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At least 541 records · Page 30

Full waveform inversion of solar interior flows

The inference of flows of material in the interior of the Sun is a subject of major interest in helioseismology. Here, we apply techniques of full waveform inversion (FWI) to synthetic data to test flow inversions. In this idealized setup, we do not model seismic realization noise, training the focus entirely on the problem of whether a chosen supergranulation flow model can be seismically recovered. We define the misfit functional as a sum of L {sub 2} norm deviations in travel times between prediction and observation, as measured using short-distance filtered f and p {sub 1} and large-distance unfiltered p modes. FWI allows for the introduction of measurements of choice and iteratively improving the background model, while monitoring the evolution of the misfit in all desired categories. Although the misfit is seen to uniformly reduce in all categories, convergence to the true model is very slow, possibly because it is trapped in a local minimum. The primary source of error is inaccurate depth localization, which, due to density stratification, leads to wrong ratios of horizontal and vertical flow velocities ({sup c}ross talk{sup )}. In the present formulation, the lack of sufficient temporal frequency and spatial resolution makes it difficult to accurately localize flow profiles at depth. We therefore suggest that the most efficient way to discover the global minimum is to perform a probabilistic forward search, involving calculating the misfit associated with a broad range of models (generated, for instance, by a Monte Carlo algorithm) and locating the deepest minimum. Such techniques possess the added advantage of being able to quantify model uncertainty as well as realization noise (data uncertainty).

79 ASTRONOMY AND ASTROPHYSICS↗

Observability Analysis of a Power System Stochastic Dynamic Model Using a Derivative-Free Approach

Serving as a prerequisite to power system dynamic state estimation, the observability analysis of a power system dynamic model has recently attracted the attention of many power engineers. However, because this model is typically nonlinear and large-scale, the analysis of its observability is a challenge to the traditional derivative-based methods. Indeed, the linear-approximation-based approach may provide unreliable results while the nonlinear-technique-based approach inevitably faces extremely complicated derivations. Furthermore, because power systems are intrinsically stochastic, the traditional deterministic approaches may lead to inaccurate observability analyses. In this work, facing these challenges, we propose a novel polynomial-chaos-based derivative-free observability analysis approach that not only is free of any linear approximations, but also accounts for the stochasticity of the dynamic model while bringing a low implementation complexity. Furthermore, this approach enables us to quantify the degree of observability of a stochastic model, what conventional deterministic methods cannot do. The excellent performance of the proposed method has been demonstrated by performing extensive simulations using a synchronous generator model with IEEE-DC1A exciter and the TGOV1 turbine governor.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Technical Report: Algorithm and Implementation for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

This report describes the design and implementation of an algorithm for estimating relative microbial abundances, together with confidence limits, using data from metagenomic DNA sequencing. For the background behind this project and a detailed discussion of our modeling approach for metagenomic data, we refer the reader to our earlier technical report, dated March 4, 2014. Briefly, we described a fully Bayesian generative model for paired-end sequence read data, incorporating the effects of the relative abundances, the distribution of sequence fragment lengths, fragment position bias, sequencing errors and variations between the sampled genomes and the nearest reference genomes. A distinctive feature of our modeling approach is the use of a Chinese restaurant process (CRP) to describe the selection of genomes to be sampled, and thus the relative abundances. The CRP component is desirable for fitting abundances to reads that may map ambiguously to multiple targets, because it naturally leads to sparse solutions that select the best representative from each set of nearly equivalent genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Measurement of the Antineutrino Double-Differential Charged-Current Quasi-Elastic Scattering Cross Section at MINERvA

Next-generation neutrino oscillation experiments, such as DUNE and Hyper-Kamiokande, hope to measure charge-parity (CP) violation in the lepton sector. In order to do this, they must dramatically reduce their current levels of uncertainty, particularly those due to neutrino-nucleus interaction models. As CP violation is a measure of the difference between the oscillation properties of neutrinos and antineutrinos, data about how the less-studied antineutrinos interact is especially valuable. We present the MINERvA experiment's first double-differential scattering cross sections for antineutrinos on scintillator, in the few-GeV range relevant to experiments such as DUNE and NOvA. We also present total antineutrino-scintillator quasi-elastic cross sections as a function of energy, which we compare to measurements from previous experiments. As well as being useful to help reduce oscillation experiments' uncertainty, our data can also be used to study the prevalence of various cor relation and final-state interaction effects within the nucleus. We compare to models produced by different model generators, and are able to draw first conclusions about the predictions of these models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Explicit environmental and vibronic effects in simulations of linear and nonlinear optical spectroscopy

