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At least 1,207 records · Page 67

Z-checker: A framework for assessing lossy compression of scientific data

Because of the vast volume of data being produced by today’s scientific simulations and experiments, lossy data compressor allowing user-controlled loss of accuracy during the compression is a relevant solution for significantly reducing the data size. However, lossy compressor developers and users are missing a tool to explore the features of scientific data sets and understand the data alteration after compression in a systematic and reliable way. To address this gap, we have designed and implemented a generic framework called Z-checker. On the one hand, Z-checker combines a battery of data analysis components for data compression. On the other hand, Z-checker is implemented as an open-source community tool to which users and developers can contribute and add new analysis components based on their additional analysis demands. In this article, we present a survey of existing lossy compressors. Then, we describe the design framework of Z-checker, in which we integrated evaluation metrics proposed in prior work as well as other analysis tools. Specifically, for lossy compressor developers, Z-checker can be used to characterize critical properties (such as entropy, distribution, power spectrum, principal component analysis, and autocorrelation) of any data set to improve compression strategies. For lossy compression users, Z-checker can detect the compression quality (compression ratio and bit rate) and provide various global distortion analysis comparing the original data with the decompressed data (peak signal-to-noise ratio, normalized mean squared error, rate–distortion, rate-compression error, spectral, distribution, and derivatives) and statistical analysis of the compression error (maximum, minimum, and average error; autocorrelation; and distribution of errors). Z-checker can perform the analysis with either coarse granularity (throughout the whole data set) or fine granularity (by user-defined blocks), such that the users and developers can select the best fit, adaptive compressors for different parts of the data set. Z-checker features a visualization interface displaying all analysis results in addition to some basic views of the data sets such as time series. To the best of our knowledge, Z-checker is the first tool designed to assess lossy compression comprehensively for scientific data sets.

97 MATHEMATICS AND COMPUTING↗

Comparing Deep Learning Approaches for Understanding Genotype × Phenotype Interactions in Biomass Sorghum

We explore the use of deep convolutional neural networks (CNNs) trained on overhead imagery of biomass sorghum to ascertain the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. We consider both CNNs trained explicitly on the classification task of predicting whether an image shows a plant with a reference or alternate version of various SNPs as well as CNNs trained to create data-driven features based on learning features so that images from the same plot are more similar than images from different plots, and then using the features this network learns for genetic marker classification. We characterize how efficient both approaches are at predicting the presence or absence of a genetic markers, and visualize what parts of the images are most important for those predictions. We find that the data-driven approaches give somewhat higher prediction performance, but have visualizations that are harder to interpret; and we give suggestions of potential future machine learning research and discuss the possibilities of using this approach to uncover unknown genotype × phenotype relationships.

Zhang, Zeyu↗

Multi-atom quasiparticle scattering interference for superconductor energy-gap symmetry determination

Complete theoretical understanding of the most complex superconductors requires a detailed knowledge of the symmetry of the superconducting energy-gap Δ$^α_k$, for all momenta k on the Fermi surface of every band α. While there are a variety of techniques for determining |Δ$^α_k$|, no general method existed to measure the signed values of Δ$^α_k$. Recently, however, a technique based on phase-resolved visualization of superconducting quasiparticle interference (QPI) patterns, centered on a single non-magnetic impurity atom, was introduced. In principle, energy-resolved and phase-resolved Fourier analysis of these images identifies wavevectors connecting all k-space regions where Δ$^α_k$ has the same or opposite sign. But use of a single isolated impurity atom, from whose precise location the spatial phase of the scattering interference pattern must be measured, is technically difficult. Here we introduce a generalization of this approach for use with multiple impurity atoms, and demonstrate its validity by comparing the Δ$^α_k$ it generates to the Δ$^α_k$ determined from single-atom scattering in FeSe where s ± energy-gap symmetry is established. Finally, to exemplify utility, we use the multi-atom technique on LiFeAs and find scattering interference between the hole-like and electron-like pockets as predicted for Δ$^α_k$ of opposite sign.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Numerical simulations and experimental measurements of steel and ice impacts on concrete for acoustic interrogation of delaminations in bridge decks

