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At least 397 records · Page 22

Atmospheric Flow Development and Associated Changes in Turbulent Sensible Heat Flux over a Patchy Mountain Snow Cover

In this study, the small-scale boundary layer dynamics and the energy balance over a fractional snow cover are numerically investigated. The atmospheric boundary layer flows over a patchy snow cover were calculated with an atmospheric model (Advanced Regional Prediction System) on a very high spatial resolution of 5 m. The numerical results revealed that the development of local flow patterns and the relative importance of boundary layer processes depend on the snow patch size distribution and the synoptic wind forcing. Energy balance calculations for quiescent wind situations demonstrated that well-developed katabatic winds exerted a major control on the energy balance over the patchy snow cover, leading to a maximum in the mean downward sensible heat flux over snow for high snow-cover fractions. This implies that if katabatic winds develop, total melt of snow patches may decrease for low snow-cover fractions despite an increasing ambient air temperature, which would not be predicted by most hydrological models. In contrast, stronger synoptic winds increased the effect of heat advection on the catchment’s melt behavior by enhancing the mean sensible heat flux over snow for lower snow-cover fractions. A sensitivity analysis to grid resolution suggested that the grid size is a critical factor for modeling the energy balance of a patchy snow cover. The comparison of simulation results from coarse (50 m) and fine (5 m) horizontal resolutions revealed a difference in the spatially averaged turbulent heat flux over snow of 40%–70% for synoptic cases and 95% for quiescent cases.

17 WIND ENERGY↗

Effective Cloud Detection and Segmentation Using a Gradient-Based Algorithm for Satellite Imagery: Application to Improve PERSIANN-CCS

The effective identification of clouds and monitoring of their evolution are important toward more accurate quantitative precipitation estimation and forecast. In this study, a new gradient-based cloud-image segmentation algorithm is developed using image processing techniques. This method integrates morphological image gradient magnitudes to separate cloud systems and patches boundaries. A varying scale kernel is implemented to reduce the sensitivity of image segmentation to noise and to capture objects with various finenesses of the edges in remote sensing images. The proposed method is flexible and extendable from single to multispectral imagery. Case studies were carried out to validate the algorithm by applying the proposed segmentation algorithm to synthetic radiances for channels of the Geostationary Operational Environmental Satellite ( GOES-16) simulated by a high-resolution weather prediction model. The proposed method compares favorably with the existing cloud-patch-based segmentation technique implemented in the Precipitation Estimation from Remotely Sensed Information Using Artificial Neural Networks–Cloud Classification System (PERSIANN-CCS) rainfall retrieval algorithm. Evaluation of event-based images indicates that the proposed algorithm has potentials comparing to the conventional segmentation technique used in PERSIANN-CCS to improve rain detection and estimation skills with an accuracy rate of up to 98% in identifying cloud regions.

54 ENVIRONMENTAL SCIENCES↗

Cloud, Aerosol and Boundary Layer Structure across the Northeast Pacific Stratocumulus-Cumulus Transition as observed during CSET

During the Cloud System Evolution in the Trades (CSET) field study, 14 research flights of the National Science Foundation G-V sampled the stratocumulus-cumulus transition between Northern California and Hawaii and its synoptic variability. The G-V made vertically resolved measurements of turbulence, cloud microphysics, aerosol characteristics, and trace gases. It also carried dropsondes and a vertically pointing W-band radar and lidar. This paper summarizes these observations with the goals of fostering novel comparisons with theory, models and reanalyses, and satellite-derived products. A longitude-height binning and compositing strategy mitigates limitations of sparse sampling and spatiotemporal variability. Typically, a 1-km-deep decoupled stratocumulus-capped boundary layer near California evolved into 2-km-deep precipitating cumulus clusters surrounded by patches of thin stratus that dissipated toward Hawaii. Low cloud cover was correlated with estimated inversion strength more than with cloud droplet number, even though the thickest clouds were generally precipitating and ultraclean layers indicative of aerosol-cloud-precipitation interaction were common west of 140 degrees W. Accumulation-mode aerosol concentration correlated well with collocated cloud droplet number concentration and was typically largest near the surface. Aitken mode aerosol concentration was typically larger in the free troposphere. Wildfire smoke produced spikes of aerosol and trace gases on some flights. CSET data are compared with space-time collocated output from MERRA-2 reanalysis and from the CAM6 climate model run with winds and temperature nudged toward this reanalysis. The reanalysis compares better with the observed relative humidity than does nudged CAM6. Both vertically diffuse the stratocumulus cloud layer versus observations. MERRA-2 slightly underestimates in situ carbon monoxide measurements and underestimates ozone depletion within the boundary layer.

