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At least 631 records · Page 35

Relaxation algorithms for matrix completion, with applications to seismic travel-time data interpolation

Travel time tomography is used to infer the underlying three-dimensional wavespeed structure of the Earth by fitting seismic travel time data collected at surface stations. Data interpolation and denoising techniques are important pre-processing steps that use prior knowledge about the data, including parsimony in the frequency and wavelet domains, low-rank structure of matricizations, and local smoothness. In this work, we show how local smoothness structure can be combined with low rank constraints using level-set optimization formulations, and develop a new relaxation algorithm that can efficiently solve these joint problems. In the seismology setting, we use the approach to interpolate missing stations and de-noise observed stations. The new approach is competitive with alternative algorithms, and offers new functionality to interpolate observed data using both smoothness and low rank structure in the presence of data fitting constraints.

constrained optimization↗

Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters

Abstract Background The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAST to find identical sequences between the two. The typical millions of database and query sequences make BLAST computationally challenging but also well suited for parallelization on high-performance computing clusters. The efficacy of parallelization depends on the data partitioning, where the optimal data partitioning relies on an accurate performance model. In previous studies, a BLAST job was sped up by 27 times by partitioning the database and query among thousands of processor nodes. However, the optimality of the partitioning method was not studied. Unlike BLAST performance models proposed in the literature that usually have problem size and hardware configuration as the only variables, the execution time of a BLAST job is a function of database size, query size, and hardware capability. In this work, the nucleotide BLAST application BLASTN was profiled using three methods: shell-level profiling with the Unix “time” command, code-level profiling with the built-in “profiler” module, and system-level profiling with the Unix “gprof” program. The runtimes were measured for six node types, using six different database files and 15 query files, on a heterogeneous HPC cluster with 500+ nodes. The empirical measurement data were fitted with quadratic functions to develop performance models that were used to guide the data parallelization for BLASTN jobs. Results Profiling results showed that BLASTN contains more than 34,500 different functions, but a single function, RunMTBySplitDB, takes 99.12% of the total runtime. Among its 53 child functions, five core functions were identified to make up 92.12% of the overall BLASTN runtime. Based on the performance models, static load balancing algorithms can be applied to the BLASTN input data to minimize the runtime of the longest job on an HPC cluster. Four test cases being run on homogeneous and heterogeneous clusters were tested. Experiment results showed that the runtime can be reduced by 81% on a homogeneous cluster and by 20% on a heterogeneous cluster by re-distributing the workload. Discussion Optimal data partitioning can improve BLASTN’s overall runtime 5.4-fold in comparison with dividing the database and query into the same number of fragments. The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.

59 BASIC BIOLOGICAL SCIENCES↗

Biomembrane Structure and Material Properties Studied With Neutron Scattering

Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An initial analysis of the data from the Polar Orbiting Geophysical (POGS) Satellite

The Polar Orbiting Geophysical Satellite (POGS) was launched in 1990 to measure the geomagnetic field. POGS data from selected magnetically quiet days was chosen, quality checked and deleted where thought to be erroneous. A time and position correction was applied. The resulting data was fit to a degree 13 spherical harmonic model. Evaluation of the quality of the data indicates that it is sufficient for definition of the low degree (approximately less than 8) portion of the geomagnetic field. Further correction of the data time and position may improve this quality.

Langel, R. A.↗

GVIPS Models and Software

Two reports discuss, respectively, (1) the generalized viscoplasticity with potential structure (GVIPS) class of mathematical models and (2) the Constitutive Material Parameter Estimator (COMPARE) computer program. GVIPS models are constructed within a thermodynamics- and potential-based theoretical framework, wherein one uses internal state variables and derives constitutive equations for both the reversible (elastic) and the irreversible (viscoplastic) behaviors of materials. Because of the underlying potential structure, GVIPS models not only capture a variety of material behaviors but also are very computationally efficient. COMPARE comprises (1) an analysis core and (2) a C++-language subprogram that implements a Windows-based graphical user interface (GUI) for controlling the core. The GUI relieves the user of the sometimes tedious task of preparing data for the analysis core, freeing the user to concentrate on the task of fitting experimental data and ultimately obtaining a set of material parameters. The analysis core consists of three modules: one for GVIPS material models, an analysis module containing a specialized finite-element solution algorithm, and an optimization module. COMPARE solves the problem of finding GVIPS material parameters in the manner of a design-optimization problem in which the parameters are the design variables.

