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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 91 records · Page 5

Toward Accelerating Discovery via Physics-Driven and Interactive Multifidelity Bayesian Optimization

Both computational and experimental material discovery bring forth the challenge of exploring multidimensional and often nondifferentiable parameter spaces, such as phase diagrams of Hamiltonians with multiple interactions, composition spaces of combinatorial libraries, processing spaces, and molecular embedding spaces. Often these systems are expensive or time consuming to evaluate a single instance, and hence classical approaches based on exhaustive grid or random search are too data intensive. This resulted in strong interest toward active learning methods such as Bayesian optimization (BO) where the adaptive exploration occurs based on human learning (discovery) objective. However, classical BO is based on a predefined optimization target, and policies balancing exploration and exploitation are purely data driven. In practical settings, the domain expert can pose prior knowledge of the system in the form of partially known physics laws and exploration policies often vary during the experiment. Here, we propose an interactive workflow building on multifidelity BO (MFBO), starting with classical (data-driven) MFBO, then expand to a proposed structured (physics-driven) structured MFBO (sMFBO), and finally extend it to allow human-in-the-loop interactive interactive MFBO (iMFBO) workflows for adaptive and domain expert aligned exploration. These approaches are demonstrated over highly nonsmooth multifidelity simulation data generated from an Ising model, considering spin–spin interaction as parameter space, lattice sizes as fidelity spaces, and the objective as maximizing heat capacity. Detailed analysis and comparison show the impact of physics knowledge injection and real-time human decisions for improved exploration with increased alignment to ground truth. Here, the associated notebooks allow to reproduce the reported analyses and apply them to other systems.

97 MATHEMATICS AND COMPUTING↗

Finite-frequency modeling of regional tropospheric infrasound using realistic atmospheres and terrain

Infrasonic waves have been observed to propagate to regional (greater than 15 km) distances through the troposphere. Infrasound propagation in the geometric acoustics approximation has shown that realistic terrain can scatter acoustic energy from tropospheric ducts; however, ray methods cannot intrinsically capture finite-frequency behavior such as diffraction. A two-dimensional finite-difference time-domain (FDTD) method has been developed to solve linearized equations for infrasound propagation with realistic terrain. Acoustic wave propagation over 100 km with both flat terrain and a Gaussian hill was first simulated in order to compare finite-frequency propagation with ray predictions. The effects of realistic terrain and atmospheres on infrasound signals from a 2012 surface explosion at the Utah Testing and Training Range are then investigated. Propagation through the troposphere is suggested by array processing results, but eigenrays are not predicted due to weak to nonexistent ducting conditions. FDTD modeling suggests that the inclusion of terrain and finite frequency effects helps explain much of the observed signal in a realistic scenario. Furthermore, these results suggest that geometric acoustics may underestimate propagation through the troposphere, and that recorded waveforms at regional distances may be noticeably affected by terrain.

58 GEOSCIENCES↗

Estimation Methodology to Evaluate Hypothetical Downwind Impacts from Fusion Plants

The continuing move toward establishing fusion systems for power generation and the associated research to that end is prompting examination of the potential health and safety impacts of such plants to the environment and human health. As many fusion facilities will have tritium inventories on site as part of the fusion fuel, evaluating the potential for downwind impacts from fusion facilities or power plants resulting from accident or routine emissions is a general requirement for assessing location and impacts to workers and the public. As part of siting considerations and permitting, the fusion facilities would be evaluated for potential for downwind concentration and dose impacts. For accident assessment scenarios, the downwind impacts are usually modeled as an instantaneous (or near-instantaneous) release of material transported following the wind. A range of meteorological conditions are usually assessed to determine a bounding case which results in a dose exceeding a specified threshold (e.g., 95 th or 99 th percentile; DOE 2015). This report provides initial estimates of the downwind dose impacts from a potential tritium release at a fusion power plant-relevant facility and identifies potential distances required to limit impacts to nearby population. This effort is meant to provide a bounding analysis and theoretical understanding of impacts of tritium releases for facilities subject to various environmental and atmospheric conditions. Using a Gaussian dispersion model to simulate a brief plume, downwind concentration and dose is projected for tritium oxide. Releases are assumed to consist entirely of tritium oxide due to the increased dose impacts from the oxide form relative to the elemental form of tritium. We also briefly identify how climatological conditions could potentially be used to support risk profile determination.

