Showing papers by "Los Alamos National Laboratory published in 2000"

The Sloan Digital Sky Survey: Technical summary

Abstract: The Sloan Digital Sky Survey (SDSS) will provide the data to support detailed investigations of the distribution of luminous and nonluminous matter in the universe: a photometrically and astrometrically calibrated digital imaging survey of π sr above about Galactic latitude 30° in five broad optical bands to a depth of g' ~ 23 mag, and a spectroscopic survey of the approximately 106 brightest galaxies and 105 brightest quasars found in the photometric object catalog produced by the imaging survey. This paper summarizes the observational parameters and data products of the SDSS and serves as an introduction to extensive technical on-line documentation.

A comparison of three methods for selecting values of input variables in the analysis of output from a computer code

Abstract: Two types of sampling plans are examined as alternatives to simple random sampling in Monte Carlo studies. These plans are shown to be improvements over simple random sampling with respect to variance for a class of estimators which includes the sample mean and the empirical distribution function.

Theoretical approaches to x-ray absorption fine structure

Abstract: Dramatic advances in the understanding of x-ray absorption fine structure (XAFS) have been made over the past few decades, which have led ultimately to a highly quantitative theory. This review covers these developments from a unified multiple-scattering viewpoint. The authors focus on extended x-ray absorption fine structure (EXAFS) well above an x-ray edge, and, to a lesser extent, on x-ray absorption near-edge structure (XANES) closer to an edge. The discussion includes both formal considerations, derived from a many-electron formulation, and practical computational methods based on independent-electron models, with many-body effects lumped into various inelastic losses and energy shifts. The main conceptual issues in XAFS theory are identified and their relative importance is assessed; these include the convergence of the multiple-scattering expansion, curved-wave effects, the scattering potential, inelastic losses, self-energy shifts, and vibrations and structural disorder. The advantages and limitations of current computational approaches are addressed, with particular regard to quantitative experimental comparisons.

Optical gain and stimulated emission in nanocrystal quantum dots.

Abstract: The development of optical gain in chemically synthesized semiconductor nanoparticles (nanocrystal quantum dots) has been intensely studied as the first step toward nanocrystal quantum dot lasers. We examined the competing dynamical processes involved in optical amplification and lasing in nanocrystal quantum dots and found that, despite a highly efficient intrinsic nonradiative Auger recombination, large optical gain can be developed at the wavelength of the emitting transition for close-packed solids of these dots. Narrowband stimulated emission with a pronounced gain threshold at wavelengths tunable with the size of the nanocrystal was observed, as expected from quantum confinement effects. These results unambiguously demonstrate the feasibility of nanocrystal quantum dot lasers.

Ultrahigh-Density Nanowire Arrays Grown in Self-Assembled Diblock Copolymer Templates

Abstract: We show a simple, robust, chemical route to the fabrication of ultrahigh-density arrays of nanopores with high aspect ratios using the equilibrium self-assembled morphology of asymmetric diblock copolymers. The dimensions and lateral density of the array are determined by segmental interactions and the copolymer molecular weight. Through direct current electrodeposition, we fabricated vertical arrays of nanowires with densities in excess of 1.9 x 10(11) wires per square centimeter. We found markedly enhanced coercivities with ferromagnetic cobalt nanowires that point toward a route to ultrahigh-density storage media. The copolymer approach described is practical, parallel, compatible with current lithographic processes, and amenable to multilayered device fabrication.

Maximum-likelihood density modification

Abstract: A likelihood-based approach to density modification is developed that can be applied to a wide variety of cases where some information about the electron density at various points in the unit cell is available. The key to the approach consists of developing likelihood functions that represent the probability that a particular value of electron density is consistent with prior expectations for the electron density at that point in the unit cell. These likelihood functions are then combined with likelihood functions based on experimental observations and with others containing any prior knowledge about structure factors to form a combined likelihood function for each structure factor. A simple and general approach to maximizing the combined likelihood function is developed. It is found that this likelihood-based approach yields greater phase improvement in model and real test cases than either conventional solvent flattening and histogram matching or a recent reciprocal-space solvent-flattening procedure [Terwilliger (1999), Acta Cryst. D55, 1863–1871].

