Showing papers by "Lawrence Berkeley National Laboratory published in 2001"

Room-temperature ultraviolet nanowire nanolasers

Abstract: Room-temperature ultraviolet lasing in semiconductor nanowire arrays has been demonstrated The self-organized, oriented zinc oxide nanowires grown on sapphire substrates were synthesized with a simple vapor transport and condensation process These wide band-gap semiconductor nanowires form natural laser cavities with diameters varying from 20 to 150 nanometers and lengths up to 10 micrometers Under optical excitation, surface-emitting lasing action was observed at 385 nanometers, with an emission linewidth less than 03 nanometer The chemical flexibility and the one-dimensionality of the nanowires make them ideal miniaturized laser light sources These short-wavelength nanolasers could have myriad applications, including optical computing, information storage, and microanalysis

The National Human Activity Pattern Survey (NHAPS): a resource for assessing exposure to environmental pollutants.

Abstract: Because human activities impact the timing, location, and degree of pollutant exposure, they play a key role in explaining exposure variation. This fact has motivated the collection of activity pattern data for their specific use in exposure assessments. The largest of these recent efforts is the National Human Activity Pattern Survey (NHAPS), a 2-year probability-based telephone survey ( n=9386) of exposure-related human activities in the United States (U.S.) sponsored by the U.S. Environmental Protection Agency (EPA). The primary purpose of NHAPS was to provide comprehensive and current exposure information over broad geographical and temporal scales, particularly for use in probabilistic population exposure models. NHAPS was conducted on a virtually daily basis from late September 1992 through September 1994 by the University of Maryland's Survey Research Center using a computer-assisted telephone interview instrument (CATI) to collect 24-h retrospective diaries and answers to a number of personal and exposure-related questions from each respondent. The resulting diary records contain beginning and ending times for each distinct combination of location and activity occurring on the diary day (i.e., each microenvironment). Between 340 and 1713 respondents of all ages were interviewed in each of the 10 EPA regions across the 48 contiguous states. Interviews were completed in 63% of the households contacted. NHAPS respondents reported spending an average of 87% of their time in enclosed buildings and about 6% of their time in enclosed vehicles. These proportions are fairly constant across the various regions of the U.S. and Canada and for the California population between the late 1980s, when the California Air Resources Board (CARB) sponsored a state-wide activity pattern study, and the mid-1990s, when NHAPS was conducted. However, the number of people exposed to environmental tobacco smoke (ETS) in California seems to have decreased over the same time period, where exposure is determined by the reported time spent with a smoker. In both California and the entire nation, the most time spent exposed to ETS was reported to take place in residential locations.

Thermal transport measurements of individual multiwalled nanotubes.

Abstract: The thermal conductivity and thermoelectric power of a single carbon nanotube were measured using a microfabricated suspended device. The observed thermal conductivity is more than 3000 W/K m at room temperature, which is 2 orders of magnitude higher than the estimation from previous experiments that used macroscopic mat samples. The temperature dependence of the thermal conductivity of nanotubes exhibits a peak at 320 K due to the onset of umklapp phonon scattering. The measured thermoelectric power shows linear temperature dependence with a value of 80 microV/K at room temperature.