54 ENVIRONMENTAL SCIENCES↗

Weak-Form Latent Space Dynamics Identification

This software showcases the enhanced capabilities of the Latent Space Dynamics Identification (LaSDI) algorithm through the application of the weak form, resulting in WLaSDI. WLaSDI first compresses the data, then projects it onto test functions, and subsequently learns the local latent space models. Notably, WLaSDI demonstrates significantly improved robustness to noise. Using weak-form equation learning techniques, WLaSDI achieves local latent space modeling. Compared to the standard sparse identification of nonlinear dynamics (SINDy) used in LaSDI, the variance reduction of the weak form ensures robust and precise latent space recovery, enabling fast, robust, and accurate simulations. We demonstrate the efficacy of WLaSDI against LaSDI using several common benchmark examples, including viscid and inviscid Burgers', radial advection, and heat conduction. For instance, in 1D inviscid Burgers' simulations with up to 100% Gaussian white noise, WLaSDI maintains relative errors consistently below 6%, whereas LaSDI errors can exceed 10,000%. Similarly, in radial advection simulations, WLaSDI keeps relative errors below 16%, compared to potential errors of up to 10,000% with LaSDI. Additionally, WLaSDI achieves significant speedups, such as a 140X speedup in 1D Burgers' simulations compared to the corresponding full order model.

Choi, Youngsoo↗

Uniform Beam Simulation Technique for Beam Scans and Machine Learning Studies at Fermilab

Fermilab's neutrino facilities, including NuMI and the upcoming LBNF, use proton beams to produce positively and negatively charged pions and kaons. Detailed simulations are necessary to study particle interactions and beam propagation. To efficiently analyze beam scan effects, we propose a technique to generate multiple simulation samples with high statistics. These samples can be used to develop beamline simulation based machine learning applications. In this technique, we generate a uniformly distributed single simulation data sample. We calculate Gaussian weights for each beam configurations and apply them to post-processing measurements. In this poster, we demonstrate the proposed simulation technique. This technique reduces simulation time and computing resources significantly.

Wickremasinghe, Athula↗

Use of Remote Sensing and In-Situ Observations to Develop and Evaluate Improved Representations of Convection and Clouds for the ACME Model

The overachieving goal of the whole CMDV-MCS project is to improve understanding of warm season continental convection and to develop treatments of convection and microphysics capable of representing mesoscale convective systems (MCSs) features in large-scale models. Our tasks for this project contributing to the overachieving goal include: (1) Improve the ice nucleation formulation for MG2 and P3 cloud microphysics schemes; (2) Improve the treatment of subgrid dynamics and thermodynamics driving the ice nucleation in E3SM; and (3) Test the performance of improved ice microphysics in E3SM with observation data. In this project, we have (1) Improved the ice nucleation parameterization for MG2 and P3 in E3SM by implementing two advanced empirical parameterizations with connection to aerosols. The two deterministic heterogeneous ice nucleation parameterizations (i.e., DeMott et al., 2015; Niemand et al., 2012) were merged with the MG2 and P3 cloud microphysics schemes in E3SM. Long-term simulations were conducted to examine the impacts of these new parameterizations on simulated cloud properties; (2) Improved the treatment of subgrid dynamics and thermodynamics driving the ice nucleation in E3SM. We evaluated the double Gaussian PDF of vertical velocity simulated by the Cloud Layers Unified By Binormals (CLUBB) and the sub-column vertical velocity sampled from the Subgrid Importance Latin Hypercube Sampler (SILHS) in E3SM. We introduced the vertical velocity variance induced by topographic gravity waves for ice nucleation and droplet activation; and (3) Tested the performance of improved ice microphysics in E3SM with observation data. We tested the new treatments of ice nucleation in the single column model (SCM) mode for the stratiform mixed-phase clouds observed during 9-10 October 2004 in the DOE ARM Mixed-Phase Arctic Cloud Experiment (M-PACE) and for the convective clouds observed on 20 May 2011 in the Midlatitude Continental Convective Clouds Experiment (MC3E). Modeled ice nucleating particles (INPs) concentrations were compared against observations collected around the globe.

