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At least 451 records · Page 25

Computationally efficient Bayesian estimation of graphical networks for omics data

Graphical networks are useful, widely-used modeling approaches to represent complex biological processes with biological measurements generated by platforms such as mass spectrometry. Bayesian analyses of graphical networks for omics data have several advantages over their frequentist counterparts, such as the inclusion of prior knowledge in the estimation of models. However, Bayesian approaches to date have only been feasible for data with a couple hundred biomolecules due to prohibitive computational time, but omics data often contains tens of thousands of biomolecules. Here, we present and illustrate a more computationally efficient approach named BPlane (Bayesian PseudoLikelihood-based Algorithm for Network Estimation) to extend Bayesian modeling capabilities for larger-sized datasets, such as most untargeted proteomics data. Via simulation, we demonstrate that BPlane produces substantial computational savings over a current state-of-the-art Bayesian algorithm while maintaining competitive edge detection accuracy. On a SARS-CoV2 proteomics data with 7000 proteins, the competing algorithm takes three times as long to complete the first iteration as BPlane takes to converge after over 100 iterations.

EM algorithm↗

Results from the Alfvén Eigenmode Active Diagnostic during the 2019-2020 JET deuterium campaign

This paper presents results of extensive analysis of mode excitation observed during the operation of the Alfvén Eigenmode Active Diagnostic (AEAD) in the JET tokamak during the 2019-2020 deuterium campaign. Here, six of eight toroidally spaced antennas, each with independent power and phasing, were successful in actively exciting stable MHD modes in 479 plasmas. In total, magnetic resonances were detected with up to fourteen fast magnetic probes. In this work, we present the calculations of resonant frequencies $f_0$, damping rates γ < 0, and toroidal mode numbers $\textit{n}$, spanning the parameter ranges $f_0$ ≈ 30–250 kHz, –γ ≈ 0–13 kHz, and $\vert n \vert \leq {30}$. In general, good agreement is seen between the resonant and the calculated toroidal Alfvén Eigenmode frequencies, and between the toroidal mode numbers applied by the AEAD and estimated of the excited resonances. We note several trends in the database: the probability of resonance detection decreases with plasma current and external heating power; the normalized damping rate increases with edge safety factor but decreases with external heating. These results provide key information to prepare future experimental campaigns and to better understand the physics of excitation and damping of Alfvén Eigenmodes in the presence of alpha particles during the upcoming DT campaign, thereby extrapolating with confidence to future tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Understanding the Impact of Data Staging for Coupled Scientific Workflows

We report the rate of data generated by cutting-edge experimental science facilities and large-scale simulations enabled by current high-performance computing (HPC) systems has continued to grow at a far greater pace than the development of the network and storage capabilities on which these systems rely. To cope with this challenge, scientist are moving toward the creation of autonomous experiments and HPC simulations using machine learning. However, efficiently moving, storing, and processing large amounts of data away from the point of origin presents an incredible challenge. In-memory computing, in situ analysis, data staging, and data streaming are recognized viable alternatives to traditional file-based methods for transferring data between coupled workflows. However, the performance trade-offs and limitations for these methods are not fully understood when used in HPC applications. This article presents a comprehensive performance assessment of the current solutions for data staging when applied to applications that are not necessary I/O intensive which makes them not ideal candidates for these methods. Our study is based on experiments running at scale on Oak Ridge National Laboratory's Summit supercomputer using applications and simulations that cover typical computational motifs and patterns. We investigated the usability and cost/benefit trade-offs of staging algorithms for HPC applications under different scenarios and highlight opportunities for optimizing the dataflow between coupled simulation workflows.

97 MATHEMATICS AND COMPUTING↗

A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements

In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I–VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers’ views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗

Model Diagnostics for Equation Oriented Models: Roadblocks and the Path Forward

This poster was presented at the Foundations of Computer Aided Process Design (FOCAPD) 2024 conference with a paper describing efforts to develop a unified workflow and toolbox for diagnosing issues in equation-oriented models as part of the IDAES modeling framework. The poster presents the work currently underway within the IDAES project to develop and integrate cutting edge model analysis techniques into a common toolbox and workflow for model developers to use.