Delaminations in bridge decks typically result from corrosion of the top mat of reinforcing steel, which leads to a localized separation of the concrete cover from the underlying concrete. Because delaminations cannot be detected using visual inspection, rapid, large-area interrogation methods are desired to characterize bridge decks without disruption to traffic, without the subjectivity inherent in existing methods, and with increased inspector safety. To this end, disposable impactors such as water droplets or ice chips can be dropped using automatic dispensers onto concrete surfaces to excite mechanical vibrations while acoustic responses can be recorded using air-coupled microphones. In this work, numerical simulations are used to characterize the flexural response of a model concrete bridge deck subject to both steel and ice impactors, and the results are compared with similar experiments performed in the laboratory on a partially delaminated concrete bridge deck slab. The simulations offer greater understanding of the kinetics of impacts and the responses of materials.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Comparison of electrical capacitance tomography and gamma densitometer measurement in viscous oil-gas flows

Multiphase flow is a common occurrence in industries such as nuclear, process, oil and gas, food and chemical. A prior knowledge of its features and characteristics is essential in the design, control and management of such processes due to its complex nature. Electrical Capacitance Tomography (ECT) and Gamma Densitometer (Gamma) are two promising approaches for multiphase visualization and characterization in process industries. In two phase oil and gas flow, ECT and Gamma are used in multiphase flow monitoring techniques due to their inherent simplicity, robustness, and an ability to withstand wide range of operational temperatures and pressures. High viscous oil (viscosity > 100 cP) is of interest because of its huge reserves, technological advances in its production and unlike conventional oil (oil viscosity < 100 cP) and gas flows where ECT and Gamma have been previously used, high viscous oil and gas flows comes with certain associated concerns which include; increased entrainment of gas bubbles dispersed in oil, shorter and more frequent slugs as well as oil film coatings on the walls of flowing conduits. This study aims to determine the suitability of both devices in the visualization and characterization of high-viscous oil and gas flow. Static tests are performed with both devices and liquid holdup measurements are obtained. Dynamic experiments were also conducted in a 1 and 3 inch facility at Cranfield University with a range of nominal viscosities (1000, 3000 and 7500 cP). Plug, slug and wavy annular flow patterns were identified by means of Probability Mass Function and time series analysis of the data acquired from Gamma and ECT devices with high speed camera used to validate the results. Measured Liquid holdups for both devices were also compared.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DYNAMICAL MODELING OF GALAXY MERGERS USING IDENTIKIT

We present dynamical models of four interacting systems: NGC 5257/8, The Mice, the Antennae, and NGC 2623. The parameter space of the encounters are constrained using the Identikit model-matching and visualization tool. Identikit utilizes hybrid N-body and test particle simulations to enable rapid exploration of the parameter space of galaxy mergers. The Identikit-derived matches of these systems are reproduced with self-consistent collisionless simulations which show very similar results. The models generally reproduce the observed morphology and H I kinematics of the tidal tails in these systems with reasonable properties inferred for the progenitor galaxies. The models presented here are the first to appear in the literature for NGC 5257/8 and NGC 2623, and The Mice and the Antennae are compared with previously published models. Based on the assumed mass model and our derived initial conditions, the models indicate that the four systems are currently being viewed 175-260 Myr after first passage and cover a wide range of merger stages. In some instances there are mismatches between the models and the data (e.g., in the length of a tail); these are likely due to our adoption of a single mass model for all galaxies. Despite the use of a single mass model, these results demonstrate the utility of Identikit in constraining the parameter space for galaxy mergers when applied to real data.