54 ENVIRONMENTAL SCIENCES↗

An ICME Modeling Framework for Titanium/Tungsten-Carbide Metal Matrix Composites

This report describes a collaborative project to develop a validated, predictive model for the high temperature mechanical properties of a titanium-matrix, tungsten-carbide/cobalt-reinforced metal matrix composite. The modeling approach was to first develop a detailed, microstructural model linking the material structure and the interfacial debonding properties to the effective properties of the material. The project then completed a throughput simulation campaign to generate a large number of simulations for discrete microstructures and different debonding parameters. Finally, the project trained a fast, Gaussian process surrogate model against this simulation database to provide a quick model linking the material compositions, structure, and processing parameters to the resulting material properties. This model was validated against high temperature tensile test data on a few particular composite compositions. The tests validate the model predictions for ultimate tensile strength and uniform elongation/ductility, meaning the final surrogate model can now be used to tune the material composition and processing parameters to identify optimal composite compositions for particular applications.

36 MATERIALS SCIENCE↗

Pathways and Mechanism of Caffeine Binding to Human Adenosine A 2A Receptor

Caffeine (CFF) is a common antagonist to the four subtypes of adenosine G-protein-coupled receptors (GPCRs), which are critical drug targets for treating heart failure, cancer, and neurological diseases. However, the pathways and mechanism of CFF binding to the target receptors remain unclear. In this study, we have performed all-atom-enhanced sampling simulations using a robust Gaussian-accelerated molecular dynamics (GaMD) method to elucidate the binding mechanism of CFF to human adenosine A 2A receptor (A 2A AR). Multiple 500–1,000 ns GaMD simulations captured both binding and dissociation of CFF in the A 2A AR. The GaMD-predicted binding poses of CFF were highly consistent with the x-ray crystal conformations with a characteristic hydrogen bond formed between CFF and residue N6.55 in the receptor. In addition, a low-energy intermediate binding conformation was revealed for CFF at the receptor extracellular mouth between ECL2 and TM1. While the ligand-binding pathways of the A 2A AR were found similar to those of other class A GPCRs identified from previous studies, the ECL2 with high sequence divergence serves as an attractive target site for designing allosteric modulators as selective drugs of the A 2A AR.

59 BASIC BIOLOGICAL SCIENCES↗

A Gaussian field approach to the planar electric double layer structures in electrolyte solutions

Here, in this work, the planar, electric, double-layer structures of non-polarizable electrodes in electrolyte solutions are studied with Gaussian field theory. A response function with two Yukawa functions is used to capture the electrostatic response of the electrolyte solution, from which the modified response function in the planar symmetry is derived analytically. The modified response function is further used to evaluate the induced charge density and the electrostatic potential near an electrode. The Gaussian field theory, combined with a two-Yukawa response function, can reproduce the oscillatory decay behavior of the electric potentials in concentrated electrolyte solutions. When the exact sum rules for the bulk electrolyte solutions and the electric double layers are used as constraints to determine the parameters of the response function, the Gaussian field theory could at least partly capture the nonlinear response effect of the surface charge density. Comparison with results for a planar electrode with fixed surface charge densities from molecular simulations demonstrates the validity of Gaussian field theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Absorptive Weak Plume Detection on Gaussian and Non-Gaussian Background Clutter

For additive signals on Gaussian clutter, the optimal detector is a linear matched filter that is adapted to the known signal and the covariance of the background. This adaptive matched filter is widely used for gas-phase plume detection, even though the effect of the plume on the background is not strictly additive. Here, a derivation of the matched filter for a strictly absorptive plume produces, in the weak plume limit, a quadratic filter. This quadratic matched filter is extended in two ways: an elliptically-contoured multivariate t distribution is used to generalize the Gaussian background clutter, and a generalized likelihood ratio test detector is derived to extend applicability to stronger plumes. In addition to detectors whose purpose is to identify presence versus absence of a plume, expressions are also derived for estimating plume strength. The performance of these various detectors is evaluated by implanting simulated plume into background images that are either real hyperspectral images or simulated images based on different (Gaussian, multivariate t, and lognormal) clutter distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

