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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 325 records · Page 18
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DOE OSTI2023

Improved quality metrics for association and reproducibility in chromatin accessibility data using mutual information

Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when comparing values between replicated sequencing experiments that probe chromatin accessibility, such as assays for transposase-accessible chromatin via sequencing (ATAC-seq). Such data can possess several regions across the human genome with little to no sequencing depth and are thus non-normal with a large portion of zero values. Despite distributed use in the epigenomics field, few studies have evaluated and benchmarked how correlation and association statistics behave across ATAC-seq experiments with known differences or the effects of removing specific outliers from the data. Here, we developed a computational simulation of ATAC-seq data to elucidate the behavior of correlation statistics and to compare their accuracy under set conditions of reproducibility. Using these simulations, we monitored the behavior of several correlation statistics, including the Pearson’s R and Spearman’s ρ coefficients as well as Kendall’s τ and Top–Down correlation. We also test the behavior of association measures, including the coefficient of determination R 2 , Kendall’s W, and normalized mutual information. Our experiments reveal an insensitivity of most statistics, including Spear man’s ρ, Kendall’s τ, and Kendall’s W, to increasing differences between simulated ATAC-seq replicates. The removal of co-zeros (regions lacking mapped sequenced reads) between simulated experiments greatly improves the estimates of correlation and association. After removing co-zeros, the R 2 coefficient and normalized mutual information display the best performance, having a closer one-to-one relationship with the known portion of shared, enhanced loci between simulated replicates. When comparing values between experimental ATAC-seq data using a random forest model, mutual information best predicts ATAC-seq replicate relationships. Collectively, this study demonstrates how measures of correlation and association can behave in epigenomics experiments. We provide improved strategies for quantifying relationships in these increasingly prevalent and important chromatin accessibility assays.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Effective Resistivity in Relativistic Collisionless Reconnection

Magnetic reconnection can power spectacular high-energy astrophysical phenomena by producing nonthermal energy distributions in highly magnetized regions around compact objects. By means of two-dimensional fully kinetic particle-in-cell (PIC) simulations, we investigate relativistic collisionless plasmoid-mediated reconnection in magnetically dominated pair plasmas with and without a guide field. In X-points, where diverging flows result in a nondiagonal thermal pressure tensor, a finite residence time for particles gives rise to a localized collisionless effective resistivity. Here, for the first time for relativistic reconnection in a fully developed plasmoid chain, we identify the mechanisms driving the nonideal electric field using a full Ohm law by means of a statistical analysis based on our PIC simulations. We show that the nonideal electric field is predominantly driven by gradients of nongyrotropic thermal pressures. We propose a kinetic physics motivated nonuniform effective resistivity model that is negligible on global scales and becomes significant only locally in X-points. It captures the properties of collisionless reconnection with the aim of mimicking its essentials in nonideal magnetohydrodynamic descriptions. This effective resistivity model provides a viable opportunity to design physically grounded global models for reconnection-powered high-energy emission.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Molecular dynamics simulation of metallic Al–Ce liquids using a neural network machine learning interatomic potential

Al-rich Al-Ce alloys have the possibility of replacing heavier steel and cast-irons for use in high-temperature applications. Knowledge about the structures and properties of Al-Ce alloys at liquid state is vital for optimizing the manufacture process to produce desired allows. However, reliable molecular dynamics simulation of Al-Ce alloy systems remains a great challenge due to the lack of accurate Al-Ce interatomic potential. In this work, an artificial neural network (ANN) deep machine learning (ML) method is used to develop a reliable interatomic potential for Al-Ce alloy. Ab initio molecular dynamics (AIMD) simulation data on Al-Ce liquid with small unit cell (~200 atoms) and on the known Al-Ce crystalline compounds are collected to train the interatomic potential using ANN-ML. The obtained ANN-ML model reproduces well the energies, forces, and atomic structure of Al 90 Ce 10 liquid and crystalline phases of Al-Ce compounds in comparison with ab initio results. The developed ANN-ML potential is applied in molecular dynamics simulations to study the structures and properties of metallic Al 90 Ce 10 liquid, which would provide useful insight for guiding experimental process to produce desired Al-Ce allows.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Model-observation discrepancies in Arctic moisture intrusions: causes and pathways for improved simulation

