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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

TX$^2$: Transformer eXplainability and eXploration

The Transformer eXplainability and eXploration (Martindale & Stewart, 2021), or TX 2 software package, is a library designed for artificial intelligence researchers to better understand the performance of transformer models (Vaswani et al., 2017) used for sequence classification. The tool is capable of integrating with a trained transformer model and a dataset split into training and testing populations to produce an ipywidget (Project Jupyter Contributors, 2021) dashboard with a number of visualizations to understand model performance with an emphasis on explainability and interpretability. The TX 2 package is primarily intended to integrate into a workflow centered around Jupyter Notebooks (Kluyver et al., 2016), and currently assumes the use of PyTorch (Paszke et al., 2019) and Hugging Face transformers library (Wolf et al., 2020). The dashboard includes visualization and data exploration features to aid researchers, including an interactive UMAP embedding graph (McInnes et al., 2018) to understand classification clusters, a word salience map that can be updated as researchers alter textual entries in near real time, a set of tools to understand word frequency and importance based on the clusters in the UMAP embedding graph, and a set of traditional confusion matrix analysis tools.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Antireflective Multi‐Dielectric Metasurfaces Operating in the Visible

Abstract As increasingly more demanding photonics applications are brought on‐chip, more complex design solutions are employed to deliver enhanced performance: e.g., meta‐molecules, inverse‐designed freeform structures, and multilayer metasurfaces. Instead, this study introduces anti‐reflective metasurfaces fabricated in a single nanolithography step that follows deposition of multiple dielectrics onto a substrate. Anti‐reflective metasurfaces offer fundamentally better transmission efficiencies compared to conventional equivalents. Conventional and anti‐reflective metalenses, both fabricated in the Ta 2 O 5 /SiO 2 material platform for 461 nm operation, show an improvement in focusing efficiencies from ≈ 55% to ≈ 90% at low numerical apertures and from ≈ 35% to ≈ 65% at high numerical apertures. Simulations of ideal and imperfect metalenses indicate that anti‐reflective metasurfaces not only improve transmission at the design library level, but also reduce spurious diffraction and protect against higher‐order scattering.

Optics↗
DOE OSTI2025

Quantum Electrodynamics Coupled-Cluster at Scale: High-Performance Implementation for Complex Systems

Coupled-cluster theory (CC) is a highly accurate and versatile method for simulating complex interactions within quantum systems. The extension of CC theory to model mixed electron-photon processes with quantum electrodynamics (QED) has improved our capability to predict cavity-modified chemistry, a field where photons are used as cost-effective and eco-friendly alternatives to catalyze/inhibit chemical reactions. However, calculations with CC methods, even without incorporating QED effects, are often prohibitively expensive. Simulations of larger systems require scalable infrastructures that exist for traditional CC methods but not for QED-CC methods. As such, we present a GPU-enabled, high-performance, open-source implementation of the quantum electrodynamics coupled-cluster method with single and double excitations (QED-CCSD) within the ExaChem quantum chemistry software package. ExaChem relies on the Tensor Algebra for Many-body Methods (TAMM) infrastructure: a parallel heterogeneous tensor library designed to achieve scalable performance on modern heterogeneous supercomputing platforms. Furthermore, we discuss theoretical foundations, algorithmic details, and numerical benchmarks to showcase the larger systems that ExaChem can simulate and how the integration of photonic degrees-of-freedom alters their ground-state properties.