Lee, Andrew↗

Scientific challenges to characterizing the wind resource in the marine atmospheric boundary layer

Abstract. With the increasing level of offshore wind energy investment, it is correspondingly important to be able to accurately characterize the wind resource in terms of energy potential as well as operating conditions affecting wind plant performance, maintenance, and lifespan. Accurate resource assessment at a particular site supports investment decisions. Following construction, accurate wind forecasts are needed to support efficient power markets and integration of wind power with the electrical grid. To optimize the design of wind turbines, it is necessary to accurately describe the environmental characteristics, such as precipitation and waves, that erode turbine surfaces and generate structural loads as a complicated response to the combined impact of shear, atmospheric turbulence, and wave stresses. Despite recent considerable progress both in improvements to numerical weather prediction models and in coupling these models to turbulent flows within wind plants, major challenges remain, especially in the offshore environment. Accurately simulating the interactions among winds, waves, wakes, and their structural interactions with offshore wind turbines requires accounting for spatial (and associated temporal) scales from O(1 m) to O(100 km). Computing capabilities for the foreseeable future will not be able to resolve all of these scales simultaneously, necessitating continuing improvement in subgrid-scale parameterizations within highly nonlinear models. In addition, observations to constrain and validate these models, especially in the rotor-swept area of turbines over the ocean, remains largely absent. Thus, gaining sufficient understanding of the physics of atmospheric flow within and around wind plants remains one of the grand challenges of wind energy, particularly in the offshore environment. This paper provides a review of prominent scientific challenges to characterizing the offshore wind resource using as examples phenomena that occur in the rapidly developing wind energy areas off the United States. Such phenomena include horizontal temperature gradients that lead to strong vertical stratification; consequent features such as low-level jets and internal boundary layers; highly nonstationary conditions, which occur with both extratropical storms (e.g., nor'easters) and tropical storms; air–sea interaction, including deformation of conventional wind profiles by the wave boundary layer; and precipitation with its contributions to leading-edge erosion of wind turbine blades. The paper also describes the current state of modeling and observations in the marine atmospheric boundary layer and provides specific recommendations for filling key current knowledge gaps.

17 WIND ENERGY↗

Model Diagnostics for Equation Oriented Models: Roadblocks and the Path Forward

Conference paper for FOCAPD24 describing efforts to develop a unified workflow and toolbox for diagnosing issues in equation-oriented models as part of the IDAES modeling framework. The paper presents the work currently underway within the IDAES project to develop and integrate cutting edge model analysis techniques into a common toolbox and workflow for model developers to use.

Lee, Andrew↗

Results from the Alfven Eigenmode Active Diagnostic during the 2019-2020 JET deuterium campaign

This paper presents results of extensive analysis of mode excitation observed during the operation of the Alfven Eigenmode Active Diagnostic (AEAD) in the JET tokamak during the 2019-2020 deuterium campaign. Six of eight toroidally spaced antennas, each with independent power and phasing, were successful in actively exciting stable MHD modes in 479 plasmas. In total, 4768 magnetic resonances were detected with up to fourteen fast magnetic probes. In this work, we present the calculations of resonant frequencies f0, damping rates \gamma < 0, and toroidal mode numbers n, spanning the parameter range f0 = 30 - 250 kHz, -\gamma = 0 - 13 kHz, and |n| < 30. In general, good agreement is seen between the resonant and the calculated toroidal Alfven Eigenmode frequencies, and between the toroidal mode numbers applied by the AEAD and estimated of the excited resonances. We note several trends in the database: the probability of resonance detection decreases with plasma current and external heating power; the normalized damping rate increases with edge safety factor but decreases with external heating. These results provide key information to prepare future experimental campaigns and to better understand the physics of excitation and damping of Alfven Eigenmodes in the presence of alpha particles during the upcoming DT campaign, thereby extrapolating with confidence to future tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Investigation of rotor blade element airloads for a teetering rotor in the blade stall regime

A model of a teetering rotor was tested in a low speed wind tunnel. Blade element airloads measured on an articulated model rotor were compared with the teetering rotor and showed that the teetering rotor is subjected to less extensive flow separation. Retreating blade stall was studied. Results show that stall, under the influence of unsteady aerodynamic effects, consists of four separate stall events, each associated with a vortex shed from the leading edge and sweeping over the upper surface of the rotor blade. Current rotor performance prediction methodology was evaluated through computer simulation.

Dadone, L. U.↗

Influence of the electron source distribution on field-aligned currents

The field-aligned current density above a discrete auroral arc has been deduced from the downward electron flux and magnetic field measurements onboard the rocket Porcupine flight 4. Both measurements show that the field-aligned current density is, in spite of decreasing peak energies towards the edge of the arc, about 4 times higher there than in the center of the arc. This can be explained by using the single particle description for an anisotropic electron source distribution.