Bretherton, Christopher S.↗

Characterizing post-fire delayed tree mortality with remote sensing: sizing up the elephant in the room

Abstract Background Despite recent advances in understanding the drivers of tree-level delayed mortality, we lack a method for mapping delayed mortality at landscape and regional scales. Consequently, the extent, magnitude, and effects of delayed mortality on post-fire landscape patterns of burn severity are unknown. We introduce a remote sensing approach for mapping delayed mortality based on post-fire decline in the normalized burn ratio (NBR). NBR decline is defined as the change in NBR between the first post-fire measurement and the minimum NBR value up to 5 years post-fire for each pixel. We validate the method with high-resolution aerial photography from six wildfires in California, Oregon, and Washington, USA, and then compare the extent, magnitude, and effects of delayed mortality on landscape patterns of burn severity among fires and forest types. Results NBR decline was significantly correlated with post-fire canopy mortality (r 2 = 0.50) and predicted the presence of delayed mortality with 83% accuracy based on a threshold of 105 NBR decline. Plots with NBR decline greater than 105 were 23 times more likely to experience delayed mortality than those below the threshold (p < 0.001). Delayed mortality occurred across 6–38% of fire perimeters not affected by stand-replacing fire, generally affecting more areas in cold (22–41%) and wet (30%) forest types than in dry (1.7–19%) types. The total area initially mapped as unburned/very low-severity declined an average of 38.1% and generally persisted in smaller, more fragmented patches when considering delayed mortality. The total area initially mapped as high-severity increased an average of 16.2% and shifted towards larger, more contiguous patches. Conclusions Differences between 1- and 5-year post-fire burn severity maps depict dynamic post-fire mosaics resulting from delayed mortality, with variability among fires reflecting a range of potential drivers. We demonstrate that tree-level delayed mortality scales up to alter higher-level landscape patterns of burn severity with important implications for forest resilience and a range of fire-driven ecological outcomes. Our method can complement existing tree-level studies on drivers of delayed mortality, refine mapping of fire refugia, inform estimates of habitat and carbon losses, and provide a more comprehensive assessment of landscape and regional scale fire effects and trends.

Environmental Sciences & Ecology↗

Risso's dolphins plan foraging dives

ABSTRACT Humans remember the past and use that information to plan future actions. Lab experiments that test memory for the location of food show that animals have a similar capability to act in anticipation of future needs, but less work has been done on animals foraging in the wild. We hypothesized that planning abilities are critical and common in breath-hold divers who adjust each dive to forage on prey varying in quality, location and predictability within constraints of limited oxygen availability. We equipped Risso's dolphins with sound-and-motion recording tags to reveal where they focus their attention through their externally observable echolocation and how they fine tune search strategies in response to expected and observed prey distribution. The information from the dolphins was integrated with synoptic prey data obtained from echosounders on an underwater vehicle. At the start of the dives, whales adjusted their echolocation inspection ranges in ways that suggest planning to forage at a particular depth. Once entering a productive prey layer, dolphins reduced their search range comparable to the scale of patches within the layer, suggesting that they were using echolocation to select prey within the patch. On ascent, their search range increased, indicating that they decided to stop foraging within that layer and started searching for prey in shallower layers. Information about prey, learned throughout the dive, was used to plan foraging in the next dive. Our results demonstrate that planning for future dives is modulated by spatial memory derived from multi-modal prey sampling (echoic, visual and capture) during earlier dives.