Accurately simulating the linear and nonlinear electronic spectra of condensed phase systems and accounting for all physical phenomena contributing to spectral line shapes presents a significant challenge. Vibronic transitions can be captured through a harmonic model generated from the normal modes of a chromophore, but it is challenging to also include the effects of specific chromophore–environment interactions within such a model. We work to overcome this limitation by combining approaches to account for both explicit environment interactions and vibronic couplings for simulating both linear and nonlinear optical spectra. We present and show results for three approaches of varying computational cost for combining ensemble sampling of chromophore–environment configurations with Franck–Condon line shapes for simulating linear spectra. We present two analogous approaches for nonlinear spectra. Simulated absorption spectra and two-dimensional electronic spectra (2DES) are presented for the Nile red chromophore in different solvent environments. Furthermore, employing an average Franck–Condon or 2DES line shape appears to be a promising method for simulating linear and nonlinear spectroscopy for a chromophore in the condensed phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗

Positive-Sequence Phasor Modeling of Droop-Controlled, Grid-Forming Inverters with Fault Current Limiting Function

Traditional positive-sequence phasor models of droop-controlled, grid-forming inverters do not have the fault current limiting function. During a short-circuit fault the model generates unrealistic high fault current making the simulation results less practical. This paper develops a fault current limiting function for the positive-sequence phasor model of droop-controlled, grid-forming inverters, which can effectively limit the inverter output current at the predefined maximum during faults. A user-written model has been developed for the commercially-available software Siemens/PTI PSS/E. Fault studies on a modified IEEE 39-bus system with all grid-forming inverters verify the effectiveness of the developed fault current limiting function. The proposed model can be used to evaluate how the limited fault currents of droop-controlled, grid-forming inverters impact the bulk power system transient stability under fault conditions.

Du, Wei↗

On Parallelizing Single Dynamic Simulation Using HPC Techniques and APIs of Commercial Software

Time-domain simulations are heavily used in today’s planning and operation practices to assess power system transient stability and post-transient voltage/frequency profiles following severe contingencies to comply with industry standards. Because of the increased modeling complexity, it is several times slower than real time for state-of-the-art commercial packages to complete a dynamic simulation for a large-scale model. With the growing stochastic behavior introduced by emerging technologies, power industry has seen a growing need for performing security assessment in real time. This paper presents a parallel implementation framework to speed up a single dynamic simulation by leveraging the existing stability model library in commercial tools through their application programming interfaces (APIs). Several high performance computing (HPC) techniques are explored such as parallelizing the calculation of generator current injection, identifying fast linear solvers for network solution, and parallelizing data outputs when interacting with APIs in the commercial package, TSAT. The proposed method has been tested on a WECC planning base case with detailed synchronous generator models and exhibits outstanding scalable performance with sufficient accuracy.

Diao, Ruisheng↗

Spatial Patterns and Intensity of the Surface Storm Tracks in CMIP5 Models

To improve the understanding of storm tracks and western boundary current (WBC) interactions, surface storm tracks in 12 CMIP5 models are examined against ERA-Interim. All models capture an equatorward displacement toward the WBCs in the locations of the surface storm tracks’ maxima relative to those at 850 hPa. An estimated storm-track metric is developed to analyze the location of the surface storm track. It shows that the equatorward shift is influenced by both the lower-tropospheric instability and the baroclinicity. Basin-scale spatial correlations between models and ERA-Interim for the storm tracks, near-surface stability, SST gradient, and baroclinicity are calculated to test the ability of the GCMs’ match reanalysis. An intermodel comparison of the spatial correlations suggests that differences (relative to ERA-Interim) in the position of the storm track aloft have the strongest influence on differences in the surface storm-track position. However, in the North Atlantic, biases in the surface storm track north of the Gulf Stream are related to biases in the SST. An analysis of the strength of the storm tracks shows that most models generate a weaker storm track at the surface than 850 hPa, consistent with observations, although some outliers are found. A linear relationship exists among the models between storm-track amplitudes at 500 and 850 hPa, but not between 850 hPa and the surface. In total, the work reveals a dual role in forcing the surface storm track from aloft and from the ocean surface in CMIP5 models, with the atmosphere having the larger relative influence.