Bruening, K.↗

Experimental study of the vortex flow behavior on a generic fighter wing at subsonic and transonic speeds

A subsonic and transonic investigation of the vortex flow behavior of a generic fighter configuration with 55-deg cropped delta wing has been conducted in order to improve current understanding of vortical motions on a wing with deflected leading edge flap at moderate and high angles-of-attack. The leading edge vortex strength was reduced, and the vortex was flatter and closer to the wing surface, as the Mach number increased. Transonically, at high angles-of-attack, the test data suggested the development of a cross-flow shock wave above the vortex sheet which coexisted with a rear shock wave. Subsonically, a deflected leading edge flap was able to sustain a concentrated vortex on the forward-facing surface.

Erickson, Gary E.↗

NbN/MgO/NbN SIS tunnel junctions for submm wave mixers

The authors report on the fabrication and testing of all-refractory NbN/MgO/NbN SIS (superconductor-insulator-superconductor) tunnel junctions for use as high-frequency mixers. Progress in the development of techniques for the fabrication of submicron-area tunnel junctions is described. Junction structures which have been investigated include mesa, crossline, and edge geometries. Using reactive sputtering techniques, NbN tunnel junctions with critical currents in excess of 104 A/sq cm have been fabricated with Vm values as high as 65 mV and areas down to 0.1 sq micron. Specific capacitance measurements on NbN/MgO/NbN mesa-type tunnel junctions give values in the range 60-90 fF/sq micron. These SIS tunnel junctions have been integrated with antennas and coupling structures for mixer tests in a waveguide receiver at 207 GHz. Preliminary mixer results are reported.

Stern, J. A.↗

Spatial variations in ac susceptibility and microstructure for the YBa2Cu3O(7-x) superconductor and their correlation with room-temperature ultrasonic measurements

The spatial (within-sample) uniformity of superconducting behavior and microstructure in YBa2Cu3O(7-x) specimens over the pore fraction range of 0.10 to 0.25 was examined. The viability of using a room-temperature, nondestructive characterization method (ultrasonic velocity imaging) to predict spatial variability was determined. Spatial variations in superconductor properties were observed for specimens containing 0.10 pore fraction. An ultrasonic velocity image constructed from measurements at 1 mm increments across one such specimen revealed microstructural variation between edge and center locations that correlated with variations in alternating-current shielding and loss behavior. Optical quantitative image analysis on sample cross-sections revealed pore fraction to be the varying microstructural feature.

Roth, Don J.↗

Spatial variations in a.c. susceptibility and microstructure for the YBa2Cu3O(7-x) superconductor and their correlation with room-temperature ultrasonic measurements

The spatial (within-sample) uniformity of superconducting behavior and microstructure in YBa2Cu30(7-x) specimens over the pore fraction range of 0.10 to 0.25 was examined. The viability of using a room-temperature, nondestructive characterization method (ultrasonic velocity imaging) to predict spatial variability was determined. Spatial variations in superconductor properties were observed for specimens containing 0.10 pore fraction. An ultrasonic velocity image constructed from measurements at 1 mm increments across one such specimen revealed microstructural variation between edge and center locations that correlated with variations in alternating-current shielding and loss behavior. Optical quantitative image analysis on sample cross-sections revealed pore fraction to be the varying microstructural feature.

Roth, Don J.↗

Evaluation and Validation of the Messinger Freezing Fraction

One of the most important non-dimensional parameters used in ice-accretion modeling and scaling studies is the freezing fraction defined by the heat-balance analysis of Messinger. For fifty years this parameter has been used to indicate how rapidly freezing takes place when super-cooled water strikes a solid body. The value ranges from 0 (no freezing) to 1 (water freezes immediately on impact), and the magnitude has been shown to play a major role in determining the physical appearance of the accreted ice. Because of its importance to ice shape, this parameter and the physics underlying the expressions used to calculate it have been questioned from time to time. Until now, there has been no strong evidence either validating or casting doubt on the current expressions. This paper presents experimental measurements of the leading-edge thickness of a number of ice shapes for a variety of test conditions with nominal freezing fractions from 0.3 to 1.0. From these thickness measurements, experimental freezing fractions were calculated and compared with values found from the Messinger analysis as applied by Ruff. Within the experimental uncertainty of measuring the leading-edge thickness, agreement of the experimental and analytical freezing fraction was very good. It is also shown that values of analytical freezing fraction were entirely consistent with observed ice shapes at and near rime conditions: At an analytical freezing fraction of unity, experimental ice shapes displayed the classic rime shape, while for conditions producing analytical freezing fractions slightly lower than unity, glaze features started to appear.