79 ASTRONOMY AND ASTROPHYSICS↗

Towards time-resolved MicroED grid preparation using mix-and-inject gas dynamic virtual nozzles

Recent progress in gas dynamic virtual nozzle (GDVN) technologies in combination with high-brilliance synchrotron and X-ray free-electron lasers (XFELs) has allowed the visualization of protein dynamics in crystallo by mixing macromolecular protein crystals with a substrate using tunable mixing times on the order of milliseconds to seconds prior to serial X-ray diffraction data collection. This has become the method of choice for high-resolution structure determination of intermediate states. However, such experiments require large counts of crystals of proper sizes for high-resolution data collection, and premium beam times for screening efforts. Cryogenic microcrystal electron diffraction (MicroED) represents a complementary technique that may be a more accessible avenue for time-resolved nanocrystallography compared with serial X-ray diffraction experiments. MicroED can produce full diffraction datasets from just a few submicrometre-thick crystals, and the approach is more readily accessible, requiring standard cryogenic transmission electron microscopy (TEM) equipment available at many universities and institutes. Cryogenic MicroED, like other forms of cryo-EM, begins with rapidly freezing biological material on electron microscopy grids. In the case of MicroED, micro- to nano-crystals (<500 nm thick) are deposited onto electron microscopy grids and plunge-frozen for subsequent electron diffraction data collection. Here, we have incorporated GDVN technology developed originally for XFEL experiments into the freezing process as a first step towards time-resolved studies. We describe the limited deposition efficiency of the model MicroED protein proteinase K on TEM grids using GDVNs, preceding sample vitrification and successful MicroED data collection. We discuss both the initial results from such experiments and the methodological challenges in developing this approach into a reliable workflow for millisecond-to-second time-resolved structural studies of macromolecules. Our results promise a strategy to deposit crystals on grids using GDVNs and determine high-resolution structures by MicroED, constituting a first step towards development of time-resolved MicroED experiments.

MicroED↗

Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits

This paper describes a hierarchical stochastic simulation algorithm, which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but there are many disadvantages associated with this approach. First, the memory required to represent the model can quickly expand in the process. Second, the flattening process is computationally expensive. Finally, when modeling a dynamic cellular population within iBioSim, inlining the hierarchy of the model is inefficient since models must grow dynamically over time. This paper discusses a new approach to handle hierarchy on the fly to make the tool faster and more memory-efficient. This approach yields significant performance improvements as compared to the former flat analysis method.

60 APPLIED LIFE SCIENCES↗

Accurate in vivo tumor detection using plasmonic-enhanced shifted-excitation Raman difference spectroscopy (SERDS)

For the majority of cancer patients, surgery is the primary method of treatment. In these cases, accurately removing the entire tumor without harming surrounding tissue is critical; however, due to the lack of intraoperative imaging techniques, surgeons rely on visual and physical inspection to identify tumors. Surface-enhanced Raman scattering (SERS) is emerging as a non-invasive optical alternative for intraoperative tumor identification, with high accuracy and stability. However, Raman detection requires dark rooms to work, which is not consistent with surgical settings. Methods: Herein, we used SERS nanoprobes combined with shifted-excitation Raman difference spectroscopy (SERDS) detection, to accurately detect tumors in xenograft murine model. Results: We demonstrate for the first time the use of SERDS for in vivo tumor detection in a murine model under ambient light conditions. We compare traditional Raman detection with SERDS, showing that our method can improve sensitivity and accuracy for this task. Conclusion: Our results show that this method can be used to improve the accuracy and robustness of in vivo Raman/SERS biomedical application, aiding the process of clinical translation of these technologies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Mechanochemically responsive polymer enables shockwave visualization

Abstract Understanding the physical and chemical response of materials to impulsive deformation is crucial for applications ranging from soft robotic locomotion to space exploration to seismology. However, investigating material properties at extreme strain rates remains challenging due to temporal and spatial resolution limitations. Combining high-strain-rate testing with mechanochemistry encodes the molecular-level deformation within the material itself, thus enabling the direct quantification of the material response. Here, we demonstrate a mechanophore-functionalized block copolymer that self-reports energy dissipation mechanisms, such as bond rupture and acoustic wave dissipation, in response to high-strain-rate impacts. A microprojectile accelerated towards the polymer permanently deforms the material at a shallow depth. At intersonic velocities, the polymer reports significant subsurface energy absorption due to shockwave attenuation, a mechanism traditionally considered negligible compared to plasticity and not well explored in polymers. The acoustic wave velocity of the material is directly recovered from the mechanochemically-activated subsurface volume recorded in the material, which is validated by simulations, theory, and acoustic measurements. This integration of mechanochemistry with microballistic testing enables characterization of high-strain-rate mechanical properties and elucidates important insights applicable to nanomaterials, particle-reinforced composites, and biocompatible polymers.