Arranz, Patricia↗

Raw electron microscopy images for "The Importance of Nano-edges in Atomic Stencilling and Chiroptically Active Assembly of Patchy Gold Tetrahedra"

This dataset contains the raw transmission electron microscopy (TEM) and scanning electron microscopy (SEM) images used in the main figures of the paper “The Importance of Nano-edges in Atomic Stencilling and Chiroptically Active Assembly of Patchy Gold Tetrahedra (2026).” All the images were acquired at the Materials Research Laboratory, University of Illinois at Urbana-Champaign, by Qian Chen group. 1. We provide five subfolders, each named according to the corresponding figure numbers in the paper. 2. All files in the subfolders for Figures 1–3 and 5 are named as "Panel [letter]_*", where [letter] (e.g., a, b, c) represents the raw images used for the corresponding panels. 3. All files in the subfolder for Figure 4 correspond to panel f and show the configurations of patchy tetrahedra synthesized at varying concentrations of iodide and 2-naphthalenethiol. They are named "Experiment_[number]", where [number] represents the corresponding data points in the phase diagram. 4. In TEM images, the bright and dark regions indicate the polymer patches and nanoparticle cores, respectively. 5. In SEM images, the bright and dark regions indicate the nanoparticle cores and polymer patches, respectively. 6. Abbreviations in file names: HAADF-STEM (high-angle annular dark-field scanning transmission electron microscopy), PINEM (photon-induced near-field electron microscopy), and RCP/LCP (left-/right-handed circularly polarized).

chirality↗

Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II

The calcium calmodulin-dependent protein kinase II (CaMKII) is a dodecameric holoenzyme important for encoding memory. Its activation, triggered by binding of calcium-calmodulin, persists autonomously after calmodulin dissociation. One (receiver) kinase captures and subsequently phosphorylates the regulatory domain peptide of a donor kinase forming a chained dimer as the first stage of autonomous activation. Protein dynamics simulations examined the conformational changes triggered by dimer formation and phosphorylation, aimed to provide a molecular rationale for human mutations that result in learning disabilities. Ensembles generated from X-ray crystal structures were characterized by network centrality and community analysis. Mutual information related collective motions to local fragment dynamics encoded with a structural alphabet. Implicit solvent tCONCOORD conformational ensembles revealed the dynamic architecture of inactive kinase domains was co-opted in the activated dimer but the network hub shifted from the nucleotide binding cleft to the captured peptide. Explicit solvent molecular dynamics (MD) showed nucleotide and substrate binding determinants formed coupled nodes in long-range signal relays between regulatory peptides in the dimer. Strain in the extended captured peptide was balanced by reduced flexibility of the receiver kinase C-lobe core. The relays were organized around a hydrophobic patch between the captured peptide and a key binding helix. The human mutations aligned along the relays. Thus, these mutations could disrupt the allosteric network alternatively, or in addition, to altered binding affinities. Non-binding protein sectors distant from the binding sites mediated the allosteric signalling; providing possible targets for inhibitor design. Phosphorylation of the peptide modulated the dielectric of its binding pocket to strengthen the patch, non-binding sectors, domain interface and temporal correlations between parallel relays. These results provide the molecular details underlying the reported positive kinase cooperativity to enrich the discussion on how autonomous activation by phosphorylation leads to long-term behavioural effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Analyzing and modeling the kinetics of amyloid beta pores associated with Alzheimer’s disease pathology

Amyloid beta (Aβ) oligomers associated with Alzheimer’s disease (AD) form Ca 2+ -permeable plasma membrane pores, leading to a disruption of the otherwise well-controlled intracellular calcium (Ca 2+ ) homeostasis. The resultant up-regulation of intracellular Ca 2+ concentration has detrimental implications for memory formation and cell survival. The gating kinetics and Ca 2+ permeability of Aβ pores are not well understood. We have used computational modeling in conjunction with the ability of optical patch-clamping for massively parallel imaging of Ca 2+ flux through thousands of pores in the cell membrane of Xenopus oocytes to elucidate the kinetic properties of Aβ pores. The fluorescence time-series data from individual pores were idealized and used to develop data-driven Markov chain models for the kinetics of the Aβ pore at different stages of its evolution. Our study provides the first demonstration of developing Markov chain models for ion channel gating that are driven by optical-patch clamp data with the advantage of experiments being performed under close to physiological conditions. As a result, we demonstrate the up-regulation of gating of various Ca 2+ release channels due to Aβ pores and show that the extent and spatial range of such up-regulation increases as Aβ pores with low open probability and Ca 2+ permeability transition into those with high open probability and Ca 2+ permeability.

