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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Implementation and analysis of quantum computing application to Higgs boson reconstruction at the large Hadron Collider

With the advent of the High-Luminosity Large Hadron Collider (HL-LHC) era, high energy physics (HEP) event selection will require new approaches to rapidly and accurately analyze vast databases. The current study addresses the enormity of HEP databases in an unprecedented manner—a quantum search using Grover’s Algorithm (GA) on an unsorted database, ATLAS Open Data, from the ATLAS detector. A novel method to identify rare events at 13 TeV in CERN’s LHC using quantum computing (QC) is presented. As indicated by the Higgs boson decay channel H→ZZ*→4l , the detection of four leptons in one event may be used to reconstruct the Higgs boson and, more importantly, evince Higgs boson decay to some new phenomena, such as H→ZZ d →4l . Searching the dataset for collisions resulting in detection of four leptons using a Jupyter Notebook, a classical simulation of GA, and several quantum computers with multiple qubits, the current application was found to make the proper selection in the unsorted dataset. Quantum search efficacy was analyzed for the incoming HL-LHC by implementing the QC method on multiple classical simulators and IBM’s quantum computers with the IBM Qiskit Open Source Software. The current QC application provides a novel, high-efficiency alternative to classical database searches, demonstrating its potential utility as a rapid and increasingly accurate search method in HEP.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Discovering invariant spatial features in electron energy loss spectroscopy images on the mesoscopic and atomic levels

Over the last two decades, Electron Energy Loss Spectroscopy (EELS) imaging with a scanning transmission electron microscope has emerged as a technique of choice for visualizing complex chemical, electronic, plasmonic, and phononic phenomena in complex materials and structures. The availability of the EELS data necessitates the development of methods to analyze multidimensional data sets with complex spatial and energy structures. Traditionally, the analysis of these data sets has been based on analysis of individual spectra, one at a time, whereas the spatial structure and correlations between individual spatial pixels containing the relevant information of the physics of underpinning processes have generally been ignored and analyzed only via the visualization as 2D maps. Here, we develop a machine learning-based approach and workflows for the analysis of spatial structures in 3D EELS data sets using a combination of dimensionality reduction and multichannel rotationally invariant variational autoencoders. This approach is illustrated for the analysis of both the plasmonic phenomena in a system of nanowires and in the core excitations in functional oxides using low loss and core-loss EELS, respectively. The code developed in this manuscript is open sourced and freely available and provided as a Jupyter notebook for the interested reader.

36 MATERIALS SCIENCE↗
DOE OSTI2024

PigmentHunter: A point-and-click application for automated chlorophyll-protein simulations

Chlorophyll proteins (CPs) are the workhorses of biological photosynthesis, working together to absorb solar energy, transfer it to chemically active reaction centers, and control the charge-separation process that drives its storage as chemical energy. Yet predicting CP optical and electronic properties remains a serious challenge, driven by the computational difficulty of treating large, electronically coupled molecular pigments embedded in a dynamically structured protein environment. To address this challenge, we introduce here an analysis tool called PigmentHunter, which automates the process of preparing CP structures for molecular dynamics (MD), running short MD simulations on the nanoHUB.org science gateway, and then using electrostatic and steric analysis routines to predict optical absorption, fluorescence, and circular dichroism spectra within a Frenkel exciton model. Inter-pigment couplings are evaluated using point-dipole or transition-charge coupling models, while site energies can be estimated using both electrostatic and ring-deformation approaches. The package is built in a Jupyter Notebook environment, with a point-and-click interface that can be used either to manually prepare individual structures or to batch-process many structures at once. Here, we illustrate PigmentHunter’s capabilities with example simulations on spectral line shapes in the light harvesting 2 complex, site energies in the Fenna–Matthews–Olson protein, and ring deformation in photosystems I and II.

