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At least 1,585 records · Page 88

Efficient electronic structure theory via hierarchical scale-adaptive coupled-cluster formalism: I. Theory and computational complexity analysis

In this work, a novel reduced-scaling, general-order coupled-cluster approach is formulated by exploiting hierarchical representations of many-body tensors, combined with the recently suggested formalism of scale-adaptive tensor algebra. Inspired by the hierarchical techniques from the renormalization group approach, H/H 2 -matrix algebra and fast multipole method, the computational scaling reduction in our formalism is achieved via coarsening of quantum many-body interactions at larger interaction scales, thus imposing a hierarchical structure on many-body tensors of coupled-cluster theory. In our approach, the interaction scale can be defined on any appropriate Euclidean domain (spatial domain, momentum-space domain, energy domain, etc.). Additionally, we show that the hierarchically resolved many-body tensors reduce the storage requirements to O(N), where N is the number of simulated quantum particles. Subsequently, we prove that any connected many-body diagram with arbitrary-order tensors, e.g., an arbitrary coupled-cluster diagram, can be evaluated in O(NlogN) floating-point operations. On top of that, we elaborate an additional approximation to further reduce the computational complexity of higher-order coupled-cluster equations, i.e., equations involving higher than double excitations, which otherwise would introduce a large prefactor into formal O(NlogN) scaling.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Zonal shear layer collapse and the power scaling of the density limit: old L-H wine in new bottles

Edge shear layer collapse causes edge cooling and aggravates radiative effects. This paper details on the microscopic dynamics of the emergence of power (Q) scaling of density limit (DL) from the shear layer collapse transport bifurcation scenario. The analysis is based on a novel 4-field model, which evolves turbulence energy, zonal flow energy, temperature gradient and density, including the neoclassical screening of zonal flow response. Bifurcation analysis yields power scaling of critical density for shear layer collapse as $n_{crit}\sim Q^{1/3}$. The favorable Q scaling of the DL emerges from the fact that the shear layer strength increases with Q, thus preventing shear layer collapse. This in turn reduces particle transport and improves particle confinement. RMP induced ambient stochastic fields degrade the shear layer by inducing decoherence in the Reynolds stress. As a result the particle transport increases and particle confinement degrades. This leads to the emergence of unfavorable stochastic field intensity ($b_{st}^{2}$) scaling of the critical density as $n_{crit}\sim(1+b_{st}^{2})^{-5/3}$. All fields, including zonal flow shear, exhibit hysteresis when the power (Q) is ramped cyclically across the bifurcation point. The hysteresis is due to dynamical delay in bifurcation on account of critical slowing down. Furthermore, the dynamical hysteresis here is fundamentally different from the hysteresis associated with the existence of bi-stable states.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Coupled wave-current modeling for hydrodynamic load analysis of macroalgae cultivation farms

Large-scale cultivation of macroalgae is one of the most promising biofuel sources that could reduce our consumption of fossil fuels and would be particularly economically competitive when grown for the co-production of additional goods such as food and textiles. Current production of biofuel from algal biomass is limited by labor costs and lack of data on potential impacts of cultivation and harvesting on marine and coastal environments as well as a comprehensive characterization of the impact of environmental conditions on macroalgal feedstock and their bioproduct and biofuel yield and quality. Awarded by the United States (U.S.) Department of Energy Advanced Research Projects Agency-Energy (ARPA-E) Macroalgae Research Inspiring Novel Energy Resources (MARINER) program, which seeks to enable the U.S. as a global leader in the production of marine biomass, the Marine Biological Laboratory (MBL) has been developing a test system for tropical seaweed cultivation in the Gulf of Mexico and the Caribbean. An integral step in designing macroalgae cultivation farms is to adequately characterize the hydrodynamic climate at potential growth sites. In regions like the Gulf of Mexico and the Caribbean, which are highly exposed to tropical cyclones, it is critical to not only consider the day-to-day hydrodynamic conditions but to also assess the risk of extreme sea states to ensure the survivability of future macroalgae farms. Under these considerations, the Pacific Northwest National Laboratory (PNNL) is providing modeling support for MBL to inform the design and siting of the farm systems that have been proposed for their ARPA-E MARINER project. This report describes the development of a high-resolution coupled storm surge and wave model to simulate the hydrodynamics and wave climate at proposed macroalgae cultivation sites selected by MBL in Florida and Puerto Rico. Model results, including model validation, water level, current distributions, and sea states, are discussed for both selected sites in Florida and Puerto Rico coast. These simulations provide an accurate insight into the hydrodynamic conditions that a macroalgae farm is likely to experience during its operational lifetime, including current information to support fine-scale hydrodynamic load modeling, risk analysis and system design.

