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At least 973 records · Page 54

Conditional Latent Diffusion for High-Resolution Prediction of Electrochemical Surface Morphology

A conditionally guided generative latent diffusion process that is trained on a set of experimental processing parameters and their associated resulting electron microscope images of the electrodeposition process is able to interpolate between processing parameters in a physically consistent way. Electrodeposition of rhenium with pulse and pulse-reverse waveforms is used as a model system, and the process is adaptable to other electrodeposition, electropolishing, or corrosion processes. The method is able to extrapolate, predicting estimates of material morphologies for experimental setups unseen in the training data. The results are demonstrated with experimental data.

36 MATERIALS SCIENCE↗

The updated ITPA global H-mode confinement database: description and analysis

The multi-machine ITPA Global H-mode Confinement Database has been upgraded with new data from JET with the ITER-like wall and ASDEX Upgrade with the full tungsten wall. This paper describes the new database and presents results of regression analysis to estimate the global energy confinement scaling in H-mode plasmas using a standard power law. Various subsets of the database are considered, focusing on type of wall and divertor materials, confinement regime (all H-modes, ELMy H or ELM-free) and ITER-like constraints. Apart from ordinary least squares, two other, robust regression techniques are applied, which take into account uncertainty on all variables. Regression on data from individual devices shows that, generally, the confinement dependence on density and the power degradation are weakest in the fully metallic devices. Using the multi-machine scalings, predictions are made of the confinement time in a standard ELMy H-mode scenario in ITER. The uncertainty on the scaling parameters is discussed with a view to practically useful error bars on the parameters and predictions. One of the derived scalings for ELMy H-modes on an ITER-like subset is studied in particular and compared to the IPB98(y,2) confinement scaling in engineering and dimensionless form. Transformation of this new scaling from engineering variables to dimensionless quantities is shown to result in large error bars on the dimensionless scaling. Regression analysis in the space of dimensionless variables is therefore proposed as an alternative, yielding acceptable estimates for the dimensionless scaling. The new scaling, which is dimensionally correct within the uncertainties, suggests that some dependencies of confinement in the multi- machine database can be reconciled with parameter scans in individual devices. This includes vanishingly small dependence of confinement on line-averaged density and normalized plasma pressure (β), as well as a noticeable, positive dependence on effective atomic mass and plasma triangularity. Extrapolation of this scaling to ITER yields a somewhat lower confinement time compared to the IPB98(y, 2) prediction, possibly related to the considerably weaker dependence on major radius in the new scaling (slightly above linear). Further studies are needed to compare more flexible regression models with the power law used here. In addition, data from more devices concerning possible ‘hidden variables’ could help to determine their influence on confinement, while adding data in sparsely populated areas of the parameter space may contribute to further disentangling some of the global confinement dependencies in tokamak plasmas.

Database↗

Hylia: Time-Series Library for Network Operations (Hylia) v1

The ability to analyze time-series data in network operations is critical to ensure optimal operations and management in wide area networks, sensor networks, and cloud networks. Hylia is a collection of multiple time-series prediction algorithms designed specifically to work with network monitoring data sets such as SNMP, NETFLOW and other monitoring data. It is designed to recognize these features and perform the extrapolation of the data.

Kiran, Mariam↗

AADL: Anderson Accelerated Deep Learning

We propose a stable, distributed approach to perform AA that accelerates the convergence rate of stochastic first-order optimizers to train neural networks. Differently from previous works, we do not alter neither the scheme to perform AA nor the loss function minimized during the training. To improve robustness against stagnation, we customize general guidelines that suggest to relax the frequency of AA corrections by performing AA only at the end of an entire training epoch. To improve robustness of AA against the stochastic oscillations of first-order optimizers, we average the gradients computed on consecutive stochastic optimization updates. The improved regularity of the converging sequence and the reduced amplitude of stochastic oscillations across consecutive optimization steps allows AA to efficiently extrapolate an improved converging sequence, thereby overcoming limitations of existing approaches to perform AA on stochastic optimization.

Lupo Pasini, Massimiliano [Oak Ridge National Lab.↗

QGLab v0.0.1

A software program for experimenting with holographic teleportation protocol on quantum computers. The code implements the protocol that was proposed in https://arxiv.org/abs/1911.06314. The code is an end-to-end software solution that facilitates conducting the holographic teleportation experiments on state-of-the-art and emergent generations of QPUs supported by the Qiskit and tket SDKs. The code bundles all stages of an experiment as a single configurable workflow allowing faster development and experimentation cycles. Features: 1. Easy switching between Qiskit and tket quantum compilers. 2. Semi-automatic facilities for finding optimal compilation solutions beyond what Qiskit and tket provide by default. 3. Experiment resolution scaling (based on automatic jobs' batching). 4. Automatic experiment scaling over qubits. 5. Automatic readout error mitigation. 6. Automatic reproducibility analysis. 7. Standalone error-mitigation tools (randomized compiling, mitigation with estimation circuits, zero-noise extrapolation)

Shapoval, Illya↗

Scalable Reduced Order Model with Discontinuous Galerkin Domain Decomposition

scaleupROM is a scalable, physics-constrained reduced order model (ROM). It aims to provide robust, accelerated physics predictions at extrapolated scales, based on the small, component-level data. This is implemented by combining projection-based ROM with discontinuous Galerkin domain decomposition, in the framework of MFEM and libROM. It currently supports the Poisson equation and Stokes flow equation, and more work is in progress toward general, nonlinear physics systems.