59 BASIC BIOLOGICAL SCIENCES↗

Methane and CO2 chamber fluxes and porewater concentrations US-OWC Ameriflux wetland site, 2015-2018

The data measurements of CH4 and CO2 at different patch types (classified by dominant macrophyte vegetation or hydrological state). CH4 and CO2 data include 3 types of measurements: 1) Surface flux measurements from chamber measurements. 2) Leaf flux measurements from plant chambers, providing the rate per leaf area of methane flow through three species of macropyte aerenchemous plants (Water Lily, American Lotus, and Cattail) with the corresponding flux of CO2 at the same leaves. 3) Pore water concentrations of dissolved CO2 and CH4 concentrations. These are measured along vertical profiles at varying depths from the soil-water interface using in-situ porewater dialysis profiles (peepers). Observations of 1 and 3 are available monthly for most months of the growing season (May-September) of 2015, 2016 and 2018. Leaf flux measurements (plant chambers) are available only in June, July and August of 2018. We also included the patch type classification maps during 2015, 2017 and 2018 the relative water elevation map (bathymetry) for the site.In 8/23/2020 we added the data file ChamberFluxes_2018_Separated_Diffusive_Ebullitive_Fluxes.xlsx with observation related to chamber measurements in OWC during September 2018. In these observations, we partitioned the methane flux to its diffusive and ebullitive components, using an analysis approach we describe in section 5 of the methods "Ebullition and diffusion partitioning".

54 ENVIRONMENTAL SCIENCES↗

NGEE Arctic 2019 Alder Ground Truth Survey, Seward Peninsula AK

In July 2019 we made traveled the road system outside of Nome, AK and detailed the GPS coordinates of alder shrublands for the purpose of ground-truthing alder maps of the region. Both visual and ground-based observations were made for patches of alder shrublands greater 5x5m and larger, ideally 10x10m. Visual observations were made from the car and GPS coordinates are approximate, placed by dropping pins on georeferenced pdfs using the Avenza app. Visual observations included positive identified alder shrublands as well as thickets of non-alder shrubs. Ground Observations were made at a subset of locations where we were able to hike to alders shrubland areas. Ground observations include GPS points (made with Garmin InReach) as well as relevant features of a centrally located, representative alder shrub in the patch (max height, basal diameter of all ramets, soil depth). Aboveground biomass (weight dry mass) of the surveyed shrub was calculated based on alder-specific allometric equations in Berner et al 2015 which our team checked for accuracy for the Seward Peninsula as part of Salmon et al 2019. This dataset contains three data files, three data dictionaries, and one file-level metadata file all in*.csv format plus one *.txt README file. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Post-fire soil respiration in late growing season (2023 and 2024), Kougarok Fire Complex, Seward Peninsula, Alaska

Field soil respiration data collected in 2023 and 2024 from burned and unburned tussock tundra sites in the Kougarok Fire Complex, near Nome, on the Seward Peninsula of Alaska. Specifically, we measured soil properties and late-growing season CO2 fluxes in patches of unique plant functional types (forbs, shrubs, and graminoids) across two years in tundra recovering from repeated wildfires over the decade. The goal was to identify the main drivers of soil respiration in Arctic tundra underlain by discontinuous permafrost that is recovering from two recent, repeated wildfires that differed in fire age and number of times burned, thereby resulting in different levels of vegetation and subsurface property changes (i.e., successional trajectories). There are five files in *.csv format with one data file and four data description files including data, dictionary, methods, terminology, and file-level metadata. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), is a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic Phase 3 project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