The HalfDome multi-survey cosmological simulations: N-body simulations

Upcoming cosmological surveys have the potential to reach groundbreaking discoveries on multiple fronts, including the neutrino mass, dark energy, and inflation. Most of the key science goals require the joint analysis of datasets from multiple surveys to break parameter degeneracies and calibrate systematics. To realize such analyses, a large set of mock simulations that realistically model correlated observables is required. In this paper we present the N-body component of the HalfDome cosmological simulations, designed for the joint analysis of Stage-IV cosmological surveys, such as Rubin LSST, Euclid, SPHEREx, Roman, DESI, PFS, Simons Observatory, CMB-S4, and LiteBIRD. Our 300TB initial data release includes full-sky lightcones and halo catalogs between z = 0–4 for 11 fixed cosmology realizations, as well as an additional run with local primordial non-Gaussianity (f NL = 20). The simulations evolve 61443 particles in a 3.75 h -1 Gpc box, reaching a minimum halo mass of ∼6 × 1012 h -1 M ⊙ and maximum scale of k ∼ h Mpc-1. Our data is publicly available: instructions to access the data and plans for future data releases can be found at https://halfdomesims.github.io.

Bayer, Adrian E↗

Mechanistic Insights into Peptide Binding and Deactivation of an Adhesion G Protein-Coupled Receptor

Adhesion G protein-coupled receptors (ADGRGs) play critical roles in the reproductive, neurological, cardiovascular, and endocrine systems. In particular, ADGRG2 plays a significant role in Ewing sarcoma cell proliferation, parathyroid cell function, and male fertility. In 2022, a cryo-EM structure was reported for the active ADGRG2 bound by an optimized peptide agonist IP15 and the Gs protein. The IP15 peptide agonist was also modified to antagonists 4PH-E and 4PH-D with mutations of the 4PH residue to Glu and Asp, respectively. However, experimental structures of inactive antagonist-bound ADGRs remain to be resolved, and the activation mechanism of ADGRs such as ADGRG2 is poorly understood. Here, we applied Gaussian accelerated molecular dynamics (GaMD) simulations to probe conformational dynamics of the agonist- and antagonist-bound ADGRG2. By performing GaMD simulations, we were able to identify important low-energy conformations of ADGRG2 in the active, intermediate, and inactive states, as well as explore the binding conformations of each peptide. Moreover, our simulations revealed critical peptide-receptor residue interactions during the deactivation of ADGRG2. In conclusion, through GaMD simulations, we uncovered mechanistic insights into peptide (agonist and antagonist) binding and deactivation of the ADGRG2. These findings will potentially facilitate rational design of new peptide modulators of ADGRG2 and other ADGRs.

59 BASIC BIOLOGICAL SCIENCES↗

Learning likelihood ratios with neural network classifiers

The likelihood ratio is a crucial quantity for statistical inference in science that enables hypothesis testing, construction of confidence intervals, reweighting of distributions, and more. Many modern scientific applications, however, make use of data- or simulation-driven models for which computing the likelihood ratio can be very difficult or even impossible. By applying the so-called “likelihood ratio trick,” approximations of the likelihood ratio may be computed using clever parametrizations of neural network-based classifiers. A number of different neural network setups can be defined to satisfy this procedure, each with varying performance in approximating the likelihood ratio when using finite training data. We present a series of empirical studies detailing the performance of several common loss functionals and parametrizations of the classifier output in approximating the likelihood ratio of two univariate and multivariate Gaussian distributions as well as simulated high-energy particle physics datasets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mechanism of tethered agonist-mediated signaling by polycystin-1

Mutations of polycystin-1 (PC1) are the major cause (85% of cases) of autosomal dominant polycystic kidney disease (ADPKD), which is the fourth leading cause of kidney failure. PC1 is thought to function as an atypical G protein-coupled receptor, yet the mechanism by which PC1 regulates G-protein signaling remains poorly understood. A significant portion of ADPKD mutations of PC1 encode a protein with defects in maturation or reduced function that may be amenable to functional rescue. In this work, we have combined complementary biochemical and cellular assay experiments and accelerated molecular simulations, which revealed an allosteric transduction pathway in activation of the PC1 C-terminal fragment. Our findings will facilitate future rational drug design efforts targeting the PC1 signaling function. Polycystin-1 (PC1) is an important unusual G protein-coupled receptor (GPCR) with 11 transmembrane domains, and its mutations account for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 shares multiple characteristics with Adhesion GPCRs. These include a GPCR proteolysis site that autocatalytically divides these proteins into extracellular, N-terminal, and membrane-embedded, C-terminal fragments (CTF), and a tethered agonist (TA) within the N-terminal stalk of the CTF that is suggested to activate signaling. However, the mechanism by which a TA can activate PC1 is not known. Here, we have combined functional cellular signaling experiments of PC1 CTF expression constructs encoding wild type, stalkless, and three different ADPKD stalk variants with all-atom Gaussian accelerated molecular dynamics (GaMD) simulations to investigate TA-mediated signaling activation. Correlations of residue motions and free-energy profiles calculated from the GaMD simulations correlated with the differential signaling abilities of wild type and stalk variants of PC1 CTF. They suggested an allosteric mechanism involving residue interactions connecting the stalk, Tetragonal Opening for Polycystins (TOP) domain, and putative pore loop in TA-mediated activation of PC1 CTF. Key interacting residues such as N3074–S3585 and R3848–E4078 predicted from the GaMD simulations were validated by mutagenesis experiments. Together, these complementary analyses have provided insights into a TA-mediated activation mechanism of PC1 CTF signaling, which will be important for future rational drug design targeting PC1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

