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At least 1,207 records · Page 67

Time-dependent behavioral data from zebrafish reveals novel signatures of chemical toxicity using point of departure analysis

High-content imaging of embryonic zebrafish behavior can be used as a screening approach to rapidly evaluate the relative potential for chemicals to cause toxicity. However, most statistical methods applied to these data so far transform movement values to incidence-based “hits” and calculate lowest effect levels (LELs), which loses individual fish resolution of behavior and defies hazard ranking due to reliance on applied dose levels. Here, we have developed and parallelized a workflow to calculate benchmark dose (BMD) values from dynamic, high-content zebrafish behavior data that scales for high-throughput chemical screening. To appropriately capture the dynamics of zebrafish response from light to dark stimulus, we summarized time-dependent data using both area under the curve and immediate change at the transition point into two novel metrics that characterized abnormal behavior as a function of chemical concentration. The BMD workflow was applied to calculate BMD 10 values of 1,060 ToxCast chemicals for 24 zebrafish endpoints, including behavior, mortality and morphology. The BMD 10 values provided better precision and separation than LELs for clustering chemicals since they were derived from models that best-fit their concentration-response curves. Clustering analysis revealed behavioral signatures as the most sensitive endpoints. High concordance in chemical activity was observed between ToxCast assays and zebrafish behavioral endpoints, however ToxPi analysis indicated that rankings based on in vitro data was not a reliable predictor of in vivo rankings for lower potency chemicals. The methods developed in this work will enable the use of high-content zebrafish behavioral screening data for BMD analysis in toxicological hazard assessment.

59 BASIC BIOLOGICAL SCIENCES↗

Energy-efficient mapping of large-scale workflows under deadline constraints in big data computing systems

Large-scale workflows for big data analytics have become a main consumer of energy in data centers where moldable parallel computing models such as MapReduce are widely applied to meet high computational demands with time-varying computing resources. The granularity of task partitioning in each moldable job of such big data workflows has a significant impact on energy efficiency, which remains largely unexplored. In this paper, we analyze the properties of moldable jobs and formulate a workflow mapping problem to minimize the dynamic energy consumption of a given workflow request under a deadline constraint in big data systems. Since this problem is strongly NP-hard, we design a fully polynomial-time approximation scheme (FPTAS) for a special case with a pipeline-structured workflow on a homogeneous cluster and a heuristic for the generalized problem with an arbitrary workflow on a heterogeneous cluster. The performance superiority of the proposed solution in terms of dynamic energy saving and deadline missing rate is illustrated by extensive simulation results in comparison with existing algorithms, and further validated by real-life workflow implementation and experimental results in Hadoop/YARN systems.

97 MATHEMATICS AND COMPUTING↗

Dual-pace transient heat conduction in vertically aligned carbon nanotube arrays induced by structure separation

Vertically aligned arrays of carbon nanotubes (CNTs) are attractive for a wide range of macroscopic applications which can exploit the remarkable properties of individual nanotubes. In this work, an abnormal behavior of CNT bundles in heat conduction is discovered under the transient electro-thermal characterization. The measured voltage change over the sample shows a dual-pace thermal response (DTR), which could not be fitted using a single thermal diffusivity heat transfer model. Instead, two thermal diffusivities are determined from the DTR phenomenon. Three rounds of cryogenic experiments are conducted to investigate the physics behind DTR phenomenon. It starts to emerge when the temperature is reduced to a certain level. After two rounds of cryogenic experiments, the DTR phenomenon becomes permanent from 295 K to 10 K. The nano-scale structure separation induced by the increased thermal strain leads to macroscale structure separation, which results in two parallel heat conduction paths responsible for the DTR phenomenon. By building a new parallel heat transfer model taking both the transient and steady-state electrical and thermal response into consideration, the area ratio of separated CNTs is determined. Furthermore, this result uncovers the existence of coiled morphology and nano-structure evolution of CNTs under cryogenic state and its effect on thermal and electrical transport, especially on their transient behaviors. Knowledge of the thermal transport in these CNTs arrays is important considering the fact that transient thermal response strongly affects their mechanical, optical, and electrical behaviors.