Basis sets↗
DOE OSTI2026

Sequence-based generative AI design of versatile tryptophan synthases

Enzymes are powerful and sustainable catalysts, but their widespread application is limited by the difficulty of identifying functional starting points for optimization, creating a major bottleneck in early- stage biocatalyst discovery. Designing libraries of such starting enzymes remains particularly challenging. Here, we use the GenSLM protein language model to generate novel β-subunit of tryptophan synthase (TrpB) enzymes that express in Escherichia coli and are both stable and catalytically active. Many generated TrpBs also display significant substrate promiscuity, outperforming their natural counterparts on non-native substrates. Some even surpass laboratory-evolved TrpBs. Comparison of the most-active and most-promiscuous generated TrpB to its closest natural homolog confirms that the enhanced versatility is absent from the natural enzyme, highlighting the creative potential of generative models. These results demonstrate that the generated TrpBs not only preserve natural structure and function but also acquire non-natural properties, establishing generative models as powerful tools for biocatalyst discovery and engineering.

biocatalysis↗
DOE OSTI2022

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns of biochemical annotations and provide a better understanding of the mechanisms underpinning protein and nucleic acid function at the atomic level. We present a new library designed to display fully customizable interactive views between 1D positional features of protein and/or nucleic acid sequences and their 3D structures as isolated chains or components of macromolecular assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Open-source library for performance-portable neutrino reaction rates: Application to neutron star mergers

A realistic and detailed description of neutrinos in binary neutron star (BNS) mergers is essential to build reliable models of such systems. To this end, we present bns_nurates, a novel open-source numerical library designed for the efficient on-the-fly computation of neutrino interactions, with particular focus on regimes relevant to BNS mergers. bns_nurates targets a higher level of accuracy and realism in the implementation of commonly employed reactions by accounting for relevant microphysics effects on the interactions, such as weak magnetism and mean field effects. It also includes the contributions of inelastic neutrino scattering off electrons and positrons and (inverse) nucleon decays. Finally, it offers a way to reconstruct the neutrino distribution function in the framework of moment-based transport schemes. As a first application, we compute both energy-dependent and energy-integrated neutrino emissivities and opacities for conditions extracted from a BNS merger simulation with m1 transport scheme. We find some qualitative differences in the results when considering the impact of the additional relevant reactions and of microphysics effects. For example, neutrino-electron/positron scattering reactions are important for the energy exchange of heavy-type neutrinos as they do not undergo semileptonic charged-current processes, when μ± are not accounted for. Moreover, weak magnetism and mean field effects can significantly modify the contribution of β processes for electron-type (anti)neutrinos, increasing at the same time the importance of (inverse) neutron decays. Here, the improved treatment for the reaction rates also modifies the conditions at which neutrinos decouple from matter in the system, potentially affecting their emission spectra.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

PyFaults: A Python Toolkit for Stacking Fault Screening

PyFaults is an open-source Python library designed to model stacking fault disorder in crystalline materials and qualitatively assess the characteristic selective broadening effects in powder X-ray diffraction (PXRD). Here, the main capabilities of PyFaults are presented, including unit cell and supercell model construction, PXRD pattern calculation, assessment against experimental PXRD, and methods for rapid screening of candidate models within a set of possible stacking vectors and fault occurrence probabilities. This program aims to serve as a computationally inexpensive tool for identifying and screening potential stacking fault models in materials with planar disorder. Three diverse case studies, involving GaN, Li2MnO3 and Li3YCl6, are presented to illustrate the program functionality across a range of structure types and stacking fault modalities.

MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Deeplynx-loader

'deeplynx-timeseries-loader' is a library designed to make it as easy as possible for users to download and access timeseries or tabular data from DeepLynx.

Darrington, John↗
DOE OSTI2023

BuildStockQuery [SWR-23-58]

BuildStockQuery is a python library designed to simplify and streamline the process of querying massive, terabyte-scale datasets generated by ResStock(TM). ResStock (SWR-19-15) is a U.S. DOE-supported, NREL-built, national residential building energy stock model that enables a new approach to large-scale residential energy analysis across the U.S. by combining large public and private data sources, statistical sampling, detailed sub-hourly building simulations, and high-performance computing. BuildStockQuery offers an intuitive Object-Oriented Programming (OOP) interface to the ResStock output dataset allowing users to easily perform common queries and receive results in familiar pandas DataFrame format, abstracting away the need for complex SQL query. By initializing a query object with the pertinent Athena database and table names, users can easily query for various kinds of insights, for example, timeseries electricity for an end use for a given state grouped by building types.