Arnold, Steven M.↗

Long‐term variation in environmental conditions influences host–parasite fitness

Abstract Long‐term data on host and parasite fitness are important for predicting how host–parasite interactions will be altered in an era of global change. Here, we use data collected from 1997 to 2013 to explore effects of changing environmental conditions on bird–blowfly interactions in northern New Mexico. The objectives of this study were to examine what climate variables influence blowfly prevalence and intensity and to determine whether blowflies and climate variables affect bird fledging success. We examined how temperature, precipitation, and drought affect two parasitic blowflies and their hosts, Western Bluebirds ( Sialia mexicana ) and Ash‐throated Flycatchers ( Myiarchus cinerascens ). We found that blowfly prevalence did not change over time. Blowfly intensity increased over time in bluebird nests, but not in flycatcher nests. More blowflies result in slightly higher fledging success in bluebirds, but not flycatchers. There was a significant interaction between blowflies and precipitation on bluebird fledging success. For flycatchers, there was a significant interaction between blowflies and temperature and between blowflies and drought severity on fledging success. Given that the southwest is projected to be hotter and have more frequent and prolonged droughts, we predict that flycatchers may be negatively impacted by blowflies if these trends continue. Future work should focus on investigating the role of both blowflies and climate on fledging success. Climate patterns may negatively impact host fitness through altered parasite pressure.

54 ENVIRONMENTAL SCIENCES↗

LASSO for CALPHAD Model Selection Enables Data-Efficient Thermodynamic Modeling: An Application in Thermochemical Hydrogen Production Materials

Phenomenological CALPHAD (CALculation of PHAse Diagrams) models, widely used for multicomponent materials, often contain a considerable number of parameters and require fitting using data from a relatively small number of experimental measurements or theoretical calculations. Sometimes these parameters are introduced for the purpose of improving model fits but without clear physical justification, which leads to overparametrized models with poor generalization performance. Automated approaches for optimal model selection based on the available data therefore become critical. Here, in this work, a least absolute shrinkage and selection operator (LASSO)-based approach is developed for model selection by leveraging the linearity of the CALPHAD model with respect to its parameters to convert the model selection and fitting to a LASSO minimization problem. We demonstrate its utility for thermodynamic modeling of thermochemical hydrogen (TCH) production materials using lanthanum strontium manganite (LSM) as an example. Various TCH-relevant properties, including oxygen stoichiometry as a function of oxygen partial pressure, enthalpy of reduction, and entropy of reduction, are successfully predicted with reasonable accuracy using a minimal set of model parameters. Importantly, the model selection and fitting involve minimal human decision; it can therefore be applied to high-throughput DFT defect calculations and yield efficient workflows for TCH material modeling and optimization.

CALPHAD↗

Acid-base properties of the Fe(CN){sub 6}{sup 3-}/Fe(CN){sub 6}{sup 4-} redox couple in the presence of various background mineral acids and salts

The acid-base behavior of Fe(CN){sub 6}{sup 4-} was investigated by measuring the formal potentials of the Fe(CN){sub 6}{sup 3-}/Fe(CN){sub 6}{sup 4-} couple over a wide range of acidic and neutral solution compositions. The experimental data were fitted to a model taking into account the protonated forms of Fe(CN){sub 6}{sup 4-} and using values of the activities of species in solution, calculated with a simple solution model and a series of binary data available in the literature. The fitting needed to take account of the protonated species HFe(CN){sub 6}{sup 3-} and H{sub 2}Fe(CN){sub 6}{sup 2-}, already described in the literature, but also the species H{sub 3}Fe(CN){sub 6}{sup -} (associated with the acid-base equilibrium H{sub 3}Fe(CN){sub 6}{sup -} ↔ H{sub 2}Fe(CN){sub 6}{sup 2-} + H{sup +}). The acidic dissociation constants of HFe(CN){sub 6}{sup 3-}, H{sub 2}Fe(CN){sub 6}{sup 2-} and H{sub 3}Fe(CN){sub 6}{sup -} were found to be pK(1)(II) = 3.9 ± 0.1, pK(2)(II) = 2.0 ± 0.1, and pK(3)(II) = 0.0 ± 0.1, respectively. These constants were determined by taking into account that the activities of the species are independent of the ionic strength. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Testing relativity with solar system dynamics

A major breakthrough is described in the accuracy of Solar System dynamical tests of relativistic gravity. The breakthrough was achieved by factoring in ranging data from Viking Landers 1 and 2 from the surface of Mars. Other key data sources included optical transit circle observations, lunar laser ranging, planetary radar, and spacecraft (Mariner 9 to Mars and Mariner 10 to Mercury). The Solar System model which is used to fit the data and the process by which such fits are performed are explained and results are discussed. The results are fully consistent with the predictions of General Relativity.