Santos, Fernanda [ORNL] (ORCID:0000000191555623)↗

AmeriFlux US-An2 Anaktuvuk River Moderate Burn

This is the AmeriFlux version of the carbon flux data for the site US-An2 Anaktuvuk River Moderate Burn. Site Description - The Anaktuvuk River fire on the North Slope of Alaska started on July 16, 2007 by lightning. It continued until the end of September when nearby lakes had already frozen over and burned >256,000 acres, creating a mosaic of patches that differed in burn severity. The Anaktuvuk River Severe Burn, Moderate Burn, and Unburned sites are 40 km to the west of the nearest road and were selected in late May 2008 to determine the effects of the fire on carbon, water, and energy exchanges during the growing season. Because the fire had burned through September of the previous year, initial deployment of flux towers occurred prior to any significant vegetative regrowth, and our sampling campaign captured the full growing season in 2008. The Moderate Burn site consisted of a large area with small patches of completely and partially burned tundra intermixed across the landscape.

Rocha, Adrian↗

AmeriFlux MX-Aog Alamos Old-Growth tropical dry forest

This is the AmeriFlux version of the carbon flux data for the site MX-Aog Alamos Old-Growth tropical dry forest. Site Description - This tower is located at a patch of remnant old growth tropical dry forest where the dominant vegetation are leguminous trees and a notorious presence of the genus Brusera. The site is at about 18 km from the municipality of Alamos Sonora Mexico within a private ranch managed by the NGO Nature Culture International. The area is also within a federally protected land named “Area de Proteccion de Flora y Fauna Sierra de Alamos Rio-Cuchijaqui" in the catalog of the “Comision Nacional de Areas Naturales Protegidas (CONANP-Mexico)”. The preserved ranch is surrounded by a mosaic of forest patches with different successional stages of tropical dry forest, and some places that are used for local agriculture and livestock. This ecosystem lies in a highly seasonal region under the influence of the North American Monsoon that brings about 70% of the rains from July to September.

Yepez, Enrico A.↗

AmeriFlux FLUXNET-1F MX-Aog Alamos Old-Growth tropical dry forest

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site MX-Aog Alamos Old-Growth tropical dry forest. This is the FLUXNET version of the carbon flux data for the site MX-Aog Alamos Old-Growth tropical dry forest produced by applying the standard ONEFlux (1F) software. Site Description - This tower is located at a patch of remnant old growth tropical dry forest where the dominant vegetation are leguminous trees and a notorious presence of the genus Brusera. The site is at about 18 km from the municipality of Alamos Sonora Mexico within a private ranch managed by the NGO Nature Culture International. The area is also within a federally protected land named “Area de Proteccion de Flora y Fauna Sierra de Alamos Rio-Cuchijaqui" in the catalog of the “Comision Nacional de Areas Naturales Protegidas (CONANP-Mexico)”. The preserved ranch is surrounded by a mosaic of forest patches with different successional stages of tropical dry forest, and some places that are used for local agriculture and livestock. This ecosystem lies in a highly seasonal region under the influence of the North American Monsoon that brings about 70% of the rains from July to September.

Yepez, Enrico A. [Instituto Tecnologico de Sonora]↗

Refinements to the Graves–Pitarka Kinematic Rupture Generator, Including a Dynamically Consistent Slip-Rate Function, Applied to the 2019 Mw 7.1 Ridgecrest Earthquake

The main objective of this study is to develop physics–based constraints on the spatiotemporal variation of the slip–rate function using a simplified dynamic rupture model. First, we performed dynamic rupture modeling of the 2019 M w 7.1 Ridgecrest, California, earthquake, to analyze the effects of depth–dependent stress and material friction on slip rate. Then, we used our modeling results to guide refinements to the slip–rate function that were implemented in the Graves–Pitarka kinematic rupture generation technique. The dynamic ruptures were computed on a surface–rupturing, planar strike–slip fault that includes a weak (negative to low–stress–drop) zone in the upper 4 km of the crust. Below the weak zone, we placed high–stress–drop patches designed to mirror the large–slip areas seen in various rupture model inversions of the event. The locations of the high–stress–drop patches and the hypocenter were varied in multiple realizations to investigate how changing the dynamic conditions affected the resulting rupture kinematics, in particular, the slip rate. From these simulations, we observed a systematic change in the shape of the slip–rate function from Kostrov type below the weak zone to a predominantly symmetric shape within the weak zone, along with a depth–dependent reduction of peak slip rate. We generalized these shallow rupture features into a depth–dependent parametric variation of the slip–rate function and implemented it in the Graves–Pitarka kinematic rupture model generator. The performance of the updated kinematic approach was then verified in 0–4 Hz simulations of the M w 7.1 Ridgecrest earthquake, which showed that incorporating the depth–dependent variation in the shape of the slip–rate function improves the fit to the observed near–fault ground motions in the 0.5–3 s period range.