Catalytic Growth of Zinc Oxide Nanowires by Vapor Transport

Abstract: nanoparticles in dimethylsulfoxide onto the PLL film for about 20 min, after which it was rinsed in dimethylsulfoxide and then dichloromethane. From the molecular weight, the average length of the PLL is about 30 nm. Therefore, each polymer can accommodate about seven or eight nanoparticles. [20] L. Clarke, M. N. Wybourne, M. Yan, S. X. Cai, J. F. W. Keana, Appl. Phys. Lett. 1997, 71, 617. [21] A. A. Middleton, N. S. Wingreen, Phys. Rev. Lett. 1993, 71, 3198. [22] G. Y. Hu, R. F. O'Connell, Phys. Rev. B 1994, 49, 16 773. [23] A. J. Rimberg, T. R. Ho, J. Clarke, Phys. Rev. Lett. 1995, 74, 4714. [24] L. Clarke, M. N. Wybourne, M. Yan, S. X. Cai, L. O. Brown, J. Hutchison, J. F. W. Keana, J. Vac. Sci. Technol. B 1997, 15, 2925. [25] The capacitance matrix was calculated for different chain lengths using the software package FastCap MIT (1992). We used the nanoparticle dimensions given in the text and a ligand shell dielectric constant of 3. For nanoclusters away from the end of the chains we obtain Cdd » 0.04 aF and Cg » 0.17 aF. As expected, the value of Cg is slightly larger than the value calculated for an isolated metal sphere of radius a coated with a dielectric shell, Cg» (4pee0a)/(1 + (a/d)(e±1)) = 0.14 aF, where d is the total radius of the core plus ligand shell. [26] Simulations were carried out using both MOSES (Monte-Carlo SingleElectronics Simulator, R. H. Chen) and SIMON (Simulation of Nano Structures, C. Wasshuber). [27] S. Chen, R. S. Ingram, M. J. Hostetler, J. J. Pietron, R. W. Murray, T. G. Schaaff, J. T. Khoury, M. M. Alvarez, R. L. Whetton, Science 1998, 280, 2098. [28] L. Y. Gorelik, A. Isacsson, M. V. Voinova, B. Kasemo, R. I. Shekhter, M. Jonson, Phys. Rev. Lett. 1998, 80, 4526. [29] O. D. Häberlen, S. C. Chung, M. Stener, N. Rösch, J. Chem. Phys. 1997, 106, 5189. [30] Y. Awakuni, J. H. Calderwood, J. Phys. D: Appl. Phys. 1972, 5, 1038. [31] G. Markovich, C. P. Collier, J. R. Heath, Phys. Rev. Lett. 1998, 80, 3807. [32] C. P. Collier, R. J. Saykally, J. J. Shiang, S. E. Hendrichs, J. R. Heath, Science 1997, 277, 1978. [33] N. Mott, Metal Insulator Transitions, Taylor and Francis, London 1990.

Putting tumours in context

Abstract: The interactions between cancer cells and their micro- and macroenvironment create a context that promotes tumour growth and protects it from immune attack. The functional association of cancer cells with their surrounding tissues forms a new 'organ' that changes as malignancy progresses. Investigation of this process might provide new insights into the mechanisms of tumorigenesis and could also lead to new therapeutic targets.

Crystal structure of the ribosome at 5.5 A resolution

Abstract: We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.

Measurement of the rate of ve + d → p + p + e- interactions produced by 8B solar neutrinos at the sudbury neutrino observatory

Abstract: Solar neutrinos from the decay of 8B have been detected at the Sudbury Neutrino Observatory (SNO) via the charged current (CC) reaction on deuterium and by the elastic scattering (ES) of electrons. The CC reaction is sensitive exclusively to νe, while the ES reaction also has a small sensitivity to νμ and ντ. The flux of νe from 8B decay measured by the CC reaction rate is φCC(ν e )=[1.75±0.07(stat.) −0.11 +0.12 (syst.)×0.05(theor.)]×106cm−2s−1. Assuming no flavor transformation, the flux inferred from the ES reaction rate is φES(ν x )=[2.39±0.34(stat.) −0.14 +0.16 (syst.)]×106cm−2s−1. Comparison of φCC(νe) to the Super-Kamiokande collaboration’s precision value of φES(νx) yields a 3.3σ difference, assuming the systematic uncertainties are normally distributed, providing evidence that there is a nonelectron flavor active neutrino component in the solar flux. The total flux of active 8B neutrinos is thus determined to be (5.44±0.99)×106 cm−2 s−1, in close agreement with the predictions of solar models.

Senescent fibroblasts promote epithelial cell growth and tumorigenesis: a link between cancer and aging.