Arctic moisture intrusions (MIs), narrow filaments of strong moisture transport, are key drivers of poleward moisture flux and Arctic weather extremes, yet their representation in climate models is poorly understood. Using a new Arctic MI detection algorithm, we document persistent biases across three CMIP generations (CMIP3–CMIP6): models overestimate MI occurrence over the Pacific sector and underestimate it over the Atlantic sector. These errors stem from misrepresented midlatitude westerly jets, with an equatorward North Atlantic jet associated with too few Atlantic MIs, and a poleward, weakened North Pacific jet linked to too many Pacific MIs. Experiments that correct sea surface temperature and sea ice concentration biases and increase atmospheric resolution improve jet structure and MI statistics, while a cloud-locking simulation indicates that better high-frequency cloud–radiation–circulation interactions can yield further gains. Our results clarify pathways to reducing long-standing MI and jet biases, providing guidance for improving simulations of Arctic and midlatitude climate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Multiscale spatial analysis of fracture arrangement and pattern reconstruction using Ripley's K-function

This work presents novel multiscale spatial data analytics using Ripley's K-function, as a measure of spatial interaction, to study one-dimensional arrangement of fractures. Fracture spatial arrangements are classified into clustered, anticlustered, or indistinguishable from random by testing statistical significance of the calculated Ripley's K-function. Characterizations of fracture arrangements are performed as a function of length scale and position. Analysis of the K-function along the study interval identifies where fracture clustering and anticlustering occur. Here, a simulation technique is also introduced here to statistically reconstruct spatial arrangements and to generate fracture realizations that are spatially similar to the fractures observed in the field. With this simulation technique, one can also fill spatial gaps in fracture measurements where data are absent, unreliable, or unused. Synthetic as well as field-measured 1D fracture datasets are used for testing and demonstration. Methods introduced in this work can be readily applied to fracture datasets observed in outcrops, borehole image logs, and cores.

58 GEOSCIENCES↗
DOE OSTI2022

Computation of conventional and alternative jet fuel sensitivity to lean blowout

Large Eddy Simulations (LES) are performed to compute the sensitivity of a conventional (A-2) and an alternate bio-jet (C-1) fuel to Lean Blowout (LBO). A realistic aviation gas turbine engine combustor configuration is considered. Reliable experimental LBO data and OH* chemiluminescence data for the conventional and alternate jet fuel in the combustor configuration have recently become available. The present work utilizes a highly automated, on-the-fly meshing strategy, along with adaptive mesh refinement, to demonstrate the feasibility of capturing the realistic combustion processes. A Lagrangian framework, with initial conditions specified using measurements of spray statistics, is used to model the fuel spray. Newly developed compact reaction mechanisms based on fuel surrogates are validated for the A-2 and the C-1 fuels. The compact reaction mechanisms are implemented using a detailed finite rate chemistry solver. Spray statistics computed by the present LES simulations compare well with available measurements at stable flame conditions near the lean blowout limit. The computed shape of the stable flame as represented by line integrated OH concentrations compares well with the experimental OH* chemiluminescence data. Lean blowout is reached by gradually decreasing the fuel flow rate in the computations, similar to that in the experiments. The results of the LES simulations effectively capture the fuel composition effects and estimate the sensitivity of the LBO limits to the fuel type. The computed trends in LBO limits agree within engineering accuracy with the experimental results for conventional and alternative aviation fuels. The methodology for predicting the fuel composition effects on the lean blowout limits in a fully resolved realistic, complex combustor is established for the first time.

Adaptive mesh refinement↗
DOE OSTI2023

The Aemulus Project. V. Cosmological Constraint from Small-scale Clustering of BOSS Galaxies

We analyze clustering measurements of BOSS galaxies using a simulation-based emulator of two-point statistics. We focus on the monopole and quadrupole of the redshift-space correlation function, and the projected correlation function, at scales of 0.1 ~ 60 h -1 Mpc. Although our simulations are based on wCDM with general relativity (GR), we include a scaling parameter of the halo velocity field, γ f , defined as the amplitude of the halo velocity field relative to the GR prediction. We divide the BOSS data into three redshift bins. After marginalizing over other cosmological parameters, galaxy bias parameters, and the velocity scaling parameter, we find fσ 8 (z = 0.25) = 0.413 ± 0.031, fσ 8 (z = 0.4) = 0.470 ± 0.026, and fσ 8 (z = 0.55) = 0.396 ± 0.022. Compared with Planck observations using a flat Lambda cold dark matter model, our results are lower by 1.9σ, 0.3σ, and 3.4σ, respectively. These results are consistent with other recent simulation-based results at nonlinear scales, including weak lensing measurements of BOSS LOWZ galaxies, two-point clustering of eBOSS LRGs, and an independent clustering analysis of BOSS LOWZ. All these results are generally consistent with a combination of ${\gamma }_{f}^{1/2}{\sigma }_{8}\approx 0.75$. We note, however, that the BOSS data is well fit assuming GR, i.e., γf = 1. We cannot rule out an unknown systematic error in the galaxy bias model at nonlinear scales, but near-future data and modeling will enhance our understanding of the galaxy–halo connection, and provide a strong test of new physics beyond the standard model.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Direct numerical simulations of three-component Rayleigh–Taylor mixing and an improved model for multicomponent reacting mixtures