Quantization of multiparticle auger rates in semiconductor quantum dots

Abstract: We have resolved single-exponential relaxation dynamics of the 2-, 3-, and 4-electron-hole pair states in nearly monodisperse cadmium selenide quantum dots with radii ranging from 1 to 4 nanometers. Comparison of the discrete relaxation constants measured for different multiple-pair states indicates that the carrier decay rate is cubic in carrier concentration, which is characteristic of an Auger process. We observe that in the quantum-confined regime, the Auger constant is strongly size-dependent and decreases with decreasing the quantum dot size as the radius cubed.

The Catalytic Pathway of Cytochrome P450Cam at Atomic Resolution

Abstract: Members of the cytochrome P450 superfamily catalyze the addition of molecular oxygen to nonactivated hydrocarbons at physiological temperature-a reaction that requires high temperature to proceed in the absence of a catalyst. Structures were obtained for three intermediates in the hydroxylation reaction of camphor by P450cam with trapping techniques and cryocrystallography. The structure of the ferrous dioxygen adduct of P450cam was determined with 0.91 angstrom wavelength x-rays; irradiation with 1.5 angstrom x-rays results in breakdown of the dioxygen molecule to an intermediate that would be consistent with an oxyferryl species. The structures show conformational changes in several important residues and reveal a network of bound water molecules that may provide the protons needed for the reaction.

Timing the ancestor of the HIV-1 pandemic strains.

Abstract: HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.

Generating solitons by phase engineering of a bose-einstein condensate

Abstract: Quantum phase engineering is demonstrated with two techniques that allow the spatial phase distribution of a Bose-Einstein condensate (BEC) to be written and read out. A quantum state was designed and produced by optically imprinting a phase pattern onto a BEC of sodium atoms, and matter-wave interferometry with spatially resolved imaging was used to analyze the resultant phase distribution. An appropriate phase imprint created solitons, the first experimental realization of this nonlinear phenomenon in a BEC. The subsequent evolution of these excitations was investigated both experimentally and theoretically.

HIV-1 Nomenclature Proposal

Abstract: A clear and consistent genetic classification of human immunodeficiency virus-type 1 (HIV-1) strains continues to be of great utility in epidemiological tracking of the AIDS pandemic and in vaccine design. It also provides a foundation for detecting any biological differences that may have evolved

Optical Nonlinearities and Ultrafast Carrier Dynamics in Semiconductor Nanocrystals

Abstract: Femtosecond transient absorption in the visible and infrared spectral ranges has been applied to study carrier dynamics and mechanisms for resonant optical nonlinearities in CdSe nanocrystals (NCs) with a variety of surface passivations. Sequential filling of the 1S, 1P, and 1D atomic-like electron orbitals, governed by Fermi statistics, is clearly observed in the NC bleaching spectra recorded at progressively higher pump intensities. We observe that electron−hole (e−h) spatial separation strongly affects electron intraband dynamics. Such dependence indicates a nonphonon energy relaxation mechanism involving e−h interactions. A strong difference in electron and hole relaxation behavior in the stage following initial intraband relaxation is observed. In contrast to electron relaxation, which is sensitive to the quality of surface passivation (i.e., is affected by trapping at surface defects), depopulation dynamics of the initially-excited hole states are identical in NCs with different surface properties, ...

Radiation tolerance of complex oxides

Abstract: The radiation performance of a variety of complex oxides is predicted on the basis of a material's propensity to accommodate lattice point defects. The calculations indicate that a particular class of oxides possessing the fluorite crystal structure should accept radiation-induced defects into their lattices far more readily than a structurally similar class of oxides based on the pyrochlore crystal structure. Preliminary radiation damage experiments substantiate the prediction that fluorites are inherently more radiation resistant than pyrochlores. These results may permit the chemical durability and radiation tolerance of potential hosts for actinides and radioactive wastes to be tailored.