Science & Technology - Other Topics↗

Updimensioning strategy derived from synthetic equiaxed grain structures for approximating 3D grain size distributions from 2D visualizations with 1D parameters

We generated synthetic equiaxed grain structures using computer graphics software to explore the relationship between various grain size determination methods and true three-dimensional (3D) grain diameters. Mirroring grain measurement techniques, the synthetic 3D grain structures are imaged as 2D micrographs which are measured to yield 1D grain size parameters. Synthetic grain structures provide data at a mass scale and permit exploration of both polished and fractured surface micrographs, revealing one-to-one correspondence between exposed 2D grain cross-sections and individual 3D grains. Analysis of this correspondence yielded a procedure to approximate 3D equiaxed grain size and volume distributions based on the mode of the 2D fractograph grain size distribution. The 3D approximation procedure is shown to be less susceptible to different imaging conditions that affect small, undiscernible grains compared to the standard planimetric and linear intercept methods, which by design also tend to underestimate the 3D grain diameter. The procedure requires larger sample sizes to lower variance and a deeper analysis which could become more practical with machine learning (ML) models for grain boundary segmentation, which synthetic grain structures can help train. This work lays the foundation for analyzing other grain distributions such as columnar and composite grains in similar depth.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Photon-dominated region modeling of the [C I], [C II], and CO Line Emission From A Boundary In The Taurus molecular cloud

We present [C I] and [C II] observations of a linear edge region in the Taurus molecular cloud, and model this region as a cylindrically symmetric photon-dominated region (PDR) exposed to a low-intensity UV radiation field. The sharp, long profile of the linear edge makes it an ideal case to test PDR models and determine cloud parameters. We compare observations of the [C I], {sup 3} P {sub 1} → {sup 3} P {sub 0} (492 GHz), [C I] {sup 3} P {sub 2} → {sup 3} P {sub 1} (809 GHz), and [C II] {sup 2} P {sub 3/2} → {sup 2} P {sub 1/2} (1900 GHz) transitions, as well as the lowest rotational transitions of {sup 12}CO and {sup 13}CO, with line intensities produced by the RATRAN radiative transfer code from the results of the Meudon PDR code. We constrain the density structure of the cloud by fitting a cylindrical density function to visual extinction data. We study the effects of variation of the FUV field, {sup 12}C/{sup 13}C isotopic abundance ratio, sulfur depletion, cosmic ray ionization rate, and inclination of the filament relative to the sky-plane on the chemical network of the PDR model and resulting line emission. We also consider the role of suprathermal chemistry and density inhomogeneities. We find good agreement between the model and observations, and that the integrated line intensities can be explained by a PDR model with an external FUV field of 0.05 G {sub 0}, a low ratio of {sup 12}C to {sup 13}C ∼43, a highly depleted sulfur abundance (by a factor of at least 50), a cosmic ray ionization rate (3-6) × 10{sup –17} s{sup –1}, and without significant effects from inclination, clumping or suprathermal chemistry.

79 ASTRONOMY AND ASTROPHYSICS↗

Optical follow-up observation for GW event S190510g using Subaru/Hyper Suprime-Cam

Abstract A gravitational wave event, S190510g, which was classified as a binary-neutron-star coalescence at the time of preliminary alert, was detected by LIGO/Virgo collaboration on 2019 May 10. At 1.7 hours after the issue of its preliminary alert, we started a target-of-opportunity imaging observation in the Y band to search for its optical counterpart using the Hyper Suprime-Cam (HSC) on the Subaru Telescope. The observation covers a 118.8 deg2 sky area corresponding to $11.6\%$ confidence in the localization skymap released in the preliminary alert and $1.2\%$ in the updated skymap. We divided the observed area into two fields based on the availability of HSC reference images. For the fields with the HSC reference images, we applied an image subtraction technique; for the fields without the HSC reference images, we sought individual HSC images by matching a catalog of observed objects with the PS1 catalog. The search depth is 22.28 mag in the former method and the limit of search depth is 21.3 mag in the latter method. Subsequently, we performed visual inspection and obtained 83 candidates using the former method and 50 candidates using the latter method. Since we only have the one-day photometric data, we evaluated the probability of candidates being located inside the 3D skymap by estimating their distances with photometry of associated extended objects. We found three candidates are likely located inside the 3D skymap and concluded they could be a counterpart of S190510g, while most of the 133 candidates were likely to be supernovae because the number density of candidates was consistent with the expected number of supernova detections. By comparing our observational depth with a light-curve model of such a kilonova reproducing AT2017gfo, we show that early deep observations with the Subaru/HSC can capture the rising phase of the blue component of a kilonova at the estimated distance of S190510g (∼230 Mpc).