Abstract: Mammalian cells can respond to damage or stress by entering a state of arrested growth and altered function termed cellular senescence. Several lines of evidence suggest that the senescence response suppresses tumorigenesis. Cellular senescence is also thought to contribute to aging, but the mechanism is not well understood. We show that senescent human fibroblasts stimulate premalignant and malignant, but not normal, epithelial cells to proliferate in culture and form tumors in mice. In culture, the growth stimulation was evident when senescent cells comprised only 10% of the fibroblast population and was equally robust whether senescence was induced by replicative exhaustion, oncogenic RAS, p14ARF, or hydrogen peroxide. Moreover, it was due at least in part to soluble and insoluble factors secreted by senescent cells. In mice, senescent, much more than presenescent, fibroblasts caused premalignant and malignant epithelial cells to form tumors. Our findings suggest that, although cellular senescence suppresses tumorigenesis early in life, it may promote cancer in aged organisms, suggesting it is an example of evolutionary antagonistic pleiotropy.

Indian Ocean Experiment: An integrated analysis of the climate forcing and effects of the great Indo-Asian haze

Abstract: Every year, from December to April, anthropogenic haze spreads over most of the North Indian Ocean, and South and Southeast Asia. The Indian Ocean Experiment (INDOEX) documented this Indo-Asian haze at scales ranging from individual particles to its contribution to the regional climate forcing. This study integrates the multiplatform observations (satellites, aircraft, ships, surface stations, and balloons) with one- and four-dimensional models to derive the regional aerosol forcing resulting from the direct, the semidirect and the two indirect effects. The haze particles consisted of several inorganic and carbonaceous species, including absorbing black carbon clusters, fly ash, and mineral dust. The most striking result was the large loading of aerosols over most of the South Asian region and the North Indian Ocean. The January to March 1999 visible optical depths were about 0.5 over most of the continent and reached values as large as 0.2 over the equatorial Indian ocean due to long-range transport. The aerosol layer extended as high as 3 km. Black carbon contributed about 14% to the fine particle mass and 11% to the visible optical depth. The single-scattering albedo estimated by several independent methods was consistently around 0.9 both inland and over the open ocean. Anthropogenic sources contributed as much as 80% (±10%) to the aerosol loading and the optical depth. The in situ data, which clearly support the existence of the first indirect effect (increased aerosol concentration producing more cloud drops with smaller effective radii), are used to develop a composite indirect effect scheme. The Indo-Asian aerosols impact the radiative forcing through a complex set of heating (positive forcing) and cooling (negative forcing) processes. Clouds and black carbon emerge as the major players. The dominant factor, however, is the large negative forcing (-20±4 W m^(−2)) at the surface and the comparably large atmospheric heating. Regionally, the absorbing haze decreased the surface solar radiation by an amount comparable to 50% of the total ocean heat flux and nearly doubled the lower tropospheric solar heating. We demonstrate with a general circulation model how this additional heating significantly perturbs the tropical rainfall patterns and the hydrological cycle with implications to global climate.

Carbon dioxide emissions from the global cement industry

Abstract: ▪ Abstract The cement industry contributes about 5% to global anthropogenic CO2 emissions, making the cement industry an important sector for CO2-emission mitigation strategies. CO2 is emitted from the calcination process of limestone, from combustion of fuels in the kiln, as well as from power generation. In this paper, we review the total CO2 emissions from cement making, including process and energy-related emissions. Currently, most available data only includes the process emissions. We also discuss CO2 emission mitigation options for the cement industry. Estimated total carbon emissions from cement production in 1994 were 307 million metric tons of carbon (MtC), 160 MtC from process carbon emissions, and 147 MtC from energy use. Overall, the top 10 cement-producing countries in 1994 accounted for 63% of global carbon emissions from cement production. The average intensity of carbon dioxide emissions from total global cement production is 222 kg of C/t of cement. Emission mitigation options include en...

Linearly Polarized Emission from Colloidal Semiconductor Quantum Rods

Abstract: Colloidal quantum rods of cadmium selenide (CdSe) exhibit linearly polarized emission. Empirical pseudopotential calculations predict that slightly elongated CdSe nanocrystals have polarized emission along the long axis, unlike spherical dots, which emit plane-polarized light. Single-molecule luminescence spectroscopy measurements on CdSe quantum rods with an aspect ratio between 1 and 30 confirm a sharp transition from nonpolarized to purely linearly polarized emission at an aspect ratio of 2. Linearly polarized luminescent chromophores are highly desirable in a variety of applications.