Predicting fault incidence using software change history

Abstract: This paper is an attempt to understand the processes by which software ages. We define code to be aged or decayed if its structure makes it unnecessarily difficult to understand or change and we measure the extent of decay by counting the number of faults in code in a period of time. Using change management data from a very large, long-lived software system, we explore the extent to which measurements from the change history are successful in predicting the distribution over modules of these incidences of faults. In general, process measures based on the change history are more useful in predicting fault rates than product metrics of the code: For instance, the number of times code has been changed is a better indication of how many faults it will contain than is its length. We also compare the fault rates of code of various ages, finding that if a module is, on the average, a year older than an otherwise similar module, the older module will have roughly a third fewer faults. Our most successful model measures the fault potential of a module as the sum of contributions from all of the times the module has been changed, with large, recent changes receiving the most weight.

Pressure-induced superconductivity in quasi-2D CeRhIn5

Abstract: CeRhIn5 is a new heavy-electron material that crystallizes in a quasi-2D structure that can be viewed as alternating layers of CeIn3 and RhIn2 stacked sequentially along the tetragonal c axis. Application of hydrostatic pressure induces a first-order-like transition from an unconventional antiferromagnetic state to a superconducting state with T(c) = 2.1 K.

Multiple-Locus Variable-Number Tandem Repeat Analysis Reveals Genetic Relationships within Bacillus anthracis

Abstract: Bacillus anthracis is one of the most genetically homogeneous pathogens described, making strain discrimination particularly difficult. In this paper, we present a novel molecular typing system based on rapidly evolving variable-number tandem repeat (VNTR) loci. Multiple-locus VNTR analysis (MLVA) uses the combined power of multiple alleles at several marker loci. In our system, fluorescently labeled PCR primers are used to produce PCR amplification products from eight VNTR regions in the B. anthracis genome. These are detected and their sizes are determined using an ABI377 automated DNA sequencer. Five of these eight loci were discovered by sequence characterization of molecular markers (vrrC1, vrrC2, vrrB1, vrrB2, and CG3), two were discovered by searching complete plasmid nucleotide sequences (pXO1-aat and pXO2-at), and one was known previously (vrrA). MLVA characterization of 426 B. anthracis isolates identified 89 distinct genotypes. VNTR markers frequently identified multiple alleles (from two to nine), with Nei's diversity values between 0.3 and 0.8. Unweighted pair-group method arithmetic average cluster analysis identified six genetically distinct groups that appear to be derived from clones. Some of these clones show worldwide distribution, while others are restricted to particular geographic regions. Human commerce doubtlessly has contributed to the dispersal of particular clones in ancient and modern times.

Theory of quantum error correction for general noise

Abstract: A measure of quality of an error-correcting code is the maximum number of errors that it is able to correct. We show that a suitable notion of "number of errors" e makes sense for any quantum or classical system in the presence of arbitrary interactions. Thus, e-error-correcting codes protect information without requiring the usual assumptions of independence. We prove the existence of large codes for both quantum and classical information. By viewing error-correcting codes as subsystems, we relate codes to irreducible representations of operator algebras and show that noiseless subsystems are infinite-distance error-correcting codes.

Tau neutrinos favored over sterile neutrinos in atmospheric muon neutrino oscillations.

Abstract: The previously published atmospheric neutrino data did not distinguish whether muon neutrinos were oscillating into tau neutrinos or sterile neutrinos, as both hypotheses fit the data. Using data recorded in 1100 live days of the Super-Kamiokande detector, we use three complementary data samples to study the difference in zenith angle distribution due to neutral currents and matter effects. We find no evidence favoring sterile neutrinos, and reject the hypothesis at the $99%$ confidence level. On the other hand, we find that oscillation between muon and tau neutrinos suffices to explain all the results in hand.