14 SOLAR ENERGY↗
DOE OSTI2020

Veridical data science

Building and expanding on principles of statistics, machine learning, and scientific inquiry, we propose the predictability, computability, and stability (PCS) framework for veridical data science. Our framework, composed of both a workflow and documentation, aims to provide responsible, reliable, reproducible, and transparent results across the data science life cycle. The PCS workflow uses predictability as a reality check and considers the importance of computation in data collection/storage and algorithm design. It augments predictability and computability with an overarching stability principle. Stability expands on statistical uncertainty considerations to assess how human judgment calls impact data results through data and model/algorithm perturbations. As part of the PCS workflow, we develop PCS inference procedures, namely PCS perturbation intervals and PCS hypothesis testing, to investigate the stability of data results relative to problem formulation, data cleaning, modeling decisions, and interpretations. We illustrate PCS inference through neuroscience and genomics projects of our own and others. Moreover, we demonstrate its favorable performance over existing methods in terms of receiver operating characteristic (ROC) curves in high-dimensional, sparse linear model simulations, including a wide range of misspecified models. Finally, we propose PCS documentation based on R Markdown or Jupyter Notebook, with publicly available, reproducible codes and narratives to back up human choices made throughout an analysis. The PCS workflow and documentation are demonstrated in a genomics case study available on Zenodo.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Tracking atomic structure evolution during directed electron beam induced Si-atom motion in graphene via deep machine learning

Using electron beam manipulation, we enable deterministic motion of individual Si atoms in graphene along predefined trajectories. Structural evolution during the dopant motion was explored, providing information on changes of the Si atom neighborhood during atomic motion and providing statistical information of possible defect configurations. The combination of a Gaussian mixture model and principal component analysis applied to the deep learning-processed experimental data allowed disentangling of the atomic distortions for two different graphene sublattices. This approach demonstrates the potential of e-beam manipulation to create defect libraries of multiple realizations of the same defect and explore the potential of symmetry breaking physics. The rapid image analytics enabled via a deep learning network further empowers instrumentation for e-beam controlled atom-by-atom fabrication. Here, the analysis described in the paper can be reproduced via an interactive Jupyter notebook at https://git.io/JJ3Bx.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

End-to-end AI framework for interpretable prediction of molecular and crystal properties

We introduce an end-to-end computational framework that allows for hyperparameter optimization using the DeepHyper library, accelerated model training, and interpretable AI inference. The framework is based on state-of-the-art AI models including CGCNN, PhysNet, SchNet, MPNN, MPNN-transformer, and TorchMD-NET. We employ these AI models along with the benchmark QM9, hMOF, and MD17 datasets to showcase how the models can predict user-specified material properties within modern computing environments. We demonstrate transferable applications in the modeling of small molecules, inorganic crystals and nanoporous metal organic frameworks with a unified, standalone framework. We have deployed and tested this framework in the ThetaGPU supercomputer at the Argonne Leadership Computing Facility, and in the Delta supercomputer at the National Center for Supercomputing Applications to provide researchers with modern tools to conduct accelerated AI-driven discovery in leadership-class computing environments. We release these digital assets as open source scientific software in GitLab, and ready-to-use Jupyter notebooks in Google Colab.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Deep kernel methods learn better: from cards to process optimization

Abstract The ability of deep learning methods to perform classification and regression tasks relies heavily on their capacity to uncover manifolds in high-dimensional data spaces and project them into low-dimensional representation spaces. In this study, we investigate the structure and character of the manifolds generated by classical variational autoencoder (VAE) approaches and deep kernel learning (DKL). In the former case, the structure of the latent space is determined by the properties of the input data alone, while in the latter, the latent manifold forms as a result of an active learning process that balances the data distribution and target functionalities. We show that DKL with active learning can produce a more compact and smooth latent space which is more conducive to optimization compared to previously reported methods, such as the VAE. We demonstrate this behavior using a simple cards dataset and extend it to the optimization of domain-generated trajectories in physical systems. Our findings suggest that latent manifolds constructed through active learning have a more beneficial structure for optimization problems, especially in feature-rich target-poor scenarios that are common in domain sciences, such as materials synthesis, energy storage, and molecular discovery. The Jupyter Notebooks that encapsulate the complete analysis accompany the article.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A mixed, unified forward/inverse framework for earthquake problems: fault implementation and coseismic slip estimate