58 GEOSCIENCES↗

Landscape corridors can increase invasion by an exotic species and reduce diversity of native species.

Abstract. Landscape corridors are commonly used to mitigate negative effects of habitat fragmentation, but concerns persist that they may facilitate the spread of invasive species. In a replicated landscape experiment of open habitat, we measured effects of corridors on the invasive fire ant, Solenopsis invicta, and native ants. Fire ants have two social forms: polygyne, which tend to disperse poorly but establish at high densities, and monogyne, which disperse widely but establish at lower densities. In landscapes dominated by polygyne fire ants, fire ant abundance was higher and native ant diversity was lower in habitat patches connected by corridors than in unconnected patches. Conversely, in landscapes dominated by monogyne fire ants, connectivity had no influence on fire ant abundance and native ant diversity. Polygyne fire ants dominated recently created landscapes, suggesting that these corridor effects may be transient. Our results suggest that corridors can facilitate invasion and they highlight the importance of considering species’ traits when assessing corridor utility.

Solenopsis invicta↗

A feasibility study for experimentally determining dynamic force distribution in a lap joint

Developing constitutive models of the physics in mechanical joints is currently stymied by inability to measure forces and displacements within the joint. The current state of the art estimates whole joint stiffness and energy loss per cycle from external measured force input and one or two acceleration responses. To validate constitutive models beyond this state requires a measurement of the distributed forces and displacements at the joint interface. Unfortunately, introducing measurement devices at the interface completely disrupts the desired physics. A feasibility study is presented for a non-intrusive method of solving for the interface dynamic forces from an inverse problem using full field measured responses. The responses come from the viewable surface of a beam. The noise levels associated with digital image correlation and continuous scanning laser Doppler velocimetry are evaluated from typical beam experiments. Two inverse problems are simulated. One utilizes the extended Sum of Weighted Accelerations Technique (SWAT). The second is a new approach dubbed the method of truncated orthogonal forces. These methods are much more robust if the contact patch geometry is well identified. Various approaches to identifying the contact patch are investigated, including ion marker tracking, Prussian blue and ultrasonic measurements. A typical experiment is conceived for a beam which has a lap joint at one end with a single bolt connecting it to another identical beam. In a virtual test using the beam finite element analysis, it appears that the SWAT inverse method requires evaluation of too many coefficients to adequately identify the force distribution to be viable. However, the method of truncated orthogonal forces appears viable with current digital image correlation (and probably other) imaging techniques.

47 OTHER INSTRUMENTATION↗

Parallel Block Structured Adaptive Mesh Refinement on Graphics Processing Units

Block-structured adaptive mesh refinement is a technique that can be used when solving partial differential equations to reduce the number of zones necessary to achieve the required accuracy in areas of interest. These areas (shock fronts, material interfaces, etc.) are recursively covered with finer mesh patches that are grouped into a hierarchy of refinement levels. Despite the potential for large savings in computational requirements and memory usage without a corresponding reduction in accuracy, AMR adds overhead in managing the mesh hierarchy, adding complex communication and data movement requirements to a simulation. In this paper, we describe the design and implementation of a native GPU-based AMR library, including: the classes used to manage data on a mesh patch, the routines used for transferring data between GPUs on different nodes, and the data-parallel operators developed to coarsen and refine mesh data. We validate the performance and accuracy of our implementation using three test problems and two architectures: an eight-node cluster, and over four thousand nodes of Oak Ridge National Laboratory’s Titan supercomputer. Our GPU-based AMR hydrodynamics code performs up to 4.87× faster than the CPU-based implementation, and has been scaled to over four thousand GPUs using a combination of MPI and CUDA.

97 MATHEMATICS AND COMPUTING↗