Hellings, R. W.↗

Ba 0.4 Rb 0.6 Mn 2 As 2 : A prototype half-metallic ferromagnet

Half-metallic ferromagnetism (FM) in single-crystal Ba 0.39(1) Rb 0.61(1) Mn 2 As 2 below its Curie temperature T C = 103(2) K is reported. The magnetization M versus applied magnetic field H isotherm data at 1.8 K show complete polarization of the itinerant doped-hole magnetic moments that are introduced by substituting Rb for Ba. Here, the material exhibits extremely soft FM, with unobservably small remanent magnetization and coercive field. Surprisingly, and contrary to typical itinerant FMs, the M(H) data follow the Arrott-plot paradigm that is based on a mean-field theory of local-moment FMs. The in-plane electrical resistivity data are fitted well by an activated-T 2 expression for T ≤ T C , whereas the data sharply deviate from this model for T > T C . Hence the activated-T 2 resistivity model is an excellent diagnostic for determining the onset of half-metallic FM in this compound, which in turn demonstrates the presence of a strong correlation between the electronic transport and magnetic properties of the material. Together with previous data on 40% hole-doped Ba 0.6 K 0.4 Mn 2 As 2 , these measurements establish 61%-doped Ba 0.39 Rb 0.61 Mn 2 As 2 as a prototype for a class of half-metallic ferromagnets in which all the itinerant carriers in the material are ferromagnetic.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

The Pioneer 11 1976 solar conjunction: A unique opportunity to explore the heliographic latitudinal variations of the solar corona

The 1976 Pioneer II Solar Conjunction provided the opportunity to accumulate a substantial quantity of doppler noise data over a dynamic range of signal closest approach point heliographic latitudes. The observed doppler noise data were fit to the doppler noise model ISED, and the deviations of the observed doppler noise data from the model were used to construct a (multiplicative) function to describe the effect of heliographic latitude. This expression was then incorporated into the ISED model to produce a new doppler noise model-ISEDB.

Berman, A. L.↗

Viking Orbiter Photometric Observations of the Mars Phase Function July Through November 1976

Over 7200 Viking Orbiter pictures have provided phase function information over a large range in viewing geometry. Comparison with the earlier Mariner 9 data reveals possibly significant changes. A two-component limb darkening characterization is shown to fit the data better at large phase angles than the traditional Minnaert or Lommel-Seeliger approach. The phase integral is 15% larger than the Mariner 9 observations owing in part to data obtained at larger phase angles revealing apparent condensate phenomena.

Thorpe, T. E.↗

Testing of the anemometer circuit: Data report

The following text discusses results from the electronic step testing and the beginning of velocity step testing in the shock tube. It should be kept in mind that frequency response is always measured as the time from the beginning of the event to the minimum (positive inflection) of the 'bucket' that immediately follows the response. This report is not a complete account of the results from square wave testing. Some data is still in the process of being analyzed and efforts are being made to fit the data to both Freymuth's third order theory and modelled responses from SPICE circuit simulation software.

Moen, Michael J.↗

A Combined $\nu_\mu \rightarrow \nu_e$ and $\bar \nu_\mu \rightarrow \bar \nu_e$ Oscillation Analysis of the MiniBooNE Excesses

The MiniBooNE experiment at Fermilab reports results from an analysis of the combined $\nu_e$ and $\bar \nu_e$ appearance data from $6.46 \times 10^{20}$ protons on target in neutrino mode and $11.27 \times 10^{20}$ protons on target in antineutrino mode. A total excess of $240.3 \pm 34.5 \pm 52.6$ events ($3.8 \sigma$) is observed from combining the two data sets in the energy range $200<E_\nu^{QE}<1250$ MeV. In a combined fit for CP-conserving $\nu_\mu \rightarrow \nu_e$ and $\bar{\nu}_{\mu}\rightarrow\bar{\nu}_e$ oscillations via a two-neutrino model, the background-only fit has a $\chi^2$-probability of 0.03% relative to the best oscillation fit. The data are consistent with neutrino oscillations in the $0.01 < \Delta m^2 < 1.0$ eV$^2$ range and with the evidence for antineutrino oscillations from the Liquid Scintillator Neutrino Detector (LSND).