79 ASTRONOMY AND ASTROPHYSICS↗

Dispatchable Solar Power Plant Project

As penetration of intermittent renewable power increases, grid operators must manage greater variability in the supply and demand on the grid. One result is that utilities are planning to build many new natural gas peaking power plants that provide added flexibility needed for grid management. This report discusses the development of a dispatchable solar power (DSP) plant that can be used in place of natural gas peakers. Specifically, a new molten-salt tower (MST) plant has been developed that is designed to allow much more flexible operation than typically considered in concentrating solar power plants. As a result, this plant can provide most of the capacity and ancillary benefits of a conventional natural gas peaker plant but without the carbon emissions. The DSP system presented was designed to meet the specific needs of the Arizona Public Service (APS) utility 2017 peaking capacity request for proposals (RFP). The goal of the effort was to design a MST peaker plant that had the operational capabilities required to meet the peaking requirements of the utility and be cost competitive with the natural gas alternative. The effort also addresses many perceived barriers facing the commercial deployment of MST technology in the US today. These include MST project development issues such as permitting, avian impacts, visual impacts of tower CSP projects, project schedule, and water consumption. The DSP plant design is based on considerable analyses using sophisticated solar system design tools and in-depth preliminary engineering design. The resulting DSP plant design uses a 250 MW steam power cycle, with solar field designed to fit on a square mile plot of land that has a design point thermal rating of 400 MWt. The DSP plant has an annual capacity factor of about 16% tailored to deliver greater than 90% capacity during the critical Arizona summer afternoon peak. The table below compares the All-In energy cost and capacity payment of conventional combustion turbines to DSP plants. These results estimate that the cost of the DSP plant is about 10% higher than a similarly-sized and operated frame combustion turbine and slightly cheaper than an aero derivative combustion turbine when APS reference fuel and emissions costs are included. The DSP plant cost is based on a single, first-of-a-kind plant, and it is likely that subsequent plants would be less expensive.

14 SOLAR ENERGY↗

Differences in total stem value when merchandizing with a tracked processor versus a knuckle–boom loader in Pinus taeda

Using tracked processors over knuckle–boom loaders to increase total value per tree when merchandizing timber on the landing has become a topic of interest in the southeastern region of the United States. This study compared merchantability values, product classes, and product weights of loblolly pine (Pinus taeda) for both machines to determine if there was a significant difference between machines when processing the same tree. In order to process the same tree twice, the chains from the tracked processor had to be removed from the bottom saw bar. This allowed the processor to simulate the merchandising process without actually marking or cutting the tree for a more realistic comparison. Data were analyzed using paired t–tests and two–way ANOVA models. Results depicted that when diameter and total lengths are visually estimated by the knuckle–boom loader. A significant difference in value occurs, however, once diameter and total length are modified to match the tracked processors for more accurate measurements, no difference in value was seen. Here, these results demonstrate that until mill specifications become more stringent, there is little incentive for loggers to purchase a tracked processor if their only motivation is to increase merchantability values.