Structural basis of water-specific transport through the AQP1 water channel

Abstract: Water channels facilitate the rapid transport of water across cell membranes in response to osmotic gradients. These channels are believed to be involved in many physiological processes that include renal water conservation, neuro-homeostasis, digestion, regulation of body temperature and reproduction. Members of the water channel superfamily have been found in a range of cell types from bacteria to human. In mammals, there are currently 10 families of water channels, referred to as aquaporins (AQP): AQP0–AQP9. Here we report the structure of the aquaporin 1 (AQP1) water channel to 2.2 A resolution. The channel consists of three topological elements, an extracellular and a cytoplasmic vestibule connected by an extended narrow pore or selectivity filter. Within the selectivity filter, four bound waters are localized along three hydrophilic nodes, which punctuate an otherwise extremely hydrophobic pore segment. This unusual combination of a long hydrophobic pore and a minimal number of solute binding sites facilitates rapid water transport. Residues of the constriction region, in particular histidine 182, which is conserved among all known water-specific channels, are critical in establishing water specificity. Our analysis of the AQP1 pore also indicates that the transport of protons through this channel is highly energetically unfavourable.

Evidence for ubiquitous strong electron-phonon coupling in high-temperature superconductors.

Abstract: Coupling between electrons and phonons (lattice vibrations) drives the formation of the electron pairs responsible for conventional superconductivity. The lack of direct evidence for electron-phonon coupling in the electron dynamics of the high-transition-temperature superconductors has driven an intensive search for an alternative mechanism. A coupling of an electron with a phonon would result in an abrupt change of its velocity and scattering rate near the phonon energy. Here we use angle-resolved photoemission spectroscopy to probe electron dynamics-velocity and scattering rate-for three different families of copper oxide superconductors. We see in all of these materials an abrupt change of electron velocity at 50-80 meV, which we cannot explain by any known process other than to invoke coupling with the phonons associated with the movement of the oxygen atoms. This suggests that electron-phonon coupling strongly influences the electron dynamics in the high-temperature superconductors, and must therefore be included in any microscopic theory of superconductivity.

Direct Observation of Vapor-Liquid-Solid Nanowire Growth

Abstract: Nanotubes and semiconductor nanowires are of fundamental importance to the study of sizeand dimensionality-dependent chemical and physical phenomena. 1,2 How to rationally synthesize these 1-dimensional nanostructures has been a major challenge, although several strategies have been pursued recently. 3-16 For example, carbon nanotubes have been prepared via condensation of hot carbon plasmas in the presence of certain metals, although the real growth mechanism has been elusive. 3-5 Recently, semiconductor nanowires with different compositions have been successfully synthesized using either vapor 6-12 or solution-based methodologies. 13-16 One key feature of these syntheses is the promotion of anisotropic crystal growth using metal nanoparticles as catalysts. The growth mechanism has been extrapolated from the vapor -liquid-solid (VLS) mechanism which was proposed in the 1960s -1970s for large whisker growth, 17-19 although an oxide-assisted growth mechanism has also been proposed. 2,20

Oxygen Reduction Reaction on Pt and Pt Bimetallic Surfaces: A Selective Review

Abstract: In this review we selectively summarize recent progress, primarily from our laboratory, in the development of the oxygen reduction reaction (ORR) catalysis on well-defined surfaces. The focus is on two type of metallic surfaces: platinum single crystals and bimetallic surfaces based on platinum. The single crystal results provide insight into the effects of the platinum structure on the kinetics of the ORR, and create a fundamental link between the specific activity of Pt (rate per unit area) and particle size (for various particle shapes). The results show that the structure sensitive kinetics of the ORR arise primarily due to structure sensitive adsorption of anions. In the absence of specific adsorption, such as in Nafion polymer electrolyte, no particle size effect is expected. The knowledge of the electrocatalysis of the ORR on model bimetallic surfaces on Pt-Ni and Pt-Co bulk alloys was used to resolve the enhanced ORR kinetics on supported Pt-Ni and Pt-Co catalysts. Finally, we show that the ORR on platinum modified with pseudomorphic Pd metal film in alkaline solution is the best catalysts ever used in O2 reduction. For both bimetallic systems, we demonstrated that the ability to make a controlled and well characterized arrangement of two elements in the electrode surface region presage a new era of advances in the ORR electrocatalysis.