09 BIOMASS FUELS↗

Surface Variability Mapping and Roughness Analysis of the Moon Using a Coarse–Graining Decomposition

The lunar surface contains a wide variety of topographic shapes and features, each with different distributions and scales, and any analysis technique to objectively measure roughness must respect these qualities. Coarse-graining is a naturally scale-dependent filtering technique that preserves scale-dependent symmetries and produces coarse elevation maps that gradually erase the smaller features from the original topography. In this study of the lunar surface, we present two surface variability metrics obtained from coarse-graining lunar topography: fine elevation and coarse curvature. Both metrics are isotropic, deterministic, slope-independent, and coordinate-agnostic. Fine (detrended) elevation is acquired by subtracting the coarse elevation from the original topography and contains features that are smaller than the coarse-graining length-scale. Coarse curvature is the Laplacian of coarsened topography, and naturally quantifies the curvature at any scale and indicates whether a location is elevated or depressed relative to its neighborhood at that scale. We find that highlands and maria have distinct roughness characteristics at all length-scales. Our topographic spectra reveal four scale-breaks that mark characteristic shifts in surface roughness: 100, 300, 1,000, and 4,000 km. Comparing fine elevation distributions between maria and highlands, we show that maria fine elevation is biased toward smaller-magnitude elevations and that the maria–highland discrepancies are more pronounced at larger length-scales. Here, we also provide local examples of selected regions to demonstrate that these metrics can successfully distinguish geological features of different length-scales.

58 GEOSCIENCES↗

Large Scale Comparative Visualisation of Regulatory Networks with TRNDiff

The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond those of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.

Bioinformatics, Visualisation, Transcription, Regu↗

Enhancements to Engineering-scale Reactor Pressure Vessel Fracture Capabilities in Grizzly

The Grizzly code is being developed to model the effect of aging in nuclear power plant systems, components, and structures. A significant part of this effort has been to develop capabilites to model the effects of embrittlement in reactor pressure vessels on their integrity. This includes both modeling of microstructure and engineering property evolution, and engineering-scale probabilistic fracture mechanics analysis. This report documents recent advances to the engineering-scale fracture mechanics capability for evaluation of RPV integrity under transient loading in Grizzly. These developments are in three areas: probabilistic fracture mechanics, general reduced order models for fracture a flaw locations, and improvments to the XFEM capability used in Grizzly for fracture mechanics analysis. The combination of these developments brings Grizzly closer to a state where it can be applied in production as a general tool for engineering-scale fracture mechanics analysis. The probabilistic fracture mechanics capabilities are included in the 1.5 testing version of Grizzly, and will be further refined in preparation for production use in the 2.0 released planned for fiscal year 2018.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for 13 C Metabolic Flux Analysis

Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) and Two-Scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) are two techniques used to determine such fluxes. Both operate on the simplifying approximation that metabolic flux from peripheral metabolism into central “core” carbon metabolism is minimal, and can be omitted when modeling isotopic labeling in core metabolism. The validity of this “two-scale” or “bow tie” approximation is supported both by the ability to accurately model experimental isotopic labeling data, and by experimentally verified metabolic engineering predictions using these methods. However, the boundaries of core metabolism that satisfy this approximation can vary across species, and across cell culture conditions. Here, we present a set of algorithms that (1) systematically calculate flux bounds for any specified “core” of a genome-scale model so as to satisfy the bow tie approximation and (2) automatically identify an updated set of core reactions that can satisfy this approximation more efficiently. First, we leverage linear programming to simultaneously identify the lowest fluxes from peripheral metabolism into core metabolism compatible with the observed growth rate and extracellular metabolite exchange fluxes. Second, we use Simulated Annealing to identify an updated set of core reactions that allow for a minimum of fluxes into core metabolism to satisfy these experimental constraints. Together, these methods accelerate and automate the identification of a biologically reasonable set of core reactions for use with 13 C MFA or 2S- 13 C MFA, as well as provide for a substantially lower set of flux bounds for fluxes into the core as compared with previous methods. We provide an open source Python implementation of these algorithms at https://github.com/JBEI/limitfluxtocore.