We present direct numerical simulations of a three-layer Rayleigh–Taylor instability (RTI) problem with a configuration based on the experiments of Suchandra & Ranjan ( J. Fluid Mech. , vol. 974, 2023, A35) and Jacobs & Dalziel ( J. Fluid Mech. , vol. 542, 2005, pp. 251–279). The problem consists of a layer of light fluid between two layers of heavy fluid with an Atwood number of 0.3. These simulations are first validated through comparison with available experimental data. The validated simulations are then utilized to analyse statistics in this three-component flow. First, length scales are examined utilizing spectra and two-point spatial correlations of velocity and species concentration fluctuations. Next, joint probability density functions (p.d.f.s) of species concentration are compared against several model p.d.f.s representing generalizations of the bivariate beta distribution. Notably, the joint p.d.f.s do not appear to be accurately described by a Dirichlet distribution, indicating the marginal distributions do not conform to a beta distribution. Finally, similarity of the present configuration to three-component mixing found in inertial confinement fusion (ICF) applications is exploited to develop and validate an improved model for the impact of multicomponent mixing on thermonuclear (TN) reaction rates. A single time instant from the present simulations is chosen for a TN burn calculation under the hypothetical assumption of ICF materials and temperatures. Total TN output from this second calculation is then compared against the prediction of the improved model. The new model is found to accurately predict TN reaction rates in both premixed and non-premixed configurations.

42 ENGINEERING↗
DOE OSTI2023

Sequence Design of Random Heteropolymers as Protein Mimics

Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo–Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Blinded challenge for precision cosmology with large-scale structure: Results from effective field theory for the redshift-space galaxy power spectrum

An accurate theoretical template for the galaxy power spectrum is key for the success of ongoing and future spectroscopic surveys. We examine to what extent the effective field theory (EFT) of large-scale structure is able to provide such a template and correctly estimate cosmological parameters. To that end, we initiate a blinded challenge to infer cosmological parameters from the redshift-space power spectrum of high-resolution mock catalogs mimicking the BOSS galaxy sample but covering a 100 times larger cumulative volume. This gigantic simulation volume allows us to separate systematic bias due to theoretical modeling from the statistical error due to sample variance. The challenge is to measure three unknown input parameters used in the simulation: the Hubble constant, the matter density fraction, and the clustering amplitude. We present analyses done by two independent teams, who have fitted the mock simulation data generated by yet another independent group. This allows us to avoid any confirmation bias by analyzers and to pin down possible tuning of the specific EFT implementations. Both independent teams have recovered the true values of the input parameters within subpercent statistical errors corresponding to the total simulation volume.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Long-term single-column model intercomparison of diurnal cycle of precipitation over midlatitude and tropical land

General Circulation Models (GCMs) have for decades exhibited difficulties in modelling the diurnal cycle of precipitation (DCP). This issue can be related to inappropriate representation of the processes controlling sub-diurnal phenomena like convection. In this study, 11 single-column versions of GCMs are used to investigate the interactions between convection and environmental conditions, processes that control nocturnal convections, and the transition from shallow to deep convection on a diurnal time-scale. Long-term simulations are performed over two continental land sites: the Southern Great Plains (SGP) in the USA for 12 summer months from 2004 to 2015 and the Manacapuru site at the central Amazon (MAO) in Brazil for two full years from 2014 to 2015. The analysis is done on two regimes: afternoon convective regime and nocturnal precipitation regime. Most models produce afternoon precipitation too early, likely due to the missing transition of shallow-to-deep convection in these models. At SGP, the unified convection schemes better simulate the onset time of precipitation. At MAO, models produce the heating peak in a much lower level compared with observation, indicating too shallow convection in the models. For nocturnal precipitation, models that produce most of nocturnal precipitation all allow convection to be triggered above the boundary layer. This indicates the importance of model capability to detect elevated convection for simulating nocturnal precipitation. Sensitivity studies indicate that (a) nudging environmental variables towards observations has a minor impact on DCP, (b) unified treatment of shallow and deep convection and the capability to capture mid-level convection can help models better capture DCP, and (c) the interactions of the atmosphere with other components in the climate system (e.g. land) are also important for DCP simulations in coupled models. Finally, these results provide long-term statistical insights on which physical processes are essential in climate models to simulate DCP.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Enhanced climate reproducibility testing with false discovery rate correction