Adhikari, Rajendra↗
DOE OSTI2024

A Full-Stack Exploration of Language-Based Parallelism in Fortran 2023

This poster explores native parallel features in Fortran 2023 through the lens of supporting applications with libraries, compilers, and parallel runtimes. The language revision informally named Fortran 2008 introduced parallelism in the form of Single Program Multiple Data (SPMD) execution with two broad feature sets: (1) loop-level parallelism via do concurrent and (2) a Partitioned Global Address Space (PGAS) comprised of distributed “coarray” data structures. Fortran’s native parallelism has demonstrated high performance [1] and reduced the burden of inserting what sometimes amounts to more directives than code. Several compilers support both feature sets, typically by translating do concurrent into serial do loops annotated by parallel directives and by translating SPMD/PGAS features into direct calls to a communication library. Our research focuses primarily on two questions: (1) can the compiler’s parallel runtime library be developed in the language being compiled (Fortran) and (2) can we define an interface to the runtime that liberates compilers from being hardwired to one runtime and vice versa. We are answering these questions by developing the Parallel Runtime Interface for Fortran (PRIF) [2] and the Co-Array Fortran Framework of Efficient Interfaces to Network Environments (Caffeine) [3]. Caffeine is initially targeting adoption by LLVM Flang, a new open-source Fortran compiler developed by a broad community in industry, academia, and government labs. We are also exploring the use of these features in Inference-Engine, a deep learning library designed to facilitate neural network training and inference for high-performance computing applications written in modern Fortran.

Rasmussen, Katherine↗
DOE OSTI2021

GFCCLib: Scalable and efficient coupled-cluster Green's function library for accurately tackling many-body electronic structure problems

Coupled-cluster Green’s function (GFCC) calculation has drawn much attention in the recent years for targeting the molecular and material electronic structure problems from a many-body perspective in a systematically improvable way. However, GFCC calculations on scientific computing clusters usually suffer from expensive higher di- mensional tensor contractions in the complex space, expensive inter-process communi- cation, and severe load imbalance, which limits it’s routine use for tackling electronic structure problems. Here we present a numerical library prototype that is specifically designed for large-scale GFCC calculations. The design of the library is focused on a systematically optimal computing strategy to improve its scalability and efficiency. The performance of the library is demonstrated by the relevant profiling analysis of running GFCC calculations on remote giant computing clusters. The capability of the library is highlighted by computing a wide near valence band of a fullerene C60 molecule for the first time at the GFCCSD level that shows excellent agreement with the experimental spectrum.

Peng, Bo↗
DOE OSTI2025

Terra-Populus v0.1: A Python Library for LandScan High-Definition Population Analysis and Modeling

The terra-populus library is designed for use by the LandScan HD technical team, offering a streamlined set of tools for generating and updating LandScan HD datasets from foundational building-level data, referred to as 'molecules,' provided by the building-level attribution team. This document serves as the primary technical documentation for terra-populus. Version 0.1 of the library includes the core modeling components necessary for LandScan HD production. It enables the generation of the LandScan HD Baseline dataset as well as corresponding confidence measures for the occupancy rates used. Parameters have been included for incorporating damaged building indicators and changes in population, to faciliate the creation of rapid updates for LandScan HD. Future iterations of terra-populus will introduce tools for creating a confidence index, and quantifying and propagating uncertainty, facilitating the creation of probabilistic LandScan HD outputs. This report provides an overview of the tools available in the library and the corresponding code implementations. One of the key advancements implemented in terra-populus is a redefinition of the atomic modeling unit for LandScan HD. Traditionally, the LandScan HD vector analytical framework has generated population estimates at the building sub-component (molecule) level. However, terra-populus adopts a building-level modeling approach. This shift is an operational decision aimed at aligning LandScan HD outputs with confidence measures, which are computed and validated at the building level (confidence measures are not included in this version of terra-populus, aside from those associated with the occupancy rates). Additional advancements to the LandScan HD modeling, as implemented by terra-populus, include a minimum population value parameter and an auto assignment of building floor counts. The population minimum value was implemented to prevent buildings and subsequent LandScan HD pixels that contained small values that may not rasterize in production. An 'auto' value has been included as a method for dealing with buildings lacking floor count information, where it is the average floor count of all other buildings with a residential building use type tag. The logic behind this is to remain consistent with the current logic employed for dealing with building use type null instances, where a null use type is defaulted to residential since it is the most common building type. The auto logic is intended to apply the most common building floor count of the most common type of buildings. The tools provided in terra-populus represent a significant step forward in improving the efficiency, reproducibility, and transparency of the LandScan HD modeling process. As the library evolves, it will continue to serve as a foundational resource for high-resolution population modeling.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Towards Superior Software Portability with SHAD and HPX C++ Libraries