42 ENGINEERING↗

The LSBmax algorithm for boosting resilience of electric grids post (N‐2) contingencies

Abstract A computationally improved algorithm is presented to find the best transmission switching (TS) candidate for boosting resilience of electricity grids subject to ( N ‐2) contingencies. Here, resilience is computed as the reduction in load shed after the above‐mentioned ( N‐ ) contingencies. TS is a planned line outage, and past research shows that changing the transmission system's topology changes the power flow and removes post contingency violations. Finding the best TS candidate in a computationally suitable time for effectively boosting resilience is a challenge. The best TS candidate is found using a novel heuristic method by decreasing the search space based on proximity to the bus with the maximum load shedding (LSB). The LSB algorithm is faster than existing algorithms in the literature; and, it is compatible with both the AC and DC optimal power flow formulations. To validate the authors' claims of speedup and accuracy, two metrics are used to analyze the results from the IEEE 39‐bus and 118‐bus systems. Finally, the inherent parallelism of the LSB algorithm is leveraged on a high‐performance computing platform and applied to the large‐scale Polish 2383‐bus test system to validate scalability in both size and speedup in computation time.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Flowing plasma rearrangement in the presence of static perturbing fields

Charged particles interacting with electromagnetic waves have a portion of their energy tied up in wave-driven oscillations. When these waves are localized to the exhaust of linear magnetic confinement systems, this ponderomotive effect can be utilized to enhance particle confinement. The same effect can be derived for particles moving via an E×B drift into a region of a static perturbation to the electromagnetic fields which has a large wave vector component in the direction of the motion. In this work, we use a simplified slab model to self-consistently solve for the electromagnetic fields within the fluid flowing plasma of a static flute-like (k∥=0) perturbation and evaluate the resulting ponderomotive potential. We find that two types of perturbations can exist within the flowing plasma, which are an O wave and an X wave in the frame moving with the fluid. In the case of tenuous plasma, these perturbations are magnetostatic or electrostatic multipole-analog perpendicular to the guiding magnetic field in the lab frame, respectfully. For denser plasmas, the O wave-like perturbation is screened at the electron skin depth scale, and the X wave-like perturbation is a combination of a similar perpendicular electric perturbation and parallel magnetic perturbation. The ponderomotive potential generated in the X wave-like case is gyrofrequency-dependent and can be used as either potential barriers or potential wells, depending on the direction of the flow velocity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

AI-optimized detector design for the future Electron-Ion Collider: the dual-radiator RICH case

Advanced detector R&D requires performing computationally intensive and detailed simulations as part of the detector-design optimization process. Here, we propose a general approach to this process based on Bayesian optimization and machine learning that encodes detector requirements. As a case study, we focus on the design of the dual-radiator Ring Imaging Cherenkov (dRICH) detector under development as a potential component of the particle-identification system at the future Electron-Ion Collider (EIC). The EIC is a US-led frontier accelerator project for nuclear physics, which has been proposed to further explore the structure and interactions of nuclear matter at the scale of sea quarks and gluons. We show that the detector design obtained with our automated and highly parallelized framework outperforms the baseline dRICH design within the assumptions of the current model. Our technique can be applied to any detector R&D, provided that realistic simulations are available.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Preparing sparse solvers for exascale computing

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges.

97 MATHEMATICS AND COMPUTING↗

HDF5 As a Vehicle for in Transit Data Movement

For in transit processing, one of the fundamental challenges is the efficient movement of data from producers to consumers. Exploiting the flexibility offered by the SENSEI generic in situ framework, we have developed a number of different in transit data transport mechanisms. In this work, we focus on the transport mechanism that leverages the HDF5 parallel I/O library, and investigate the performance characteristics of this transport mechanism. For in transit use cases at scale on HPC platforms, one might expect that an in transit data transport mechanism that uses faster layers of the storage hierarchy, such as DRAM memory, would always outperform a transport that uses slower layers of the storage hierarchy, such as an NVRAM-based persistent storage presented as a distributed file system. However, our test results show that the performance of the transport using NVRAM is competitive with the transport that uses socket-based data movement across varying levels of producer and consumer concurrency.}, booktitle = {Proceedings of the Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization

Gu, Junmin↗

HydraGNN v3.0

New or improved capabilities included in v3.0 release are as follows: 1. Enhancement in message passing layers through generalization of the class inheritance to enable the inclusion of a broader set of message passing policies Inclusion of equivariant message passing layers from the original implementations of: SchNet (https://pubs.aip.org/aip/jcp/article/148/24/241722/962591/SchNet-A-deep-learning-architecture-for-molecules); DimeNet++ (https://arxiv.org/abs/2011.14115); EGNN models (https://arxiv.org/pdf/2102.09844.pdf) 2. Restructuring of class inheritance for data management 3. Support of DDStore https://github.com/ORNL/DDStore capabilities for improved distributed data parallelism on large volumes of data that cannot fit on intra-node memory capacities 4. Large-scale system support for OLCF-Crusher and OLCF-Frontier