Chung, Seung Whan↗

Thermodynamics-informed latent space dynamics identification

This software showcases a latent space dynamics identification method, namely tLaSDI, that embeds the first and second principles of thermodynamics. The latent variables are learned through an autoencoder as a nonlinear dimension reduction model. The latent dynamics are constructed by a neural network-based model that precisely preserves certain structures for the thermodynamic laws through the GENERIC formalism. An abstract error estimate is established, which provides a new loss formulation involving the Jacobian computation of autoencoder. The autoencoder and the latent dynamics are simultaneously trained to minimize the new loss. Computational examples demonstrate the effectiveness of tLaSDI, which exhibits robust generalization ability, even in extrapolation. In addition, an intriguing correlation is empirically observed between a quantity from tLaSDI in the latent space and the behaviors of the full-state solution.

Cheung, Siu Wun↗

ninterp: N-dimensional interpolation Rust crate [SWR-25-25]

The ninterp crate provides multivariate interpolation over a regular, sorted, nonrepeating grid of any dimensionality. A variety of interpolation strategies are implemented, however more are likely to be added. Extrapolation beyond the range of the supplied coordinates is supported for 1-D linear interpolators, using the slope of the nearby points. There are hard-coded interpolators for lower dimensionalities (up to N = 3) for better runtime performance. All interpolation is handled through instances of the Interpolator enum, with the selected tuple variant containing relevant data. Interpolation is executed by calling Interpolator::interpolate.

Carow, Kyle↗

Regional Oil and gas Aerial Methane Synthesis model (ROAMS) v2.0

The Regional Oil and gas Aerial Methane Synthesis model is a tool to convert the results of wide-area, source-resolved aerial methane remote sensing surveys of oil and natural gas infrastructure in a given region into methane emissions inventories (estimates of the magnitude and breakdown of methane emissions from the surveyed infrastructure). The tool leverages databases of source-resolved methane emissions detected in aerial surveys, aerial survey coverage information (which areas were measured and when), data summarizing surveyed oil and natural gas infrastructure and production (derived from third-party databases), as well as state-of-the-art mechanistic emissions simulation tools to characterize emissions too small for the aerial system to see. The regional methane emissions estimates produced by this tool are much more granular in both space and asset type than common satellite- or flux tower-based regional estimates. Unlike other tools for converting site-level measurements into regional emissions estimates, our unique geostatistical approach integrates aerially measured emissions with limited need for statistical extrapolation, which can be highly sensitive to modeler assumptions. As a result, ROAMS-based estimates of regional methane emissions from oil and gas activity are widely viewed as highly credible, as evidenced by the success of Dr. Sherwin's recent paper in Nature.

Sherwin, Evan [Lawrence Berkeley National Laborato↗

Regional Oil and gas Aerial Methane Synthesis model (Analytica) (ROAMS Analytica) v1.5.2

The Regional Oil and gas Aerial Methane Synthesis model (Analytica) is a tool to convert the results of wide-area, source-resolved aerial methane remote sensing surveys of oil and natural gas infrastructure in a given region into methane emissions inventories (estimates of the magnitude and breakdown of methane emissions from the surveyed infrastructure). This version is written in the Analytica programming language, and this version accompanies a correction in preparation for submission to Sherwin et al. 2024 (Nature). The tool leverages databases of source-resolved methane emissions detected in aerial surveys, aerial survey coverage information (which areas were measured and when), data summarizing surveyed oil and natural gas infrastructure and production (derived from third-party databases), as well as state-of-the-art mechanistic emissions simulation tools to characterize emissions too small for the aerial system to see. The regional methane emissions estimates produced by this tool are much more granular in both space and asset type than common satellite- or flux tower-based regional estimates. Unlike other tools for converting site-level measurements into regional emissions estimates, our unique geostatistical approach integrates aerially measured emissions with limited need for statistical extrapolation, which can be highly sensitive to modeler assumptions. As a result, ROAMS-based estimates of regional methane emissions from oil and gas activity are widely viewed as highly credible, as evidenced by the success of Dr. Sherwin's recent paper in Nature.