Simulating the Earth's climate is an important and complex problem, thus climate models are similarly complex, comprised of millions of lines of code. In order to appropriately utilize the latest computational and software infrastructure advancements in Earth system models running on modern hybrid computing architectures to improve their performance, precision, accuracy, or all three; it is important to ensure that model simulations are repeatable and robust. This introduces the need for establishing statistical or non-bit-for-bit reproducibility, since bit-for-bit reproducibility may not always be achievable. Here, we propose a short-simulation ensemble-based test for an atmosphere model to evaluate the null hypothesis that modified model results are statistically equivalent to that of the original model. We implement this test in version 2 of the US Department of Energy's Energy Exascale Earth System Model (E3SM). The test evaluates a standard set of output variables across the two simulation ensembles and uses a false discovery rate correction to account for multiple testing. The false positive rates of the test are examined using re-sampling techniques on large simulation ensembles and are found to be lower than the currently implemented bootstrapping-based testing approach in E3SM. We also evaluate the statistical power of the test using perturbed simulation ensemble suites, each with a progressively larger magnitude of change to a tuning parameter. The new test is generally found to exhibit more statistical power than the current approach, being able to detect smaller changes in parameter values with higher confidence.

Kelleher, Michael E. [Oak Ridge National Laborator↗
DOE OSTI2021

The microscopic mechanism of bulk melting of ice

We study the initial stages of homogeneous melting of a hexagonal ice crystal at coexistence and at moderate superheating. Our trajectory-based computer simulation approach provides a comprehensive picture of the events that lead to melting, from the initial accumulation of 5+7 defects, via the formation of L-D and interstitial-vacancy pairs, to the formation of a liquid nucleus. Of the different types of defects that we observe to be involved in melting, a particular kind of 5+7 type defect (type 5) plays a prominent role as it often forms prior to the formation of the initial liquid nucleus and close to the site where the nucleus forms. Hence, like other solids, ice homogeneously melts via the prior accumulation of defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Illustrating galaxy–halo connection in the DESI era with illustrisTNG

ABSTRACT We employ the hydrodynamical simulation illustrisTNG to inform the galaxy–halo connection of the Luminous Red Galaxy (LRG) and Emission Line Galaxy (ELG) samples of the Dark Energy Spectroscopic Instrument (DESI) survey at redshift z ∼ 0.8. Specifically, we model the galaxy colours of illustrisTNG and apply sliding DESI colour–magnitude cuts, matching the DESI target densities. We study the halo occupation distribution (HOD) model of the selected samples by matching them to their corresponding dark matter haloes in the illustrisTNG dark matter run. We find the HOD of both the LRG and ELG samples to be consistent with their respective baseline models, but also we find important deviations from common assumptions about the satellite distribution, velocity bias, and galaxy secondary biases. We identify strong evidence for concentration-based and environment-based occupational variance in both samples, an effect known as ‘galaxy assembly bias’. The central and satellite galaxies have distinct dependencies on secondary halo properties, showing that centrals and satellites have distinct evolutionary trajectories and should be modelled separately. These results serve to inform the necessary complexities in modelling galaxy–halo connection for DESI analyses and also prepare for building high-fidelity mock galaxies. Finally, we present a shuffling-based clustering analysis that reveals a 10–15 ${{\ \rm per\ cent}}$ excess in the LRG clustering of modest statistical significance due to secondary galaxy biases. We also find a similar excess signature for the ELGs, but with much lower statistical significance. When a larger hydrodynamical simulation volume becomes available, we expect our analysis pipeline to pinpoint the exact sources of such excess clustering signatures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Viscosity in water from first-principles and deep-neural-network simulations