Cosmology of brane models with radion stabilization

Abstract: We analyze the cosmology of the Randall-Sundrum model and that of compact brane models in general in the presence of a radius stabilization mechanism. We find that the expansion of our Universe is generically in agreement with the expected effective four dimensional description. The constraint (which is responsible for the appearance of nonconventional cosmologies in these models) that must be imposed on the matter densities on the two branes in the theory without a stabilized radius is a consequence of requiring a static solution even in the absence of stabilization. Such constraints disappear in the presence of a stablizing potential, and the ordinary Friedmann-Robertson-Walker (FRW) equations are reproduced, with the expansion driven by the sum of the physical values of the energy densities on the two branes and in the bulk. For the case of the Randall-Sundrum model we examine the kinematics of the radion field, and find that corrections to the standard FRW equations are small for temperatures below the weak scale. We find that the radion field has renormalizable and unsuppressed couplings to standard model particles after electroweak symmetry breaking. These couplings may have important implications for collider searches. We comment on the possibility that matter off the TeV brane could serve as a dark matter candidate.

Second nearest-neighbor modified embedded-atom-method potential

Abstract: The modified embedded-atom method, a first nearest-neighbor semiempirical model for atomic potentials, can describe the physical properties of a wide range of elements and alloys with various lattice structures. However, the model is not quite successful for bcc metals in that it predicts the order among the size of low index surface energies incorrectly and that it generates a structure more stable than bcc for some bcc metals. In order to remove the problems, the formalism has been extended so that the second nearest neighbor interactions are taken into consideration. New parameters for Fe and comparisons between calculated and experimental physical properties of Fe are presented.

The evolution of mutation rates: separating causes from consequences.

Abstract: Summary Natural selection can adjust the rate of mutation in a population by acting on allelic variation affecting processes of DNA replication and repair Because mutation is the ultimate source of the genetic variation required for adaptation, it can be appealing to suppose that the genomic mutation rate is adjusted to a level that best promotes adaptation Most mutations with phenotypic effects are harmful, however, and thus there is relentless selection within populations for lower genomic mutation rates Selection on beneficial mutations can counter this effect by favoring alleles that raise the mutation rate, but the effect of beneficial mutations on the genomic mutation rate is extremely sensitive to recombination and is unlikely to be important in sexual populations In contrast, high genomic mutation rates can evolve in asexual populations under the influence of beneficial mutations, but this phenomenon is probably of limited adaptive significance and represents, at best, a temporary reprieve from the continual selection pressure to reduce mutation The physiological cost of reducing mutation below the low level observed in most populations may be the most important factor in setting the genomic mutation rate in sexual and asexual systems, regardless of the benefits of mutation in producing new adaptive variation Maintenance of mutation rates higher than the minimum set by this ‘‘cost of fidelity’’ is likely only under special circumstances BioEssays 22:1057‐ 1066, 2000 fl 2000 John Wiley & Sons, Inc

A thermoacoustic-Stirling heat engine: detailed study

Abstract: A new type of thermoacoustic engine based on traveling waves and ideally reversible heat transfer is described. Measurements and analysis of its performance are presented. This new engine outperforms previous thermoacoustic engines, which are based on standing waves and intrinsically irreversible heat transfer, by more than 50%. At its most efficient operating point, it delivers 710 W of acoustic power to its resonator with a thermal efficiency of 0.30, corresponding to 41% of the Carnot efficiency. At its most powerful operating point, it delivers 890 W to its resonator with a thermal efficiency of 0.22. The efficiency of this engine can be degraded by two types of acoustic streaming. These are suppressed by appropriate tapering of crucial surfaces in the engine and by using additional nonlinearity to induce an opposing time-averaged pressure difference. Data are presented which show the nearly complete elimination of the streaming convective heat loads. Analysis of these and other irreversibilities show which components of the engine require further research to achieve higher efficiency. Additionally, these data show that the dynamics and acoustic power flows are well understood, but the details of the streaming suppression and associated heat convection are only qualitatively understood.