A min-max cut algorithm for graph partitioning and data clustering

Abstract: An important application of graph partitioning is data clustering using a graph model - the pairwise similarities between all data objects form a weighted graph adjacency matrix that contains all necessary information for clustering. In this paper, we propose a new algorithm for graph partitioning with an objective function that follows the min-max clustering principle. The relaxed version of the optimization of the min-max cut objective function leads to the Fiedler vector in spectral graph partitioning. Theoretical analyses of min-max cut indicate that it leads to balanced partitions, and lower bounds are derived. The min-max cut algorithm is tested on newsgroup data sets and is found to out-perform other current popular partitioning/clustering methods. The linkage-based refinements to the algorithm further improve the quality of clustering substantially. We also demonstrate that a linearized search order based on linkage differential is better than that based on the Fiedler vector, providing another effective partitioning method.

An Apolipoprotein Influencing Triglycerides in Humans and Mice Revealed by Comparative Sequencing

Abstract: Comparison of genomic DNA sequences from human and mouse revealed a new apolipoprotein (APO) gene (APOAV) located proximal to the well-characterized APOAI/CIII/AIV gene cluster on human 11q23. Mice expressing a human APOAV transgene showed a decrease in plasma triglyceride concentrations to one-third of those in control mice; conversely, knockout mice lacking Apoav had four times as much plasma triglycerides as controls. In humans, single nucleotide polymorphisms (SNPs) across the APOAV locus were found to be significantly associated with plasma triglyceride levels in two independent studies. These findings indicate that APOAV is an important determinant of plasma triglyceride levels, a major risk factor for coronary artery disease.

The Farthest Known Supernova: Support for an Accelerating Universe and a Glimpse of the Epoch of Deceleration*

Abstract: We present photometric observations of an apparent Type Ia supernova (SN Ia) at a redshift of ~1.7, the farthest SN observed to date. The supernova, SN 1997ff, was discovered in a repeat observation by the Hubble Space Telescope (HST) of the Hubble Deep Field-North (HDF-N) and serendipitously monitored with NICMOS on HST throughout the Thompson et al. Guaranteed-Time Observer (GTO) campaign. The SN type can be determined from the host galaxy type: an evolved, red elliptical lacking enough recent star formation to provide a significant population of core-collapse supernovae. The classification is further supported by diagnostics available from the observed colors and temporal behavior of the SN, both of which match a typical SN Ia. The photometric record of the SN includes a dozen flux measurements in the I, J, and H bands spanning 35 days in the observed frame. The redshift derived from the SN photometry, z = 1.7 ± 0.1, is in excellent agreement with the redshift estimate of z = 1.65 ± 0.15 derived from the U300B450V606I814J110J125H160H165Ks photometry of the galaxy. Optical and near-infrared spectra of the host provide a very tentative spectroscopic redshift of 1.755. Fits to observations of the SN provide constraints for the redshift-distance relation of SNe Ia and a powerful test of the current accelerating universe hypothesis. The apparent SN brightness is consistent with that expected in the decelerating phase of the preferred cosmological model, ΩM ≈ 1/3,ΩΛ ≈ . It is inconsistent with gray dust or simple luminosity evolution, candidate astrophysical effects that could mimic previous evidence for an accelerating universe from SNe Ia at z ≈ 0.5. We consider several sources of potential systematic error, including gravitational lensing, supernova misclassification, sample selection bias, and luminosity calibration errors. Currently, none of these effects alone appears likely to challenge our conclusions. Additional SNe Ia at z > 1 will be required to test more exotic alternatives to the accelerating universe hypothesis and to probe the nature of dark energy.

Multi-class protein fold recognition using support vector machines and neural networks.