42 ENGINEERING↗

Oblique reconstructions in tomosynthesis. II. Super-resolution

Purpose: In tomosynthesis, super-resolution has been demonstrated using reconstruction planes parallel to the detector. Super-resolution allows for subpixel resolution relative to the detector. The purpose of this work is to develop an analytical model that generalizes super-resolution to oblique reconstruction planes.Methods: In a digital tomosynthesis system, a sinusoidal test object is modeled along oblique angles (i.e., “pitches”) relative to the plane of the detector in a 3D divergent-beam acquisition geometry. To investigate the potential for super-resolution, the input frequency is specified to be greater than the alias frequency of the detector. Reconstructions are evaluated in an oblique plane along the extent of the object using simple backprojection (SBP) and filtered backprojection (FBP). By comparing the amplitude of the reconstruction against the attenuation coefficient of the object at various frequencies, the modulation transfer function (MTF) is calculated to determine whether modulation is within detectable limits for super-resolution. For experimental validation of super-resolution, a goniometry stand was used to orient a bar pattern phantom along various pitches relative to the breast support in a commercial digital breast tomosynthesis system.Results: Using theoretical modeling, it is shown that a single projection image cannot resolve a sine input whose frequency exceeds the detector alias frequency. The high frequency input is correctly visualized in SBP or FBP reconstruction using a slice along the pitch of the object. The Fourier transform of this reconstructed slice is maximized at the input frequency as proof that the object is resolved. Consistent with the theoretical results, experimental images of a bar pattern phantom showed super-resolution in oblique reconstructions. At various pitches, the highest frequency with detectable modulation was determined by visual inspection of the bar patterns. The dependency of the highest detectable frequency on pitch followed the same trend as the analytical model. It was demonstrated that super-resolution is not achievable if the pitch of the object approaches 90°, corresponding to the case in which the test frequency is perpendicular to the breast support. Only low frequency objects are detectable at pitches close to 90°.Conclusions: This work provides a platform for investigating super-resolution in oblique reconstructions for tomosynthesis. In breast imaging, this study should have applications in visualizing microcalcifications and other subtle signs of cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

In‐operando crystallization study of zinc nitrate hexahydrate using zinc oxide nucleators

Abstract Supercooling (∆T Sup ) is one of the crucial problems in utilizing a phase change material (PCM), which has been attempted to overcome using nucleators possessing small lattice disregistry without comprehensive understanding of the nucleation phenomenon. Here, this work studies the interactions between nucleators and PCM via in‐operando direct visualization for the first time, to the best of our knowledge, to better understand the crystallization process during freezing of a PCM using zinc nitrate hexahydrate (ZNH) and a zinc oxide (ZnO) nucleator. According to our in‐operando study, freezing was randomly initiated by only a fraction of the nucleator particles during each thermal cycling. However, previously unresponsive nucleators also suddenly crystalized PCM when the propagating crystal encountered them, improving the crystal initiation and thereby ∆T Sup . Consequently, for equal wt% of ZnO, better nucleation behavior was obtained using uniformly distributed small nucleator particles throughout the PCM, as compared to either large or poorly distributed aggregated nucleators. DSC results using ZnO‐needle as nucleator confirmed a 38% and 33.3% lower ∆T Sup upon employing 5 wt% small (individual) particles (~4 μm on average), as compared to using equal wt% of small (aggregated) particle clusters (~200 μm) and large particles (~46 μm), respectively. Crystallization of ZNH caused additional hair‐like ZnO growth preferentially decorated along lateral faces of the original nucleator particles. The in‐operando studies are valuable tools to correlate inherent crystallization phenomena to the practical thermal energy storage properties of the system.

Chakraborty, Anirban↗

Water and chloride ions migration in porous cementitious materials: An experimental and molecular dynamics investigation

The interactions of water and chloride ions penetration into porous mortar have been investigated experimentally and modelled by molecular dynamics. The water distribution visualized by neutron radiography and chloride penetration by Electron Probe Micro-Analysis indicate that separation of chloride ions from water during the penetration process took place and water ran much deeper into the material than chloride ions. The relationship between the penetration depth of water and chloride ions can be described by a linear function despite different water-cement ratio. Furthermore, molecular dynamics attributes the different transport mechanisms of water and ions in porous cementitious materials to three reasons: the nanostructure of hydration product play filtering role to screen chloride ions with larger hydration shell; as compared with water, ions reside in the calcium silicate surface for longer time due to the strong interfacial bonding; chloride ions accumulate and form CaCl ionic cluster, slowing down the migrating rate.

36 MATERIALS SCIENCE↗