Nonlinear Elastic Wave Spectroscopy (NEWS) Techniques to Discern Material Damage, Part I: Nonlinear Wave Modulation Spectroscopy (NWMS)

Abstract: The level of nonlinearity in the elastic response of materials containing structural damage is far greater than in materials with no structural damage. This is the basis for nonlinear wave diagnostics of damage, methods which are remarkably sensitive to the detection and progression of damage in materials. Nonlinear wave modulation spectroscopy (NWMS) is one exemplary method in this class of dynamic nondestructive evaluation techniques. The method focuses on the application of harmonics and sum and difference frequency to discern damage in materials. It consists of exciting a sample with continuous waves of two separate frequencies simultaneously, and inspecting the harmonics of the two waves, and their sum and difference frequencies (sidebands). Undamaged materials are essentially linear in their response to the two waves, while the same material, when damaged, becomes highly nonlinear, manifested by harmonics and sideband generation. We illustrate the method by experiments on uncracked and crac...

Solar wind observations over Ulysses' first full polar orbit

Abstract: This study examines solar wind plasma and magnetic field observations from Ulysses' first full polar orbit in order to characterize the high-latitude solar wind under conditions of decreasing and low solar activity. By comparing observations taken over nearly all heliolatitudes and two different intervals covering the same radial distances, we are able to separate the radial and latitudinal variations in the solar wind. We find that once the radial gradients are removed, none of the high-latitude solar wind parameters show much latitudinal variation, indicating that the solar wind emanating from the polar coronal holes is extremely uniform. In addition, by examining nearly 6 years of data starting in the declining phase of the last solar cycle and extending through the most recent solar minimum, we are able to address hemispheric asymmetries in the observations. We find that these asymmetries are most likely driven by differences in the solar wind source over the solar cycle and indicate that more energy goes into the polar solar wind during the declining phase of the solar cycle than around minimum. Because the mass flux is larger in the declining phase while the speeds are very similar, we conclude that this energy is introduced at an altitude below the solar wind acceleration critical point. Finally, we provide details of the statistics of over 20 solar wind parameters so that upcoming observations from Ulysses' second polar orbit, during much more active times on the Sun, can be readily compared to the quieter first orbit results.

The decay of the latent reservoir of replication-competent HIV-1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy.

Abstract: Replication-competent HIV-1 can be isolated from infected patients despite prolonged plasma virus suppression by anti-retroviral treatment1,2,3. Recent studies have identified resting, memory CD4+ T lymphocytes as a long-lived latent reservoir of HIV-1 (refs. 4,5). Cross-sectional analyses indicate that the reservoir is rather small, between 103 and 107 cells per patient5,6. In individuals whose plasma viremia levels are well suppressed by anti-retroviral therapy, peripheral blood mononuclear cells containing replication-competent HIV-1 were found to decay with a mean half-life of approximately 6 months7, close to the decay characteristics of memory lymphocytes in humans and monkeys8,9,10. In contrast, little decay was found in a less-selective patient population11. We undertook this study to address this apparent discrepancy. Using a quantitative micro-culture assay, we demonstrate here that the latent reservoir decays with a mean half-life of 6.3 months in patients who consistently maintain plasma HIV-1 RNA levels of fewer than 50 copies/ml. Slower decay rates occur in individuals who experience intermittent episodes of plasma viremia. Our findings indicate that the persistence of the latent reservoir of HIV-1 despite prolonged treatment is due not only to its slow intrinsic decay characteristics but also to the inability of current drug regimens to completely block HIV-1 replication.

Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction

Abstract: We introduce a distance-based phylogeny reconstruction method called ‘‘weighted neighbor joining,’’ or ‘‘Weighbor’’ for short. As in neighbor joining, two taxa are joined in each iteration; however, the Weighbor criterion for choosing a pair of taxa to join takes into account that errors in distance estimates are exponentially larger for longer distances. The criterion embodies a likelihood function on the distances, which are modeled as correlated Gaussian random variables with different means and variances, computed under a probabilistic model for sequence evolution. The Weighbor criterion consists of two terms, an additivity term and a positivity term, that quantify the implications of joining the pair. The first term evaluates deviations from additivity of the implied external branches, while the second term evaluates confidence that the implied internal branch has a positive branch length. Compared with maximum-likelihood phylogeny reconstruction, Weighbor is much faster, while building trees that are qualitatively and quantitatively similar. Weighbor appears to be relatively immune to the ‘‘long branches attract’’ and ‘‘long branch distracts’’ drawbacks observed with neighbor joining, BIONJ, and parsimony.

Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis

Abstract: Rapid analysis of diversity in complex microbial communities has remained an elusive but important goal in microbial ecology. Community diversity can be examined at several levels. The most simple analyses use DNA profiles (generated by PCR and sometimes followed by restriction digestion of amplification mixtures) to identify differences in the composition of communities. More refined approaches describe differences not only in community composition but also in community organization by measuring the number (richness) and relative abundance (structure or evenness) of species or phylotypes. The richness and evenness of biological communities reflect selective pressures that shape diversity within communities. Measuring these parameters is most useful when assessing treatment effects (e.g., physical disturbance, pollution, nutrient addition, predation, climate change, etc.) on community diversity. Diversity statistics can also indicate the ability of a community to recover from disturbance and utilize resources efficiently (4). An ideal method for analysis of diversity in complex microbial communities would enable the simultaneous measurement of composition, phylotype richness, and community structure. The method would be rapid and reproducible and would permit flexible sampling of the entire microbial community. Direct amplification of bacterial 16S rRNA genes from extracted soil DNA provides the most comprehensive and flexible means of sampling bacterial communities. Analysis of clone libraries of 16S rRNA genes amplified from different environments can provide relative measures of diversity that are, in general, consistent with qualitative relationships determined from traditional culture collections (9). However, analysis of individual 16S rRNA gene clones in multiple libraries is an expensive and extremely inefficient approach for comparison of numerous bacterial communities in replicated field experiments. Other methods, such as thermal or denaturing gradient gel electrophoresis (DGGE) (12, 14, 16, 21, 23, 28), heteroduplex analysis (8, 11), or terminal restriction fragment (T-RFLP or TRF) analysis (3, 6, 18, 20), assess the diversity of 16S rRNA gene mixtures more crudely than cloning and sequencing but are far more rapid and therefore more amenable to field-scale experiments in which replication is important. DGGE and the TRF method were recently shown to identify similar relationships among marine communities (20). DGGE has also been shown to provide estimates of cyanobacterial richness consistent with estimates based on direct observation of cell morphological types in cyanobacterial mat communities (22). Although cyanobacteria comprise a small phylogenetic group, these findings support the idea that rapid fingerprinting techniques might be capable of assessing the richness and evenness of microbial communities in general. We calibrated the TRF method by comparing the composition, relative species richness, and evenness of four soil microbial communities that had been analyzed previously by cultivation and by 16S rDNA cloning (9). The four soils were from pinyon rhizosphere and between-tree (interspace) environments at two sites 19 km apart in northern Arizona (17). Both sites are pinyon-juniper woodlands but differ dramatically in soil type (7, 17). Here we show that the TRF method successfully demonstrated relationships between the four samples consistent with previous comparisons of 801 16S rRNA gene clones from the samples. However, calculations from TRF profiles provided variable values for comparison of phylotype richness and community evenness and depended on the restriction enzyme used to derive the profile. The data demonstrate both the strengths and limitations of the TRF method for analysis of natural communities that are highly complex.