SUMMARY We introduce a new finite-element (FE) based computational framework to solve forward and inverse elastic deformation problems for earthquake faulting via the adjoint method. Based on two advanced computational libraries, FEniCS and hIPPYlib for the forward and inverse problems, respectively, this framework is flexible, transparent and easily extensible. We represent a fault discontinuity through a mixed FE elasticity formulation, which approximates the stress with higher order accuracy and exposes the prescribed slip explicitly in the variational form without using conventional split node and decomposition discrete approaches. This also allows the first order optimality condition, that is the vanishing of the gradient, to be expressed in continuous form, which leads to consistent discretizations of all field variables, including the slip. We show comparisons with the standard, pure displacement formulation and a model containing an in-plane mode II crack, whose slip is prescribed via the split node technique. We demonstrate the potential of this new computational framework by performing a linear coseismic slip inversion through adjoint-based optimization methods, without requiring computation of elastic Green’s functions. Specifically, we consider a penalized least squares formulation, which in a Bayesian setting—under the assumption of Gaussian noise and prior—reflects the negative log of the posterior distribution. The comparison of the inversion results with a standard, linear inverse theory approach based on Okada’s solutions shows analogous results. Preliminary uncertainties are estimated via eigenvalue analysis of the Hessian of the penalized least squares objective function. Our implementation is fully open-source and Jupyter notebooks to reproduce our results are provided. The extension to a fully Bayesian framework for detailed uncertainty quantification and non-linear inversions, including for heterogeneous media earthquake problems, will be analysed in a forthcoming paper.

58 GEOSCIENCES↗
DOE OSTI2021

CLMM : a LSST-DESC cluster weak lensing mass modeling library for cosmology

ABSTRACT We present the v1.0 release of CLMM, an open source python library for the estimation of the weak lensing masses of clusters of galaxies. CLMM is designed as a stand-alone toolkit of building blocks to enable end-to-end analysis pipeline validation for upcoming cluster cosmology analyses such as the ones that will be performed by the Vera C. Rubin Legacy Survey of Space and Time-Dark Energy Science Collaboration (LSST-DESC). Its purpose is to serve as a flexible, easy-to-install, and easy-to-use interface for both weak lensing simulators and observers and can be applied to real and mock data to study the systematics affecting weak lensing mass reconstruction. At the core of CLMM are routines to model the weak lensing shear signal given the underlying mass distribution of galaxy clusters and a set of data operations to prepare the corresponding data vectors. The theoretical predictions rely on existing software, used as backends in the code, that have been thoroughly tested and cross-checked. Combined theoretical predictions and data can be used to constrain the mass distribution of galaxy clusters as demonstrated in a suite of example Jupyter Notebooks shipped with the software and also available in the extensive online documentation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design

Abstract Megasynthase enzymes such as type I modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) play a central role in microbial chemical warfare because they can evolve rapidly by shuffling parts (catalytic domains) to produce novel chemicals. If we can understand the design rules to reshuffle these parts, PKSs and NRPSs will provide a systematic and modular way to synthesize millions of molecules including pharmaceuticals, biomaterials, and biofuels. However, PKS and NRPS engineering remains difficult due to a limited understanding of the determinants of PKS and NRPS fold and function. We developed ClusterCAD to streamline and simplify the process of designing and testing engineered PKS variants. Here, we present the highly improved ClusterCAD 2.0 release, available at https://clustercad.jbei.org. ClusterCAD 2.0 boasts support for PKS-NRPS hybrid and NRPS clusters in addition to PKS clusters; a vastly enlarged database of curated PKS, PKS-NRPS hybrid, and NRPS clusters; a diverse set of chemical ‘starters’ and loading modules; the new Domain Architecture Cluster Search Tool; and an offline Jupyter Notebook workspace, among other improvements. Together these features massively expand the chemical space that can be accessed by enzymes engineered with ClusterCAD.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Quantifying uncertainties and correlations in the nuclear-matter equation of state