13C metabolic flux analysis↗

Geomechanical and Hydrogeological Evaluation of a Shallow Hydraulic Fracture at the Devine Fracture Pilot Site, Medina County, Texas

UT-Austin’s Devine Fracture Pilot Site, 50 miles southwest of San Antonio, Texas, has been targeted for a comprehensive, multidisciplinary development of fracture diagnostic techniques that are cross-validated by ground-truth data acquisition near a recently created, 175-ft-deep, horizontal hydraulic fracture (Ahmadian et al. 2018 Demonstration of proof of concept of electromagnetic geophysical methods for high resolution illumination of induced fracture networks. In Proceedings of the SPE Hydraulic Fracturing Technology Conference and Exhibition, The Woodlands, Texas, USA, 23–25 January 2018. SPE-189858-MS.). To evaluate the fracture diagnostic methods at this site, we conducted injection tests with a predefined volumetric flow-rate profile, resembling a diagnostic fracture injection test on September 2020. Subsequently, we developed hydrogeological and geomechanical models based on flow-rate and bottomhole-pressure measurements. History-matching efforts using a simplified layer-cake hydrogeological model resulted in the field-scale formation permeability of 9.87 × 10 –15 m 2 (10 mD) and Darcy-scale fracture permeability. The analysis of the bottomhole pressure and injection-rate history showed that (1) the newly created horizontal fracture was closed adjacent to the injection well pre-injection and (2) the initial pump-pressure increase at a nominal volumetric injection rate led to near-well fracture reopening, fluid conductivity increase, and abrupt injection-rate increase. To overcome hydrogeological-model limitations of predicting fracture reopening throughout injection, we extended the modeling to a finite-element, poroelastic analysis of horizontal-fracture growth using a cohesive-zone model. Using this fracture-reopening model, we improved the history match of the transient-pressure response during the experiment by adjusting the hydromechanical properties. Furthermore, post-injection pressure transient analyses helped reduce uncertainty in the overburden-stress gradient, and the initial hydraulic-fracturing simulation verified the plausibility of achieving the surveyed propped fracture area.

02 PETROLEUM↗

High-Temperature Oxidation of Stellite 12 Hardfacings: Effect of Mo on Characteristics of Oxide Scale

This study aims to understand the oxide scale formation on the surfaces of commercial and Mo (10 wt.%)-modified Stellite 12 hardfacings deposited on 4140 steel. For this purpose, samples of the hardfacings were isothermally oxidized in air at various temperatures in between 500 and 900 °C for 30 h. As a result of changes in the microstructure upon Mo addition, about 50% higher mass gain at all oxidation temperatures was observed. The characteristics of the developed oxide scales were examined by utilizing Raman spectroscopy, scanning electron microscopy and x-ray diffraction analysis. The oxide scale formed over Stellite 12 consisted of CoO-, Co{sub 3}O{sub 4-} and Cr{sub 2}O{sub 3}-type oxides, while additionally CoMoO{sub 4}-type complex oxide was detected on Mo-modified hardfacing, more likely at the alloy–scale interface. On the basis of findings of isothermal oxidation tests, the formation mechanisms of this complex oxide imposing better wear resistance as reported in our previous studies were explained during high-temperature wear testing, i.e., dynamic oxidation conditions.

36 MATERIALS SCIENCE↗

Coupling LAMMPS and the vl3 Framework for Co-Visualization of Atomistic Simulations

In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future research avenues based on our results.

co-visualization↗

FasTensor (FT) v0.0.1

The FasTensor implements the native array data programming mode namely SLOPE for modern data analysis tasks. It is designed to work in parallel on supercomputer and can handle terabyte data analysis tasks. It is thousand times faster than other data analysis systems such as Apache Spark and 38% faster than TensorFlow in dealing with large scale scientific data analysis. It has wide applications in image data analysis and mesh data analysis tasks in physical simulations and other fields.