Lupo Pasini, Massimiliano [Oak Ridge National Labo↗

Theoretically and practically efficient parallel nucleus decomposition

This paper studies the nucleus decomposition problem, which has been shown to be useful in finding dense substructures in graphs. We present a novel parallel algorithm that is efficient both in theory and in practice. Our algorithm achieves a work complexity matching the best sequential algorithm while also having low depth (parallel running time), which significantly improves upon the only existing parallel nucleus decomposition algorithm (Sariyüce et al. , PVLDB 2018). The key to the theoretical efficiency of our algorithm is a new lemma that bounds the amount of work done when peeling cliques from the graph, combined with the use of a theoretically-efficient parallel algorithms for clique listing and bucketing. We introduce several new practical optimizations, including a new multi-level hash table structure to store information on cliques space-efficiently and a technique for traversing this structure cache-efficiently. On a 30-core machine with two-way hyper-threading on real-world graphs, we achieve up to a 55x speedup over the state-of-the-art parallel nucleus decomposition algorithm by Sariyüce et al. , and up to a 40x self-relative parallel speedup. We are able to efficiently compute larger nucleus decompositions than prior work on several million-scale graphs for the first time.

Computer Science↗

Refueling Infrastructure Scoping and Feasibility Assessment for Hydrogen Rail Applications

The feasibility and component cost of hydrogen rail refueling infrastructure is examined. Example reference stations can inform future studies on components and systems specifically for hydrogen rail refueling facilities. All of the 5 designs considered assumed the bulk storage of liquid hydrogen on-site, from which either gaseous or liquid hydrogen would be dispensed. The first design was estimated to refuel 10 multiple unit trains per day, each train containing 260 kg of gaseous hydrogen at 350 bar on-board. The second base design targeted the refueling of 50 passenger locomotives, each with 400 kg of gaseous hydrogen on-board at 350 bar. Variations from this basic design were made to consider the effect of two different filling times, two different hydrogen compression methods, and two different station design approaches. For each design variation, components were sized, approximate costs were estimated for major components, and physical layouts were created. For both gaseous hydrogen-dispensing base designs, the design of direct-fill using a cryopump design was the lowest cost due to the high cost of the cascade storage system and gas compressor. The last three base designs all assumed that liquid hydrogen was dispensed into tender cars for freight locomotives that required 7,500 kg of liquid hydrogen, and the three different designs assumed that 5, 50, or 200 tender cars were refueled every day. The total component costs are very different for each design, because each design has a very different dispensing capacity. The total component cost for these three designs are driven by the cost of the liquid hydrogen tank; additionally, delivering that much liquid hydrogen to the refueling facility may not be practical. Many of the designs needed the use of multiple evaporators, compressors, and cryopumps operating in parallel to meet required flow rates. In the future, the components identified here can be improved and scaled-up to better fit the needs of heavy-duty refueling facilities. This study provides basic feasibility and first-order design guidance for hydrogen refueling facilities serving emerging rail applications.

08 HYDROGEN↗

The current-voltage relationship in auroral current sheets

The current-voltage relation within narrow auroral current sheets is examined through the use of high-resolution data from the high altitude Dynamics Explorer 1 satellite. The north-south perpendicular electric field and the east-west magnetic field are shown for three cases in which there are large amplitude, oppositely directed paired electric fields and narrow current sheets. These data are shown to indicate that there is a linear Ohm's law relationship between the current density and the parallel potential drop within the narrow current sheets. This linear relationship had previously been verified for large-scale auroral formations greater than 20 km wide at the ionosphere. The evidence shown here extends our knowledge down to the scale size of discrete auroral arcs.

Weimer, D. R.↗

A comparison of plasma waves produced by ion accelerators in the F-region ionosphere

Ion beams injected into the ionosphere are known to produce waves related to the normal modes of the plasma. The spectra of plasma waves produced during four sounding rocket experiments are examined. The experimental conditions were somewhat different during each experiment. The accelerated ion was either Xe(+) or Ar(+) and the experimental geometry, described by the separation vector between the plasma wave receiver and the ion accelerator, was either parallel or perpendicular to the geomagnetic field.