As hardware architectures and software stacks complexity grows, development productivity, performance and software portability, quickly evolve from desirable features to actual needs. SHAD, the Scalable High-performance Algorithms and Data-structures C++ library is designed to mitigate these issues: it provides general purpose building blocks as well as high-level custom utilities, and offers a shared-memory programming abstraction which facilitates the programming of complex systems, scaling up to High Performance Computing clusters. SHAD’s portability is achieved through an abstract runtime interface, which decouples the upper layers of the library and hides the low level details of the underlying architecture. This layer enables SHAD to interface with different runtime/threading systems, e.g. Intel TBB and Global Memory and Threading (GMT). However, current backends targeting distributed systems, rely on a centralized controller which may possibly limit scalability up to hundreds of nodes and creates a network hot spot due to all to one communication for synchronization, and possibly resulting in degraded performance at high process counts. In this research, we explore HPX, the C++ standard library for parallelism and concurrency, as an additional backend in support of the SHAD library, and present the methodologies in support of local and remote task executions in SHAD with respect to HPX. Finally, we evaluate the proposed system by comparing against existing backends of SHAD and analyzing their performance on C++ Standard Template Library algorithms.

Wu, Nanmiao↗
DOE OSTI2021

FIERRO V.X

FIERRO is a modern C++ code intended to simulate quasi-static solid mechanics problems and transient, compressible material dynamic problems with Lagrangian methods, which have meshes with constant mass elements that move with the material. FIERRO is designed to aid a) material model research that has historically been done using commercial implicit and explicit finite element codes, b) numerical methods research, and c) computer science research. FIERRO supports user developed material models that adhere to several industry standard formats by using a C++ to Fortran interface to couple the model to the numerical solvers. FIERRO is built on the ELEMENTS library that supports a diverse suite of element types, including high-order elements, and quadrature rules. The mesh class within the ELEMENTS library is designed for efficient calculations on unstructured meshes and to minimize memory usage. FIERRO is designed to readily accommodate a range of numerical methods including continuous finite element, finite volume, and discontinuous Galerkin methods. FIERRO is designed to support explicit and implicit time integration methods. FIERRO only supports a single material in an element. No physical data exists within the code.

Morgan, Nathaniel↗
DOE OSTI2024

Evaluated Nuclear Data Library, with ENDL2009.5-direct (2009.5 Rev.)