We perform statistically rigorous uncertainty quantification (UQ) for chiral effective field theory (χ EFT) applied to infinite nuclear matter up to twice nuclear saturation density. The equation of state (EOS) is based on high-order many-body perturbation theory calculations with nucleon-nucleon and three-nucleon interactions up to fourth order in the χ EFT expansion. From these calculations our newly developed Bayesian machine-learning approach extracts the size and smoothness properties of the correlated EFT truncation error. Furthermore, we then propose a novel extension that uses multitask machine learning to reveal correlations between the EOS at different proton fractions. The inferred in-medium χ EFT breakdown scale in pure neutron matter and symmetric nuclear matter is consistent with that from free-space nucleon-nucleon scattering. These significant advances allow us to provide posterior distributions for the nuclear saturation point and propagate theoretical uncertainties to derived quantities: the pressure and incompressibility of symmetric nuclear matter, the nuclear symmetry energy, and its derivative. Our results, which are validated by statistical diagnostics, demonstrate that an understanding of truncation-error correlations between different densities and different observables is crucial for reliable UQ. The methods developed here are publicly available as annotated Jupyter notebooks.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Wave-function-based emulation for nucleon-nucleon scattering in momentum space

Emulators for low-energy nuclear physics can provide fast and accurate predictions of bound-state and scattering observables for applications that require repeated calculations with different parameters, such as Bayesian uncertainty quantification. In this paper, we extend a scattering emulator based on the Kohn variational principle (KVP) to momentum space (including coupled channels) with arbitrary boundary conditions, which enable the mitigation of spurious singularities known as Kohn anomalies. We test it on a modern chiral nucleon-nucleon (N N) interaction, including emulation of the coupled channels. We provide comparisons between a Lippmann-Schwinger equation emulator and our KVP momentum-space emulator for a representative set of neutron-proton (n p) scattering observables, and also introduce a quasi-spline-based approach for the KVP-based emulator. Furthermore, our findings show that while there are some trade-offs between accuracy and speed, all three emulators perform well. Self-contained Jupyter notebooks that generate the results and figures in this paper are publicly available.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Assessing correlated truncation errors in modern nucleon-nucleon potentials

We test the BUQEYE model of correlated effective field theory (EFT) truncation errors on Reinert, Krebs, and Epelbaum's semilocal momentum-space implementation of the chiral EFT (𝜒⁢EFT ) expansion of the nucleon-nucleon (NN) potential. This Bayesian model hypothesizes that dimensionless coefficient functions extracted from the order-by-order corrections to NN observables can be treated as draws from a Gaussian process (GP). We combine a variety of graphical and statistical diagnostics to assess when predicted observables have a 𝜒⁢EFT convergence pattern consistent with the hypothesized GP statistical model. Our conclusions are that, first, the BUQEYE model is generally applicable to the potential investigated here, which enables statistically principled estimates of the impact of higher EFT orders on observables. Second, parameters defining the extracted coefficients such as the expansion parameter 𝑄 must be well chosen for the coefficients to exhibit a regular convergence pattern—a property we exploit to obtain posterior distributions for such quantities. Third, the assumption of GP stationarity across lab energy and scattering angle is not generally met; this necessitates adjustments in future work. We provide a workflow and interpretive guide for our analysis framework, and show what can be inferred about probability distributions for 𝑄, the EFT breakdown scale Λ 𝑏 , the scale associated with soft physics in the 𝜒⁢EFT potential 𝑚 eff , and the GP hyperparameters. All our results can be reproduced using a publicly available Jupyter notebook, which can be straightforwardly modified to analyze other 𝜒⁢EFT NN potentials.

Bayesian methods↗
DOE OSTI2023

Addition of tabulated equation of state and neutrino leakage support to illinoisgrmhd

Here we have added support for realistic, microphysical, finite-temperature equations of state (EOS) and neutrino physics via a leakage scheme to illinoisgrmhd, an open-source GRMHD code for dynamical spacetimes in the einstein toolkit. These new features are provided by two new, nrpy+-based codes: nrpyeos, which performs highly efficient EOS table lookups and interpolations, and nrpyleakage, which implements a new, adaptive mesh refinement (AMR)-capable neutrino leakage scheme in the einstein toolkit. We have performed a series of strenuous validation tests that demonstrate the robustness of these new codes, particularly on the Cartesian AMR grids provided by carpet. Furthermore, we show results from fully dynamical GRMHD simulations of single unmagnetized neutron stars, and magnetized binary neutron star mergers. This new version of illinoisgrmhd, as well as nrpyeos and nrpyleakage, is pedagogically documented in jupyter notebooks and fully open source. The codes will be proposed for inclusion in an upcoming version of the einstein toolkit.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Solution scattering at the Life Science X-ray Scattering (LiX) beamline