43 PARTICLE ACCELERATORS↗

Ionization Efficiency in the Dayside Ionosphere of Mars: Structure and Variability

Ionization efficiency, the ratio between photoelectron impact ionization and primary photoionization, is an important quantity from the perspective of ionospheric energy balance and as a quantity to be parameterized for use in global simulations. We investigate ionization efficiency using MAVEN in situ measurements of solar extreme ultraviolet (EUV) flux, suprathermal electron flux, and neutral density. Its behavior with respect to pressure and solar zenith angle (SZA) is explained by ionization cross-sections and photoabsorption, plus photoelectron transport near the terminator. We find similar ionization efficiencies between the species CO 2 , O, N 2 , and CO, with Argon ∼40% higher, explained largely by its higher ionization potential. Efficiency depends positively on solar activity, increasing by ∼50–100% (depending on season) from low to moderate solar EUV levels, before flattening at higher EUV levels. EUV spectral hardening appears to be responsible for only ∼15% of this increase, the remainder best explained by variability in neutral composition. We find a negligible dependence of ionization efficiency on the strength and direction of crustal magnetic fields. Efficiencies agree poorly with the theoretical model of Nicholson et al. (2009), https://doi.org/10.1111/j.1365-2966.2009.15463.x, possibly reflecting differences in model versus measured solar EUV spectrum and neutral densities. We fit the data to the empirical parameterization of Mendillo et al. (2011), https://doi.org/10.1029/2011ja016865 but find that a single fit cannot capture ionization efficiency behavior across all dayside SZA values. We believe that an empirical model of Mars ionization efficiency will require MAVEN data and validated transport modeling to reach to sufficiently high pressures to capture Mars' photochemical peaks M1 and M2

Robert Lillis↗

PCA/HEXTE Observations of Coma and A2319

The Coma cluster was observed in 1996 for 90 ks by the PCA and HEXTE instruments aboard the RXTE satellite, the first simultaneous, pointing measurement of Coma in the broad, 2-250 keV, energy band. The high sensitivity achieved during this long observation allows precise determination of the spectrum. Our analysis of the measurements clearly indicates that in addition to the main thermal emission from hot intracluster gas at kT=7.5 keV, a second spectral component is required to best-fit the data. If thermal, it can be described with a temperature of 4.7 keV contributing about 20% of the total flux. The additional spectral component can also be described by a power-law, possibly due to Compton scattering of relativistic electrons by the CMB. This interpretation is based on the diffuse radio synchrotron emission, which has a spectral index of 2.34, within the range allowed by fits to the RXTE spectral data. A Compton origin of the measured nonthermal component would imply that the volume-averaged magnetic field in the central region of Coma is B =0.2 micro-Gauss, a value deduced directly from the radio and X-ray measurements (and thus free of the usual assumption of energy equipartition). Barring the presence of unknown systematic errors in the RXTE source or background measurements, our spectral analysis yields considerable evidence for Compton X-ray emission in the Coma cluster.

Rephaeli, Yoel↗

Variational four-dimensional analysis using quasi-geostrophic constraints

A variational four-dimensional analysis technique using quasi-geostrophic models as constraints is examined using gridded fields as data. The analysis method uses a standard iterative nonlinear minimization technique to find the solution to the constraining forecast model which best fits the data as measured by a predefined functional. The minimization algorithm uses the derivative of the functional with respect to each of the initial condition values. This derivative vector is found by inserting the weighted differences between the model solution and the inserted data into a backwards integrating adjoint model. The four-dimensional analysis system was examined by applying it to fields created from a primitive equations model forecast and to fields created from satellite retrievals. The results show that the technique has several interesting characteristics not found in more traditional four-dimensional assimilation techniques. These features include a close fit of the model solution to the observations throughout the analysis interval and an insensitivity to the frequency of data insertion or the amount of data. The four-dimensional analysis technique is very versatile and can be extended to more complex problems with little theoretical difficulty.

Derber, John C.↗

A materials data framework and dataset for elastomeric foam impact mitigating materials

The availability of materials data for impact-mitigating materials has lagged behind applications-based data. For example, data describing on-field helmeted impacts are available, whereas material behaviors for the constituent impact-mitigating materials used in helmet designs lack open datasets. Here, we describe a new FAIR (findable, accessible, interoperable, reusable) data framework with structural and mechanical response data for one example elastic impact protection foam. The continuum-scale behavior of foams emerges from the interplay of polymer properties, internal gas, and geometric structure. This behavior is rate and temperature sensitive, therefore, describing structure-property characteristics requires data collected across several types of instruments. Data included are from structure imaging via micro-computed tomography, finite deformation mechanical measurements from universal test systems with full-field displacement and strain, and visco-thermo-elastic properties from dynamic mechanical analysis. These data facilitate modeling and design efforts in foam mechanics, e.g., homogenization, direct numerical simulation, or phenomenological fitting. The data framework is implemented using data services and software from the Materials Data Facility of the Center for Hierarchical Materials Design.

36 MATERIALS SCIENCE↗