Kintner, P. M.↗

The effect of random Alfven waves on the propagation of hydromagnetic waves in a finite-beta plasma

Using first-order smoothing theory, Fourier analysis and perturbation methods, the evolution equation of the wave spectrum as well as the nonlinear forces generated by random Alfven waves in a finite-beta plasma with phenomenological Landau-damping effects are obtained. The effect of microscale random Alfven waves on the propagation of large-scale hydromagnetic waves is also investigated by solving the mean-field equations. It is shown that parallel-propagating random Alfven waves are modulationally stable and that obliquely propagating random Alfven waves can be modulationally unstable when the energy of random waves is converted to slow magnetoacoustic waves that can be Landau-damped, providing a dissipation mechanism for the Alfven waves.

Hamabata, Hiromitsu↗

Conjugate-Gradient Algorithms For Dynamics Of Manipulators

Algorithms for serial and parallel computation of forward dynamics of multiple-link robotic manipulators by conjugate-gradient method developed. Parallel algorithms have potential for speedup of computations on multiple linked, specialized processors implemented in very-large-scale integrated circuits. Such processors used to stimulate dynamics, possibly faster than in real time, for purposes of planning and control.

Fijany, Amir↗

Means, Variability and Trends of Precipitation in the Global Climate as Determined by the 25-year GEWEWGPCP Data Set

The Global Precipitation Climatology Project (GPCP) 25-year precipitation data set is used as a basis to evaluate the mean state, variability and trends (or inter-decadal changes) of global and regional scales of precipitation. The uncertainties of these characteristics of the data set are evaluated by examination of other, parallel data sets and examination of shorter periods with higher quality data (e.g., TRMM). The global and regional means are assessed for uncertainty by comparing with other satellite and gauge data sets, both globally and regionally. The GPCP global mean of 2.6 mdday is divided into values of ocean and land and major latitude bands (Tropics, mid-latitudes, etc.). Seasonal variations globally and by region are shown and uncertainties estimated. The variability of precipitation year-to-year is shown to be related to ENS0 variations and volcanoes and is evaluated in relation to the overall lack of a significant global trend. The GPCP data set necessarily has a heterogeneous time series of input data sources, so part of the assessment described above is to test the initial results for potential influence by major data boundaries in the record.

Adler, R. F.↗

A Computationally Improved Heuristic Algorithm for Transmission Switching Using Line Flow Thresholds for Load Shed Reduction

We present a computationally improved heuristic algorithm for transmission switching (TS) to recover load shed. Research from the past showed that changing power system topology may control power flows and remove line congestion. Hence, TS may reduce the required load shed. One of the main challenges is to find a potential TS candidate in a suitable time. Here, we propose a novel heuristic method that is capable of finding the potential TS candidate faster than existing algorithms in literature. The proposed method is compatible with both the AC and DC optimal power flows (OPF). Three metrics are used to compare the proposed algorithm with the state-of-the-art from literature to show the speedup and accuracy achieved. The proposed method is implemented on the IEEE 30-bus system, PEGASE 89-bus system, IEEE 118-bus system, and Polish 2383- bus system. The results on the large-scale Polish 2383-bus system shows that the proposed algorithm is scalable to large real-world systems. Parallel computing is implemented to further improve the computational performance of the proposed algorithm.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Scaled experiments on cavity confined explosions in limestone and poly(methyl methacrylate)

A scaled experiment comprising a laser-driven explosion in a cavity is used to characterize the coupling of mechanical energy into the surrounding solid material. Experiments are performed using poly(methyl methacrylate) and dry Salem limestone as the explosion containment blocks materials, in which are milled scaled spherical cavities of various dimensions. Measurements of the coupled shock, taken with fiber optic probes at the cavity wall, show the critical radius where wall deformation transitions from plastic to elastic deformation. These measurements also provide a diagnostic of the air blast, which is validated against GEODYN simulation code. The measurement of the coupled shock amplitude taken farther from the wall in the linear region indicates increased coupling efficiency in small cavities over the range of scaled cavity radii from 6 to 20 m/kt 1/3 , a phenomenon not previously observed in experiments. A comparison of results taken in this experiment with a parallel experiment using high explosive (HE) as the source shows that coupled shocks generated with HE are characteristically different with much larger amplitude than those produced by a high energy density laser-driven source with the same yield. This experimental technique potentially provides a rapid and cost-effective method to analyze the consequences of a full-scale, low yield, buried explosion.

58 GEOSCIENCES↗