This work reports the instrumentation and software implementation at the Life Science X-ray Scattering (LiX) beamline at NSLS-II in support of biomolecular solution scattering. For automated static measurements, samples are stored in PCR tubes and grouped in 18-position sample holders. Unattended operations are enabled using a six-axis robot that exchanges sample holders between a storage box and a sample handler, transporting samples from the PCR tubes to the X-ray beam for scattering measurements. The storage box has a capacity of 20 sample holders. At full capacity, the measurements on all samples last for ∼9 h. For in-line size-exclusion chromatography, the beamline-control software coordinates with a commercial high-performance liquid chromatography (HPLC) system to measure multiple samples in batch mode. The beamline can switch between static and HPLC measurements instantaneously. In all measurements, the scattering data span a wide q -range of typically 0.006–3.2 Å −1 . Functionalities in the Python package py4xs have been developed to support automated data processing, including azimuthal averaging, merging data from multiple detectors, buffer scattering subtraction, data storage in HDF5 format and exporting the final data in a three-column text format that is acceptable by most data analysis tools. These functionalities have been integrated into graphical user interfaces that run in Jupyter notebooks, with hooks for external data analysis software.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

tomoCAM : fast model-based iterative reconstruction via GPU acceleration and non-uniform fast Fourier transforms

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM , is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter -based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Normality of I-V Measurements Using ML

There is an increased interest in instrument-computing ecosystems (ICEs) that support science workflows empowered by AI-automated experiments and computations in diverse areas. In particular, electrochemistry ICEs are promising for accelerating the design and discovery of electrochemical systems for energy storage and conversion, by automating significant parts of workflows that combine synthesis and characterization experiments with computations. They require the integration of flow controllers, solvent containers, pumps, fraction collectors, and potentiostats, all connected to an electrochemical cell, as illustrated in Fig. 1. These are specialized instruments with custom software that is not originally designed for network integration. We developed network and software solutions for electrochemical workflows that adapt system and instrument settings in real-time for multiple rounds of experiments. In particular, we developed Python wrappers for Application Programming Interfaces (APIs) of instrument commands and Pyro client-server modules that enable them to be executed from remote computers. The entire workflow is orchestrated by a Jupyter notebook running on a remote computer.

Al Najjar, Anees↗
DOE OSTI2025

Descriptor: High Temporal Resolution Meteorological Data at Oak Ridge Reservation (ORR-HiResMet)

Access to continuous, quality assessed meteorological data is critical for understanding the climatology and atmospheric dynamics of a region. Research facilities like Oak Ridge National Laboratory (ORNL) rely on such data to assess site-specific climatology, model potential emissions, establish safety baselines, and prepare for emergency scenarios. To meet these needs, on-site towers at ORNL collect meteorological data at 15-minute and hourly intervals. However, data measurements from meteorological towers are affected by sensor sensitivity, degradation, lightning strikes, power fluctuations, glitching, and sensor failures, all of which can affect data quality. To address these challenges, we conducted a comprehensive quality assessment and processing of five years of meteorological data collected from ORNL at 15-minute intervals, including measurements of temperature, pressure, humidity, wind, and solar radiation. The time series of each variable was pre-processed and gap-filled using established meteorological data collection and cleaning techniques, i.e., the time series were subjected to structural standardization, data integrity testing, automated and manual outlier detection, and gap-filling. The data product and highly generalizable processing workflow developed in Python Jupyter notebooks are publicly accessible online. As a key contribution of this study, the evaluated 5-year data will be used to train atmospheric dispersion models that simulate dispersion dynamics across the complex ridge-and-valley topography of the Oak Ridge Reservation in East Tennessee.

Steckler, Morgan R. [Oak Ridge National Laboratory↗