Wu, Kesheng↗

Dynamics of Subsiding Shells in Actively Growing Clouds with Vertical Updrafts

The dynamics of a subsiding shell at the edges of actively growing shallow cumulus clouds with updrafts is analyzed using direct numerical simulation. The actively growing clouds have a fixed in-cloud buoyancy and velocity. Turbulent mixing and evaporative cooling at the cloud edges generate a subsiding shell that grows with time. A self-similar regime is observed for first- and second-order moments when normalized with respective maximum values. Internal scales derived from integral properties of the flow problem are identified. A self-similarity analysis using these scales reveals that contrary to classical self-similar flows, the turbulent kinetic energy budget terms and velocity moments scale according to the buoyancy and not with the mean velocity. The shell thickness is observed to increase linearly with time. The buoyancy scale remains time invariant and is set by the initial cloud–environment thermodynamics. The shell accelerates ballistically with a magnitude set by the saturation value of the buoyancy of the cloud–environment mixture. In this regime, the shell is buoyancy driven and independent of the in-cloud velocity. Relations are obtained for predicting the shell thickness and minimum velocities by linking the internal scales with external flow parameters. The values thus calculated are consistent with the thickness and velocities observed in typical shallow cumulus clouds. The entrainment coefficient is a function of the initial state of the cloud and the environment, and is shown to be on the same order of magnitude as fractional entrainment rates calculated for large-scale models.

54 ENVIRONMENTAL SCIENCES↗

Genomics Characterization of an Engineered Corynebacterium glutamicum in Bioreactor Cultivation Under Ionic Liquid Stress

Corynebacterium glutamicum is an ideal microbial chassis for production of valuable bioproducts including amino acids and next generation biofuels. Here we resequence engineered isopentenol (IP) producing C. glutamicum BRC-JBEI 1.1.2 strain and assess differential transcriptional profiles using RNA sequencing under industrially relevant conditions including scale transition and compare the presence vs absence of an ionic liquid, cholinium lysinate ([Ch][Lys]). Analysis of the scale transition from shake flask to bioreactor with transcriptomics identified a distinct pattern of metabolic and regulatory responses needed for growth in this industrial format. These differential changes in gene expression corroborate altered accumulation of organic acids and bioproducts, including succinate, acetate, and acetoin that occur when cells are grown in the presence of 50 mM [Ch][Lys] in the stirred-tank reactor. This new genome assembly and differential expression analysis of cells grown in a stirred tank bioreactor clarify the cell response of an C. glutamicum strain engineered to produce IP.

59 BASIC BIOLOGICAL SCIENCES↗

Analytic analysis of load alignment for coning extreme‐scale rotors

Abstract Extreme‐scale wind turbines (rated powers greater than 10 MW) with large rotor diameters and conventional upwind designs must resist extreme downwind and gravity loads. This can lead to significant structural design challenges and high blade masses that can impede the reduction of levelized cost of wind energy. Herein, the theoretical basis for downwind load alignment is developed. This alignment can be addressed with active downwind coning to reduce/eliminate flapwise bending loads by balancing the transverse components of thrust, centrifugal, and gravitational force. Equations are developed herein that estimates the optimal coning angle that reduces flapwise loads by a specified amount. This analysis is then applied to a 13.2‐MW scale with 100‐m‐level wind turbine blades, where it is found that a load alignment coning schedule can substantially reduce the root flapwise bending moments. This moment reduction in this example can allow the rotor mass to be decreased significantly when compared with a conventional upwind three‐bladed rotor while maintaining structural performance and annual energy output.