LLNL’s Nuclear Data and Theory Group have created a 2009.5 revised release of the Evaluated Nuclear Data Library (ENDL2009.5). This library is designed to support LLNL’s current and future nuclear data needs and will be employed in nuclear reactor, nuclear security and stockpile stewardship simulations with ASC codes. The ENDL2009 database was the most complete nuclear database for Monte Carlo and deterministic transport of neutrons and charged particles. It was assembled with strong support from the ASC PEM and Attribution programs, leveraged with support from Campaign 4 and the DOE/Office of Science’s US Nuclear Data Program. This document lists the revisions and fixes made in a new release called ENDL2009.5, by comparing with the existing data in the previous releases ENDL2009.3 and ENDL2009.4. In addition to the legacy library ENDL2009.5 from ENDL-format files generated by Fete, an ENDL2009.5-direct library is also released, in which ENDF6-formatted sources are used wherever possible to avoid possible translation errors from Fete.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

helixCAM: A platform for programmable cellular assembly in bacteria and human cells

Interactions between cells are indispensable for signaling and creating structure. The ability to direct precise cell-cell interactions would be powerful for engineering tissues, understanding signaling pathways, and directing immune cell targeting. In humans, intercellular interactions are mediated by cell adhesion molecules (CAMs). However, endogenous CAMs are natively expressed by many cells and tend to have cross-reactivity, making them unsuitable for programming specific interactions. Here, we showcase “helixCAM,” a platform for engineering synthetic CAMs by presenting coiled-coil peptides on the cell surface. helixCAMs were able to create specific cell-cell interactions and direct patterned aggregate formation in bacteria and human cells. Based on coiled-coil interaction principles, we built a set of rationally designed helixCAM libraries, which led to the discovery of additional high-performance helixCAM pairs. Finally, we applied this helixCAM toolkit for various multicellular engineering applications, such as spherical layering, adherent cell targeting, and surface patterning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Polyubiquitin ligand-induced phase transitions are optimized by spacing between ubiquitin units

Biomolecular condensates form via multivalent interactions among key macromolecules and are regulated through ligand binding and/or posttranslational modifications. One such modification is ubiquitination, the covalent addition of ubiquitin (Ub) or polyubiquitin chains to target macromolecules. Specific interactions between polyubiquitin chains and partner proteins, including hHR23B, NEMO, and UBQLN2, regulate condensate assembly or disassembly. Here, we used a library of designed polyubiquitin hubs and UBQLN2 as model systems for determining the driving forces of ligand-mediated phase transitions. Perturbations to either the UBQLN2-binding surface of Ub or the spacing between Ub units reduce the ability of hubs to modulate UBQLN2 phase behavior. By developing an analytical model based on polyphasic linkage principles that accurately described the effects of different hubs on UBQLN2 phase separation, we determined that introduction of Ub to UBQLN2 condensates incurs a significant inclusion energetic penalty. This penalty antagonizes the ability of polyUb hubs to scaffold multiple UBQLN2 molecules and cooperatively amplify phase separation. The extent to which polyubiquitin hubs promote UBQLN2 phase separation is encoded in the spacings between Ub units. This spacing is modulated by chains of different linkages and designed chains of different architectures, thus illustrating how the ubiquitin code regulates functionality via the emergent properties of the condensate. The spacing in naturally occurring linear polyubiquitin chains is already optimized to promote phase separation with UBQLN2. We expect our findings to extend to other condensates, emphasizing the importance of ligand properties, including concentration, valency, affinity, and spacing between binding sites in studies and designs of condensates.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

A high-fidelity building performance simulation test bed for the development and evaluation of advanced controls

We present an open-source building performance simulation test bed, the Advanced Controls Test Bed (ACTB), that interfaces high-fidelity Spawn of EnergyPlus building models, with advanced controllers implemented in Python. Additionally, the ACTB leverages the Building Optimization Testing and Alfalfa platforms for managing simulations, providing an external clock, a representational state transfer (REST) application programming interface (API), and key performance indicators for evaluating the effectiveness of control strategies. The REST API allows the development of external controllers programmed in languages such as Python, which provides flexibility and a rich choice of scientific libraries for designing control sequences. We present three test cases based on the U.S. Department of Energy's Reference Small Office Building to demonstrate the ACTB's capabilities: (a) rule-based controls compliant with ASHRAE Guideline 36 control sequences; (b) an economic model predictive control implemented using do-mpc; and (c) a deep Q-network reinforcement learning agent implemented using OpenAI Gym.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