Identifying small molecules (e.g., metabolites) is key towards driving scientific advancement in metabolomics, and gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none characterize the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending the traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g., fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Improving scalability of electronic structure code for molecular simulations in the presence of environment

A scalable density functional electronic code with Gaussian basis set, called UTEP-NRLMOL, is developed to perform simulations of molecular systems in the presence of the environment with particular attention to the memory requirements. In the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for density functional calculations scale as N*N, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure codes hinder their efficient usage of these platforms. We have introduced new scaling and parallelization paradigms using MPI-3 shared-memory functionality combined with usage of sparse algebra and storage of matrices in sparse format. This extends the range of applicability of the UTEP-NRLMOL code to large systems over 10,000 atoms, or using up to 67,000 basis functions, and making use of HPC architectures using over 6,000 processors utilizing all available cores. We have also interfaced code with effective fragment potential and polarizable continuum model libraries. The code was used in simulations of several applications which are published in reputed scientific journals.

74 ATOMIC AND MOLECULAR PHYSICS↗

A Three-Dimensional, Analytical Wind Turbine Wake Model: Flow Acceleration, Empirical Correlations, and Continuity

A new, three-dimensional, analytical, steady-state wake model is presented that includes local flow acceleration near the rotor, improving the wake description compared to existing models. Wake structures such as the momentum deficit and regions of accelerated flow are concisely described with compound and normal Gaussian functions. Large-eddy simulations (LES) are used as training data to develop the model using two in-line turbines under various inflow conditions parameterized by hub-height wind speed and turbulence intensity. Mass conservation is considered by fixing two components of the wake velocity model and optimizing the third to best satisfy continuity; after which, the model performs comparably if not better than existing work with regards to both relative error and mass consistency. The final model demonstrates a high degree of flexibility, making use of empirical correlations to scale across different inflow conditions. The inclusion of these effects is capable of revealing unused opportunities for enhanced power generation by aligning wake trajectories with these regions of accelerated flow.

modeling↗

Effects of presenilin-1 familial Alzheimer’s disease mutations on γ-secretase activation for cleavage of amyloid precursor protein

Presenilin-1 (PS1) is the catalytic subunit of γ-secretase which cleaves within the transmembrane domain of over 150 peptide substrates. Dominant missense mutations in PS1 cause early-onset familial Alzheimer’s disease (FAD); however, the exact pathogenic mechanism remains unknown. Here we combined Gaussian accelerated molecular dynamics (GaMD) simulations and biochemical experiments to determine the effects of six representative PS1 FAD mutations (P117L, I143T, L166P, G384A, L435F, and L286V) on the enzyme-substrate interactions between γ-secretase and amyloid precursor protein (APP). Biochemical experiments showed that all six PS1 FAD mutations rendered γ-secretase less active for the endoproteolytic (ε) cleavage of APP. Distinct low-energy conformational states were identified from the free energy profiles of wildtype and PS1 FAD-mutant γ-secretase. The P117L and L286V FAD mutants could still sample the “Active” state for substrate cleavage, but with noticeably reduced conformational space compared with the wildtype. The other mutants hardly visited the “Active” state. The PS1 FAD mutants were found to reduce γ-secretase proteolytic activity by hindering APP residue L49 from proper orientation in the active site and/or disrupting the distance between the catalytic aspartates. Therefore, our findings provide mechanistic insights into how PS1 FAD mutations affect structural dynamics and enzyme-substrate interactions of γ-secretase and APP.

60 APPLIED LIFE SCIENCES↗