Noyes, Carlos↗

TDCOSMO - XVII. New time delays in 22 lensed quasars from optical monitoring with the ESO-VST 2.6m and MPG 2.2m telescopes

We present new time delays, the main ingredient of time delay cosmography, for 22 lensed quasars resulting from high-cadence r-band monitoring on the 2.6 m ESO VLT Survey Telescope and Max-Planck-Gesellschaft 2.2 m telescope. Each lensed quasar was typically monitored for one to four seasons, often shared between the two telescopes to mitigate the interruptions forced by the COVID-19 pandemic. The sample of targets consists of 19 quadruply and 3 doubly imaged quasars, which received a total of 1918 hours of on-sky time split into 21 581 wide-field frames, each 320 seconds long. In a given field, the 5-σ depth of the combined exposures typically reaches the 27th magnitude, while that of single visits is 24.5 mag – similar to the expected depth of the upcoming Vera-Rubin LSST. The fluxes of the different lensed images of the targets were reliably de-blended, providing not only light curves with photometric precision down to the photon noise limit, but also high-resolution models of the targets whose features and astrometry were systematically confirmed in Hubble Space Telescope imaging. This was made possible thanks to a new photometric pipeline, lightcurver, and the forward modelling method STARRED. Finally, the time delays between pairs of curves and their uncertainties were estimated, taking into account the degeneracy due to microlensing, and for the first time the full covariance matrices of the delay pairs are provided. Of note, this survey, with 13 square degrees, has applications beyond that of time delays, such as the study of the structure function of the multiple high-redshift quasars present in the footprint at a new high in terms of both depth and frequency. The reduced images will be available through the European Southern Observatory Science Portal.Key words: methods: data analysis / surveys / distance scale

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Effect of Inlet Throttling on Thermohydraulic Instability in a Large Scale Waterbased RCCS: A System-Level Analysis with RELAP5-3D

This paper presents results from system -level modeling of a water -based reactor cavity cooling system using RELAP5-3D. The computational model is benchmarked with experimental data from a half -scale RCCS test facility at Argonne National Laboratory. The model prediction is first compared with a two-phase oscillatory baseline experimental case where mixed accuracy is obtained. The model shows reasonable prediction of mass flow rate, pressure, and temperature but significant overprediction of void fraction. The model prediction is then compared with a fault case where the inlet of the risers is gradually reduced using a throttling valve. As the valve is closed, the model is able to predict some major flow phenomena observed in the experiment such as the dampening of oscillations, the reintroduction of oscillations, as well as boiling, flashing, and geysering in the risers. However, the timeline of these events are not well captured by the model. The model is also used to investigate the evolution of flow regime in the chimney. This work highlights that the semiempirical constitutive relations used in RELAP-3D could have a strong influence on the accuracy of the model in two-phase oscillatory flows.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Mapping of the Ronda peridotite massif (Spain) from AVIRIS spectro-imaging survey: A first attempt

In both AVIRIS and ISM data, through the use of mixing models, geological boundaries of the Ronda massif are identified with respect to the surrounding rocks. We can also yield first-order vegetation maps. ISM and AVIRIS instruments give consistent results. On the basis of endmember fraction images, it is then possible to discard areas highly vegetated or not belonging to the peridotite massif. Within the remaining part of the mosaic, spectro-mixing analysis reveals spectral variations in the peridotite massif between the well-exposed areas. Spatially organized units are depicted, related to differences in the relative depth of the absorption band at 1 micron, and it may be due to a different pyroxene content. At this stage, it is worth noting that, although mineralogical variations observed in the rocks are at a sub-pixel scale for the airborne analysis, we see an emerging spatial pattern in the distribution of spectral variations across the massif which might be prevailingly related to mineralogy. Although it is known from fieldwork that the Ronda peridotite massif exhibits mineralogical variations at local scale in the content of pyroxene, and at regional scale in different mineral facies, ranging from garnet-, to spinel- to plagioclase-lherzolites, no attempt has been done yet to produce a synoptic map relating the two scales of analysis. The present work is a first attempt to reach this objective, though a lot more work is still required. In particular, for the purpose of mineralogical interpretation, it is critical to relate the airborne observation to field work and laboratory spectra of Ronda rocks already obtained, with the use of image endmembers and associated reference endmembers. Also, the pretty rough linear mixing model used here is taken as a 'black-box' process which does not necessarily apply correctly to the physical situation at the sub-pixel level. One may think of using the ground-truth observations bearing on the sub-pixel statistical characteristics (texture, structural pattern, surface distribution and vegetation contribution (grass,..)) to produce a more advanced mixing model, physically appropriate to the geologic and environmental contexts.

Pinet, P. C.↗