solar neutrino energy spectra and rates. For charged current events, assuming an undistorted 8B spectrum, the night minus day rate is 14.0%+/-6.3%(+1.5%)(-1.4%) of the average rate. If the total flux of active neutrinos is additionally constrained to have no asymmetry, the nu(e) asymmetry is found to be 7.0%+/-4.9%(+1.3%)(-1.2%). A global solar neutrino analysis in terms of matter-enhanced oscillations of two active flavors strongly favors the large mixing angle solution.

Discovery of dendrimers and dendritic polymers: A brief historical perspective*

Abstract: A brief historical perspective relating the discovery of dendrimers and other dendritic polymers is presented. Dendritic polymers are recognized as the fourth major class of macromolecular architecture consisting of four sub- classes, namely, (1) random hyperbranched, (2) dendrigrafts, (3) dendrons, and (4) dendrimers. The previous literature is reviewed with anecdotal events leading to implications for dendrimers in the emerging science of nanotechnology. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2719–2728, 2002

The BABAR detector

Abstract: BABAR, the detector for the SLAC PEP-II asymmetric e+e- B Factory operating at the upsilon 4S resonance, was designed to allow comprehensive studies of CP-violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagentic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by dE/dx measurements in the tracking detectors and in a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems, VME- and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

The origin of the anomalous superconducting properties of MgB 2

Abstract: Magnesium diboride differs from ordinary metallic superconductors in several important ways, including the failure of conventional models to predict accurately its unusually high transition temperature, the effects of isotope substitution on the critical transition temperature, and its anomalous specific heat. A detailed examination of the energy associated with the formation of charge-carrying pairs, referred to as the 'superconducting energy gap', should clarify why MgB(2) is different. Some early experimental studies have indicated that MgB(2) has multiple gaps, but past theoretical studies have not explained from first principles the origin of these gaps and their effects. Here we report an ab initio calculation of the superconducting gaps in MgB(2) and their effects on measurable quantities. An important feature is that the electronic states dominated by orbitals in the boron plane couple strongly to specific phonon modes, making pair formation favourable. This explains the high transition temperature, the anomalous structure in the specific heat, and the existence of multiple gaps in this material. Our analysis suggests comparable or higher transition temperatures may result in layered materials based on B, C and N with partially filled planar orbitals.

Systematic determination of patterns of gene expression during Drosophila embryogenesis

Abstract: Background: Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription. Results: As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, we examined 2,179 genes by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos. The photomicrographs were annotated using controlled vocabularies for anatomical structures that are organized into a developmental hierarchy. We also generated a detailed time course of gene expression during embryogenesis using microarrays to provide an independent corroboration of the in situ hybridization results. All image, annotation and microarray data are stored in publicly available database. We found that the RNA transcripts of about 1% of genes show clear subcellular localization. Nearly all the annotated expression patterns are distinct. We present an approach for organizing the data by hierarchical clustering of annotation terms that allows us to group tissues that express similar sets of genes as well as genes displaying similar expression patterns. Conclusions: Analyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis. Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays.

BerkMin: A Fast and Robust Sat-Solver

Abstract: We describe a SAT-solver, BerkMin, that inherits such features of GRASP, SATO, and Chaff as clause recording, fast BCP, restarts, and conflict clause "aging". At the same time BerkMin introduces a new decision making procedure and a new method of clause database management. We experimentally compare BerkMin with Chaff, the leader among SAT-solvers used in the EDA domain. Experiments show that our solver is more robust than Chaff. BerkMin solved all the instances we used in experiments including very large CNFs from a microprocessor verification benchmark suite. On the other hand, Chaff was not able to complete some instances even with the timeout limit of 16 hours.

The snowmass Points and slopes: benchmarks for SUSY searches

Abstract: The ”Snowmass Points and Slopes” (SPS) are a set of benchmark points and parameter lines in the MSSM parameter space corresponding to different scenarios in the search for Supersymmetry at present and future experiments. This set of benchmarks was agreed upon at the 2001 ”Snowmass Workshop on the Future of Particle Physics” as a consensus based on different existing proposals.

Resonant nonlinear magneto-optical effects in atoms

Abstract: The authors review the history, current status, physical mechanisms, experimental methods, and applications of nonlinear magneto-optical effects in atomic vapors. They begin by describing the pioneering work of Macaluso and Corbino over a century ago on linear magneto-optical effects (in which the properties of the medium do not depend on the light power) in the vicinity of atomic resonances. These effects are then contrasted with various nonlinear magneto-optical phenomena that have been studied both theoretically and experimentally since the late 1960s. In recent years, the field of nonlinear magneto-optics has experienced a revival of interest that has led to a number of developments, including the observation of ultranarrow (1-Hz) magneto-optical resonances, applications in sensitive magnetometry, nonlinear magneto-optical tomography, and the possibility of a search for parity- and time-reversal-invariance violation in atoms.

High-power terahertz radiation from relativistic electrons

Abstract: Terahertz (THz) radiation, which lies in the far-infrared region, is at the interface of electronics and photonics. Narrow-band THz radiation can be produced by free-electron lasers and fast diodes. Broadband THz radiation can be produced by thermal sources and, more recently, by table-top laser-driven sources and by short electron bunches in accelerators, but so far only with low power. Here we report calculations and measurements that confirm the production of high-power broadband THz radiation from subpicosecond electron bunches in an accelerator. The average power is nearly 20 watts, several orders of magnitude higher than any existing source, which could enable various new applications. In particular, many materials have distinct absorptive and dispersive properties in this spectral range, so that THz imaging could reveal interesting features. For example, it would be possible to image the distribution of specific proteins or water in tissue, or buried metal layers in semiconductors; the present source would allow full-field, real-time capture of such images. High peak and average power THz sources are also critical in driving new nonlinear phenomena and for pump-probe studies of dynamical properties of materials.

A Four Unit Cell Periodic Pattern of Quasi-Particle States Surrounding Vortex Cores in Bi2Sr2CaCu2O8+δ

Abstract: Scanning tunneling microscopy is used to image the additional quasi-particle states generated by quantized vortices in the high critical temperature superconductor Bi2Sr2CaCu2O8+δ. They exhibit a copper-oxygen bond–oriented “checkerboard” pattern, with four unit cell (4a0) periodicity and a ∼30 angstrom decay length. These electronic modulations may be related to the magnetic field–induced, 8a0periodic, spin density modulations with decay length of ∼70 angstroms recently discovered in La1.84Sr0.16CuO4. The proposed explanation is a spin density wave localized surrounding each vortex core. General theoretical principles predict that, in the cuprates, a localized spin modulation of wavelength λ should be associated with a corresponding electronic modulation of wavelength λ/2, in good agreement with our observations.

New Limit on the Electron Electric Dipole Moment

Abstract: We present the result of our most recent search for T-violation in 205Tl, which is interpreted in terms of an electric dipole moment of the electron de. We find de = (6.9 plus/minus 7.4) times 10{sup -28} e cm. The present apparatus is a major upgrade of the atomic beam magnetic resonance device used to set the previous limit on de.

Applications of plane-wave destruction filters

Abstract: Plane‐wave destruction filters originate from a local plane‐wave model for characterizing seismic data. These filters can be thought of as a time–distance (T‐X) analog of frequency‐distance (F‐X) prediction‐error filters and as an alternative to T‐X prediction‐error filters. The filters are constructed with the help of an implicit finite‐difference scheme for the local plane‐wave equation. Several synthetic and real data examples show that finite‐difference plane‐wave destruction filters perform well in applications such as fault detection, data interpolation, and noise attenuation.