Sherwin, Evan [Lawrence Berkeley National Laborato↗

Single hepatocytes show persistence and transcriptional inactivity of hepatitis B

There is no cure for the more than 270 million people chronically infected with HBV. Nucleos(t)ide analogs (NUCs), the mainstay of anti-HBV treatment, block HBV reverse transcription. NUCs do not eliminate the intranuclear covalently closed circular DNA (cccDNA), from which viral RNAs, including pregenomic RNA (pgRNA), are transcribed. A key gap in designing a cure is understanding how NUCs affect HBV replication and transcription because serum markers yield an incomplete view of intrahepatic HBV. We applied single-cell laser capture microdissection and droplet digital PCR to paired liver biopsies collected from 5 HBV/HIV-coinfected persons who took NUCs over 2–4 years. From biopsy 1 to 2, proportions of HBV-infected hepatocytes declined with adherence to NUC treatment (P < 0.05); we extrapolated that eradication of HBV will take over 10 decades with NUCs in these participants. In individual hepatocytes, pgRNA levels diminished 28- to 73-fold during NUC treatment, corresponding with decreased tissue HBV core antigen staining (P < 0.01). In 4 out of 5 participants, hepatocytes with cccDNA but undetectable pgRNA (transcriptionally inactive) were present, and these were enriched in 3 participants during NUC treatment. Further work to unravel mechanisms of cccDNA transcriptional inactivation may lead to therapies that can achieve this in all hepatocytes, resulting in a functional cure.

59 BASIC BIOLOGICAL SCIENCES↗

Efficient Probabilistic Prediction and Uncertainty Quantification of Tropical Cyclone–Driven Storm Tides and Inundation

Abstract This study proposes and assesses a methodology to obtain high-quality probabilistic predictions and uncertainty information of near-landfall tropical cyclone–driven (TC-driven) storm tide and inundation with limited time and resources. Forecasts of TC track, intensity, and size are perturbed according to quasi-random Korobov sequences of historical forecast errors with assumed Gaussian and uniform statistical distributions. These perturbations are run in an ensemble of hydrodynamic storm tide model simulations. The resulting set of maximum water surface elevations are dimensionality reduced using Karhunen–Loève expansions and then used as a training set to develop a polynomial chaos (PC) surrogate model from which global sensitivities and probabilistic predictions can be extracted. The maximum water surface elevation is extrapolated over dry points incorporating energy head loss with distance to properly train the surrogate for predicting inundation. We find that the surrogate constructed with third-order PCs using elastic net penalized regression with leave-one-out cross validation provides the most robust fit across training and test sets. Probabilistic predictions of maximum water surface elevation and inundation area by the surrogate model at 48-h lead time for three past U.S. landfalling hurricanes (Irma in 2017, Florence in 2018, and Laura in 2020) are found to be reliable when compared to best track hindcast simulation results, even when trained with as few as 19 samples. The maximum water surface elevation is most sensitive to perpendicular track-offset errors for all three storms. Laura is also highly sensitive to storm size and has the least reliable prediction. Significance Statement The purpose of this study is to develop and evaluate a methodology that can be used to provide high-quality probabilistic predictions of hurricane-induced storm tide and inundation with limited time and resources. This is important for emergency management purposes during or after the landfall of hurricanes. Our results show that sampling forecast errors using quasi-random sequences combined with machine learning techniques that fit polynomial functions to the data are well suited to this task. The polynomial functions also have the benefit of producing exact sensitivity indices of storm tide and inundation to the forecasted hurricane properties such as path, intensity, and size, which can be used for uncertainty estimation. The code implementing the presented methodology is publicly available on GitHub.

54 ENVIRONMENTAL SCIENCES↗

Deep Learning Parameterization of Vertical Wind Velocity Variability via Constrained Adversarial Training

Atmospheric models with typical resolution in the tenths of kilometers cannot resolve the dynamics of air parcel ascent, which varies on scales ranging from tens to hundreds of meters. Small-scale wind fluctuations are thus characterized by a subgrid distribution of vertical wind velocity W with standard deviation σ W . The parameterization of σ W is fundamental to the representation of aerosol–cloud interactions, yet it is poorly constrained. Using a novel deep learning technique, this work develops a new parameterization for σ W merging data from global storm-resolving model simulations, high-frequency retrievals of W , and climate reanalysis products. The parameterization reproduces the observed statistics of σ W and leverages learned physical relations from the model simulations to guide extrapolation beyond the observed domain. Incorporating observational data during the training phase was found to be critical for its performance. The parameterization can be applied online within large-scale atmospheric models, or offline using output from weather forecasting and reanalysis products.