Abstract We report on an extensive study of the viscosity of liquid water at near-ambient conditions, performed within the Green-Kubo theory of linear response and equilibrium ab initio molecular dynamics (AIMD), based on density-functional theory (DFT). In order to cope with the long simulation times necessary to achieve an acceptable statistical accuracy, our ab initio approach is enhanced with deep-neural-network potentials (NNP). This approach is first validated against AIMD results, obtained by using the Perdew–Burke–Ernzerhof (PBE) exchange-correlation functional and paying careful attention to crucial, yet often overlooked, aspects of the statistical data analysis. Then, we train a second NNP to a dataset generated from the Strongly Constrained and Appropriately Normed (SCAN) functional. Once the error resulting from the imperfect prediction of the melting line is offset by referring the simulated temperature to the theoretical melting one, our SCAN predictions of the shear viscosity of water are in very good agreement with experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Gaussian Process Emulators for Volcanic Ash Dispersion Model Tephra2

It is necessary to predict volcanic ash deposition since falling ash is harmful to human activities. Because simulators built for this purpose are computationally expensive, it is popular to use statistical emulators for geophysical hazard analyses, where a large number of simulations are required. Gaussian stochastic process emulators are able to approximate expensive simulations in an accurate and efficient way. Using a relatively small number of simulation runs, a well-trained emulator can accurately predict simulation outputs at massive new input points in a few seconds. Under different explosive eruption conditions, we constructed Gaussian stochastic process emulators for Tephra2, a simulation tool for estimating the accumulation of volcanic ash over a region. Historical wind records are used as input wind data, without assuming a Gaussian wind speed profile or common wind direction among elevations. While there are several inputs for Tephra2, we use no more than three physically motivated variables as emulator inputs to reduce the computational cost of emulations. The emulator outputs predict the mass of tephra per unit area at 50281 grid points around a predetermined vent location.

58 GEOSCIENCES↗
DOE OSTI2024

SCALE inventory and reactivity analysis as part of the Hermes 2021 PSAR review

The readiness of SCALE for comprehensive studies of pebble-bed reactors has been demonstrated through detailed analysis of a fluoride salt–cooled, high-temperature pebble-bed reactor (PB-FHR). The methods developed for pebble-bed reactor modeling in SCALE, particularly for inventory generation, have proven effective in gaining insights into the reactor physics of this advanced reactor. Excellent agreement with another code package has been observed, further highlighting SCALE’s strong performance. The SCALE results supported the US Nuclear Regulatory Commission’s construction permit application review of the Hermes low-power PB-FHR demonstration reactor. A SCALE model of the Hermes reactor was developed at Oak Ridge National Laboratory using information from the Preliminary Safety Analysis Report (PSAR) and supplemented with publicly available data. SCALE reactivity coefficient simulations reproduced PSAR results within 1σ statistical uncertainties. Sensitivity studies emphasized the importance of graphite specifications for accurate keff predictions.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

Subsurface Nitrogen Dissociation Kinetics in Lithium Metal from Metadynamics

The dissociation of molecular nitrogen in lithium is of interest for several promising technologies, such as the catalytic synthesis of ammonia in ambient or mild conditions. In this work we simulate nitrogen dissociation in the lithium BCC (110) surface at ambient and elevated temperatures using density functional theory (DFT) metadynamics simulations. The rate constants at temperatures of 300, 400, and 500 K are calculated by statistical analysis of the reaction time distributions from the accelerated simulations. This approach finds and estimates rate constants for transition pathways out of the initial state; the required input is the stable initial state and a reasonable choice of collective variable. A single collective variable is used in this case: the N–N distance. The results are robust to changes in metadynamics parameters, and the reaction time distributions follow the expected exponential distribution. We show that the metadynamics-derived rate constants are in agreement with results from the conventional harmonic approximation approach using a climbing image nudged elastic band (NEB) transition state search. The reaction barriers from metadynamics and the NEB/harmonic approximation agree to within 0.02–0.04 eV at all temperatures studied. This paper demonstrates that the harmonic approximation provides an accurate description of the rate constants for nitrogen dissociation in lithium metal, even at temperatures near or above the melting point of lithium, lending credence to previous and future theoretical studies using this approximation. Moreover, this work demonstrates a step toward the automated exploration and discovery of reaction mechanisms and associated rate constants for elementary surface-catalyzed reactions using DFT-based metadynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