Abstract: Motivation: Protein fold recognition is an important approach to structure discovery without relying on sequence similarity. We study this approach with new multi-class classification methods and examined many issues important for a practical recognition system. Results: Most current discriminative methods for protein fold prediction use the one-against-others method, which has the well-known ‘False Positives’ problem. We investigated two new methods: the unique one-against-others and the all-against-all methods. Both improve prediction accuracy by 14‐110% on a dataset containing 27 SCOP folds. We used the Support Vector Machine (SVM) and the Neural Network (NN) learning methods as base classifiers. SVMs converges fast and leads to high accuracy. When scores of multiple parameter datasets are combined, majority voting reduces noise and increases recognition accuracy. We examined many issues involved with large number of classes, including dependencies of prediction accuracy on the number of folds and on the number of representatives in a fold. Overall, recognition systems achieve 56% fold prediction accuracy on a protein test dataset, where most of the proteins have below 25% sequence identity with the proteins used in training. Supplementary information: The protein parameter datasets used in this paper are available online (http://www.nersc.gov/∼cding/protein).

Inelastic dark matter

Abstract: Many observations suggest that much of the matter of the universe is nonbaryonic. Recently, the DAMA NaI dark matter direct detection experiment reported an annual modulation in their event rate consistent with a WIMP relic. However, the Cryogenic Dark Matter Search (CDMS) Ge experiment excludes most of the region preferred by DAMA. We demonstrate that if the dark matter can only scatter by making a transition to a slightly heavier state $(\ensuremath{\Delta}m\ensuremath{\sim}100 \mathrm{keV}),$ the experiments are no longer in conflict. Moreover, differences in the energy spectrum of nuclear recoil events could distinguish such a scenario from the standard WIMP scenario. Finally, we discuss the sneutrino as a candidate for inelastic dark matter in supersymmetric theories.

The Indian Ocean Experiment: Widespread Air Pollution from South and Southeast Asia

Abstract: The Indian Ocean Experiment (INDOEX) was an international, multiplatform field campaign to measure long-range transport of air pollution from South and Southeast Asia toward the Indian Ocean during the dry monsoon season in January to March 1999. Surprisingly high pollution levels were observed over the entire northern Indian Ocean toward the Intertropical Convergence Zone at about 6°S. We show that agricultural burning and especially biofuel use enhance carbon monoxide concentrations. Fossil fuel combustion and biomass burning cause a high aerosol loading. The growing pollution in this region gives rise to extensive air quality degradation with local, regional, and global implications, including a reduction of the oxidizing power of the atmosphere.

The Semiclassical Initial Value Representation: A Potentially Practical Way for Adding Quantum Effects to Classical Molecular Dynamics Simulations

Abstract: The semiclassical (SC) initial value representation (IVR) provides a potentially practical way for adding quantum mechanical effects to classical molecular dynamics (MD) simulations of the dynamics of complex molecular systems (i.e., those with many degrees of freedom). It does this by replacing the nonlinear boundary value problem of semiclassical theory by an average over the initial conditions of classical trajectories. This paper reviews the background and rebirth of interest in such approaches and surveys a variety of their recent applications. Special focus is on the ability to treat the dynamics of complex systems, and in this regard, the forward−backward (FB) version of the approach is especially promising. Several examples of the FB-IVR applied to model problems of many degrees of freedom show it to be capable of describing quantum effects quite well and also how these effects are quenched when some of the degrees of freedom are averaged over (“decoherence”).

Functional annotation of a full-length mouse cDNA collection

Abstract: The RIKEN Mouse Gene Encyclopaedia Project, a systematic approach to determining the full coding potential of the mouse genome, involves collection and sequencing of full-length complementary DNAs and physical mapping of the corresponding genes to the mouse genome. We organized an international functional annotation meeting (FANTOM) to annotate the first 21,076 cDNAs to be analysed in this project. Here we describe the first RIKEN clone collection, which is one of the largest described for any organism. Analysis of these cDNAs extends known gene families and identifies new ones.

Physical fitness and activity as separate heart disease risk factors: a meta-analysis

Abstract: WILLIAMS, P. T. Physical fitness and activity as separate heart disease risk factors: a meta-analysis. Med. Sci. Sports Exerc., Vol. 33, No. 5, 2001, pp. 754–761. Objective:Public health policies for physical activity presume that the greatest health benefits are achieved by increasing physical acti