54 ENVIRONMENTAL SCIENCES↗

Development of a Full-Scale Connected U-Net for Reflectivity Inpainting in Spaceborne Radar Blind Zones

CloudSat’s Cloud Profiling Radar is a valuable tool for remotely monitoring high-latitude snowfall, but its ability to observe hydrometeor activity near the Earth’s surface is limited by a radar blind zone caused by ground clutter contamination. This study presents the development of a deeply supervised U-Net-style convolutional neural network to predict cold season reflectivity profiles within the blind zone at two Arctic locations. The network learns to predict the presence and intensity of near-surface hydrometeors by coupling latent features encoded in blind zone-aloft clouds with additional context from collocated atmospheric state variables (i.e., temperature, specific humidity, and wind speed). Results show that the U-Net predictions outperform traditional linear extrapolation methods, with low mean absolute error, a 38% higher Sørensen–Dice coefficient, and vertical reflectivity distributions 60% closer to observed values. The U-Net is also able to detect the presence of near-surface cloud with a critical success index (CSI) of 72% and cases of shallow cumuliform snowfall and virga with 18% higher CSI values compared to linear methods. An explainability analysis shows that reflectivity information throughout the scene, especially at cloud edges and at the 1.2-km blind zone threshold, along with atmospheric state variables near the tropopause, are the most significant contributors to model skill. This surface-trained generative inpainting technique has the potential to enhance current and future remote sensing precipitation missions by providing a better understanding of the nonlinear relationship between blind zone reflectivity values and the surrounding atmospheric state.

54 ENVIRONMENTAL SCIENCES↗

A Lagrangian Study of Interfaces at the Edges of Cumulus Clouds

Abstract Interfaces at the edge of an idealized, nonprecipitating, warm cloud are studied using direct numerical simulation (DNS) complemented with a Lagrangian particle tracking routine. Once a shell has formed, four zones can be distinguished: the cloud core, visible shell, invisible shell, and the environment. The union of the visible and invisible regions is the shell commonly referred to in literature. The boundary between the invisible shell and the environment is the turbulent–nonturbulent interface (TNTI), which is typically not considered in cloud studies. Three million particles were seeded homogeneously across the domain and properties were recorded along individual trajectories. The results demonstrate that the traditional cloud boundary (separating cloudy and noncloudy regions using thresholds applied on liquid condensate or updraft velocity) are some distance away from the TNTI. Furthermore, there is no dynamic difference between the traditional liquid-condensate boundary and the region extending to the TNTI. However, particles crossing the TNTI exhibit a sharp jump in enstrophy and a smooth increase in buoyancy. The traditional cloud boundary coincides with the location of minimum buoyancy in the shell. The shell premixes the entraining and detraining air and analysis reveals a highly skewed picture of entrainment and detrainment at the traditional cloud boundary. A preferential entrainment of particles with velocity and specific humidity higher than the mean values in the shell is observed. Large-eddy simulation of a more realistic setup detects an interface with similar properties using the same thresholds as in the DNS, indicating that the DNS results extrapolate beyond their idealized conditions.

54 ENVIRONMENTAL SCIENCES↗

The role of shale gas in shaping the U.S. long-run CO 2 emissions

The shale gas boom in the U.S. has lowered the U.S. CO 2 emissions in recent years mainly through substitution of gas for coal in power generation. Will the shale gas boom reduce the emissions in the long-run as well? To study this, we consider a counterfactual without the shale gas boom based on a general equilibrium modeling for the 2011 U.S. economy. To enhance the power sector modeling, the supply responses of coal-fired and gas-fired generations are calibrated to existing research. We find that if gas prices remain at 2007 levels in 2011, only a model setting that allows very little reduction in electricity demand, reflecting a short-run demand response, generates an increase in economy-wide emissions. For all other cases, the higher gas price under the counterfactual will have a dampening effect on economic activities and consequently lowers economy-wide emissions, even though the power sector emissions may increase due to the gas-to-coal switch. In other words, without any policy intervention, although the shale gas boom could reduce emissions in the short run, it may lead to higher emissions in the long run if the low gas prices persist. Our finding suggests that extrapolating the current decline in emissions due to the shale gas boom to the distant future could be misleading. Instead, if curbing emissions is the goal, rather than depending upon the cheap gas, policies and measures for cutting emissions remain imperative.

Chen, Y. -H. Henry↗

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

54 ENVIRONMENTAL SCIENCES↗

Systematic correction of the density functional theory spectra via a quantum Monte Carlo approach

Numerical outputs and driver scripts supporting auxiliary-boson corrected diffusion Monte Carlo (ABCDMC) benchmarks on second-row neutral atoms, cations, and dications, plus a C2 molecule active-space study. Includes NIST reference energies, ABCDMC timestep extrapolation summaries, orbital generation inputs, singles-only CASCI driver scripts, an O-atom basis-set convergence study, and the PyQMC boson code snapshot used for the calculations.

36 MATERIALS SCIENCE↗