54 ENVIRONMENTAL SCIENCES↗

Generative unfolding with distribution mapping

Machine learning enables unbinned, highly-differential cross section measurements. A recent idea uses generative models to morph a starting simulation into the unfolded data. We show how to extend two morphing techniques, Schrödinger Bridges and Direct Diffusion, in order to ensure that the models learn the correct conditional probabilities. This brings distribution mapping (DM) to a similar level of accuracy as the state-of-the-art conditional generative unfolding methods. Numerical results are presented with a standard benchmark dataset of single jet substructure as well as for a new dataset describing a 22-dimensional phase space of Z+2 -jets.

Butter, Anja↗

Integration of real-time measurements and atomistic modeling to license nuclear components

An improved testing and data gathering method is described herein with reference to testing a new fuel, as an exemplary component to be tested for licensure purposes. The method includes generally: generating models for the new system; making samples and getting them accepted for a reactor; and testing the samples in a test or commercial reactor until the exposure time is reached for the expected cycle length of the fuel at final use. The method is preferably done concurrent to submitting a license application for commercial use of the new component to the relevant government body to expedite license testing review.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Data-Driven Algorithm for Enabling Delay Tolerance in Resilient Microgrid Controls Using Dynamic Mode Decomposition

The increased implementation of smart grid technologies in the power distribution grid presents unique opportunities that enable resiliency, but also brings challenges motivating needs for novel solutions and mitigation techniques. The bi-directional power and data flow allow for the grid to operate with increased resiliency, which is the ability to avoid discontinuity of service to end-use loads during extreme events. However, in applications where control of the distribution grid or microgrid relies on communication networks, the degradation of communication systems in the form of loss or high latency can cause maloperation and result in loss of end-use loads. Here this paper presents a novel framework to enable delay tolerance of centralized microgrid control schemes to mitigate communication system latency impacts and guarantee successful control action. We demonstrate the delay tolerance on a control scheme that operates a battery energy storage system (BESS) to offset the sudden loss of generation and maintain system frequency. During periods of severely degraded communication system performance, the proposed delay-tolerant algorithm compensates for the latency by utilizing a data-driven model generated at the device level using dynamic mode decomposition (DMD) to determine the performance of the communications. The DMD technique predicts the system’s frequency using device-level terminal measurements and provides updated control signals. The HELICS cosimulation platform evaluates the cyber-physical interaction of the power system model in GridLAB-D, the centralized control agent in Python, and the discrete network model in NS-3. The framework is tested and validated on the IEEE-123 node system modified to represent a networked remote microgrid model, and the results show an improvement in the dynamic performance

24 POWER TRANSMISSION AND DISTRIBUTION↗

A Probabilistic Autoencoder for Type Ia Supernova Spectral Time Series

We construct a physically parameterized probabilistic autoencoder (PAE) to learn the intrinsic diversity of Type Ia supernovae (SNe Ia) from a sparse set of spectral time series. The PAE is a two-stage generative model, composed of an autoencoder that is interpreted probabilistically after training using a normalizing flow. We demonstrate that the PAE learns a low-dimensional latent space that captures the nonlinear range of features that exists within the population and can accurately model the spectral evolution of SNe Ia across the full range of wavelength and observation times directly from the data. By introducing a correlation penalty term and multistage training setup alongside our physically parameterized network, we show that intrinsic and extrinsic modes of variability can be separated during training, removing the need for the additional models to perform magnitude standardization. We then use our PAE in a number of downstream tasks on SNe Ia for increasingly precise cosmological analyses, including the automatic detection of SN outliers, the generation of samples consistent with the data distribution, and solving the inverse problem in the presence of noisy and incomplete data to constrain cosmological distance measurements. We find that the optimal number of intrinsic model parameters appears to be three, in line with previous studies, and show that we can standardize our test sample of SNe Ia with an rms of 0.091 ± 0.010 mag, which corresponds to 0.074 ± 0.010 mag if peculiar velocity contributions are removed.