Anderson, David N.↗

Characterizing Weak-Link Effects in Mo/Au Transition-Edge Sensors

We are developing Mo/Au bilayer transition-edge sensors (TESs) for applications in X-ray astronomy. Critical current measurements on these TESs show they act as weak superconducting links exhibiting oscillatory, Fraunhofer-like, behavior with applied magnetic field. In this contribution we investigate the implications of this behavior for TES detectors, under operational bias conditions. This includes characterizing the logarithmic resistance sensitivity with temperature, (alpha, and current, beta, as a function of applied magnetic field and bias point within the resistive transition. Results show that these important device parameters exhibit similar oscillatory behavior with applied magnetic field, which in turn affects the signal responsivity, noise and energy resolution.

Smith, Stephen↗

Electrical NEP in Hot-Electron Titanium Superconducting Bolometers

We are presenting the current progress on the titanium (Ti) hot-electron transition-edge devices. The ultimate goal of this work is to develop a submillimeter Hot-Electron Direct Detector (HEDD) with the noise equivalent power NEP = 10(sup -1) - 10(sup -20) W/Hz(sup 1/2) for the moderate resolution spectroscopy and Cosmic Microwave Background (CMB) studies on future space telescope (e.g., SPICA, SAFIR, SPECS, CMBPol) with cryogenically cooled (approximately 4-5 K) mirrors. Recently, we have achieved the extremely low thermal conductance (approximately 20 fW/K at 300 mK and approximately 0.1 fW/K at 40 mK) due to the electron-phonon decoupling in Ti nanodevices with niobium (Nb) Andreev contacts. This thermal conductance translates into the "phonon-noise" NEP approximately equal to 3 x 10(sup -21) W/Hz(sup 1/2) at 40 mK and NEP approximately equal to 3 x 10(sup -19) W/Hz(sup 1/2) at 300 mK. These record data indicate the great potential of the hot-electron detector for meeting many application needs. Beside the extremely low phonon-noise NEP, the nanobolometers have a very low electron heat capacitance that makes them promising as detectors of single THz photons. As the next step towards the practical demonstration of the HEDD, we fabricated and tested somewhat larger than in Ref.1 devices (approximately 6 micrometers x 0.35 micrometers x 40 nm) whose critical temperature is well reproduced in the range 300-350 mK. The output electrical noise measured in these devices with a low-noise dc SQUID is dominated by the thermal energy fluctuations (ETF) aka "phonon noise". This indicates the high electrothermal loop gain that effectively suppresses the contributions of the Johnson noise and the amplifier (SQUID) noise. The electrical NEP = 6.7 x 10(sup -18) W/Hz(sup 1/2) derived from these measurements is in good agreement with the predictions based on the thermal conductance data. The very low NEP and the high speed (approximately microns) are a unique combination not found in other detectors.

transition-edge sensor↗

IceNode: A Buoyant Vehicle for Acquiring Well-Distributed, Long-Duration Melt Rate Measurements Under Ice Shelves

Antarctic ice shelves buttress the Antarctic Ice Sheet from sliding into the ocean and significantly raising global sea level. However, the accelerating dynamics of ice shelf melt in a warming environment are poorly understood, and the collapse of Antarctic ice shelves remains one of the largest sources of uncertainty in global sea level rise projections. The cavities below Antarctic ice shelves are notoriously difficult to access, making model-based hypotheses about the relationship between ocean warming and greater ice shelf melting difficult to verify because of a lack of in-situ data to constrain model parameters and examine key assumptions. We present early progress on IceNode, a novel vehicle under development at the NASA Jet Propulsion Laboratory designed to acquire well-distributed, concurrent, long-duration melt rate measurements under ice shelves. IceNodes are deployed as an array from a ship at the shelf edge, and use variable buoyancy to ride melt-driven exchange currents far into the cavity. Once underneath their target, they release a ballast weight to become highly positively buoyant and attach to the underside of the ice shelf, where they acquire in-situ measurements of basal melt rate directly at the ice-ocean interface for a year or more. Finally, IceNodes detach from their landing structure and use variable buoyancy to ride melt-driven exchange currents back to open water, where they surface and transmit their mission data home. IceNodes are designed to be relatively low-cost, expendable, and have simple logistics, enabling scientists to deploy scalable arrays that simultaneously measure co-varying ice shelf melt and ocean conditions over large spatial areas, thereby providing an unprecedented view of ice shelf melt rate variability and its drivers.

Zapien, Xavier↗