79 ASTRONOMY AND ASTROPHYSICS↗

OpenCGRA: An Open-Source Unified Framework for Modeling,Testing, and Evaluating CGRAs

Coarse-grained reconfigurable arrays (CGRAs),loosely defined as arrays of functional units (e.g, adder, sub-tractor, multiplier, divider, or larger multi-operation units, butsmaller than a general-purpose core) interconnected through aNetwork-on-Chip, provide higher flexibility than domain-specificASIC accelerators while offering increased hardware efficiencywith respect to fine-grained reconfigurable devices, such as FieldProgrammable Gate Arrays (FPGAs). The fast evolving fieldsof machine learning and edge computing, which are seeing acontinuous flow of novel algorithms and larger models, makeCGRAs ideal target architectures to allow domain specializationwithout loosing too much generality. They also generally offerquicker and more effective reconfigurability than FPGAs, po-tentially allowing adaptation during actual algorithm execution,and implement a dataflow programming paradigm that adaptswell to these emerging workloads. Designing and generating aCGRA, however, still requires to define the type and number ofthe specific functional units, implement their interconnect andthe network topology, and perform its simulation and validation,given a variety of workloads of interest.In this paper, we propose OpenCGRA, a Python-based unifiedframework that integrates generation, modeling, testing and eval-uation for CGRAs. OpenCGRA is the first open-source integratedframework able to support the full top-to-bottom design flow forspecializing and implementing CGRAs: modeling at different ab-straction levels (functional level, cycle level, register-transfer level),generation, simulation, testing at different granularities (unit test-ing, integration testing, property-based testing), and characteriza-tion (area, power, and timing). OpenCGRAs will be made availableon GitHub.

CGRA, synthesis↗

Technical Report on Modeling for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

The overall aim of this project is to develop a software package, called MetaQuant, that can determine the constituents of a complex microbial sample and estimate their relative abundances by analysis of metagenomic sequencing data. The goal for Task 1 is to create a generative model describing the stochastic process underlying the creation of sequence read pairs in the data set. The stages in this generative process include the selection of a source genome sequence for each read pair, with probability dependent on its abundance in the sample. The other stages describe the evolution of the source genome from its nearest common ancestor with a reference genome, breakage of the source DNA into short fragments, and the errors in sequencing the ends of the fragments to produce read pairs.

59 BASIC BIOLOGICAL SCIENCES↗

ASSESSING FUEL PROPERTY EFFECTS ON CAVITATION AND EROSION PROPENSITY USING A COMPUTATIONAL FUEL SCREENING TOOL

To advance compression ignition combustion strategies, researchers have evaluated fuel property effects and their impact on achieving higher efficiencies and lower emissions levels relative to current capabilities. Within the Department of Energy's Co-Optima initiative, there has been a recent focus on understanding the influence of fuel properties on fuel injection performance. To help identify candidate fuels that can meet desired injector performance metrics, a computational fuel screening tool is under development that can link fuel properties with the tendency of a given fuel to cavitate and lead to cavitation-induced erosion. In the initial development of this tool, five liquid fuel properties were selected to represent candidate fuels, namely density, viscosity, vapor pressure, surface tension, and heat of vaporization. A design of experiments methodology was employed to generate a set of pseudo fuel cases, which can represent the main effects and interactions among the fuel properties and be related to cavitation erosion predictions. Large eddy simulations were performed using a mixture modeling approach to predict the cavitation and erosion propensity of these pseudo-fuels in terms of the mean fuel vapor mole fraction and stored impact energy from repeated cloud collapse events. The low order regression models generated from this study revealed the importance of liquid fuel density on cavitation formation, whereas liquid viscosity was found to have a strong negative correlation with erosion severity. The surrogate models were then used in the fuel screening tool to rank the cavitation and erosion tendency of four candidate single-component fuels: methyl decanoate, isooctane, ethanol and n-dodecane. While the fuel screening tool was not able to quantitatively predict the cavitation and erosion response metrics, the tool was able to accurately rank the relative cavitation and erosion propensity of the four fuels. Overall, ethanol and iso-octane were observed to produce the highest levels of cavitation and erosion, respectively.

cavitation-induced erosion↗

Engagement: Hyperparameter Optimization of Generative Adversarial Network Models for High-Energy Physics Simulations

We present our SciDAC FASTMath-HEP partnership results for tuning generative adversarial models (GANs) for high energy physics applications. The GANs are used in hybrid simulations to accelerate otherwise time-consuming computations. We optimize for both, prediction accuracy and variability with the goal to find GAN architectures that are reliable and robust.

high energy physics↗