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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 667 records · Page 37

Model verification of large structural systems

A computer program for the application of parameter identification on the structural dynamic models of space shuttle and other large models with hundreds of degrees of freedom is described. Finite element, dynamic, analytic, and modal models are used to represent the structural system. The interface with math models is such that output from any structural analysis program applied to any structural configuration can be used directly. Processed data from either sine-sweep tests or resonant dwell tests are directly usable. The program uses measured modal data to condition the prior analystic model so as to improve the frequency match between model and test. A Bayesian estimator generates an improved analytical model and a linear estimator is used in an iterative fashion on highly nonlinear equations. Mass and stiffness scaling parameters are generated for an improved finite element model, and the optimum set of parameters is obtained in one step.

Lee, L. T.↗

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules ( e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

59 BASIC BIOLOGICAL SCIENCES↗

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. We present the predicted structural proteome (25,134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

59 BASIC BIOLOGICAL SCIENCES↗

Multistep modeling of protein structure: application to bungarotoxin

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

NASA Discipline Exobiology↗

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

59 BASIC BIOLOGICAL SCIENCES↗

Advanced Mirror & Modelling Technology Development

The 2020 Decadal technology survey is starting in 2018. Technology on the shelf at that time will help guide selection to future low risk and low cost missions. The Advanced Mirror Technology Development (AMTD) team has identified development priorities based on science goals and engineering requirements for Ultraviolet Optical near‐Infrared (UVOIR) missions in order to contribute to the selection process. One key development identified was lightweight mirror fabrication and testing. A monolithic, stacked, deep core mirror was fused and replicated twice to achieve the desired radius of curvature. It was subsequently successfully polished and tested. A recently awarded second phase to the AMTD project will develop larger mirrors to demonstrate the lateral scaling of the deep core mirror technology. Another key development was rapid modeling for the mirror. One model focused on generating optical and structural model results in minutes instead of months. Many variables could be accounted for regarding the core, face plate and back structure details. A portion of a spacecraft model was also developed. The spacecraft model incorporated direct integration to transform optical path difference to Point Spread Function (PSF) and between PSF to modulation transfer function. The second phase to the project will take the results of the rapid mirror modeler and integrate them into the rapid spacecraft modeler.

Effinger, Michael↗

Nondestructive construction error detection in large space structures

Continuum modeling of large space structures is extended to the problem of detecting construction errors in large space structures such as the proposed space station. First-order dynamic sensitivity equations for structures involving eigenfrequencies, modal masses, modal stiffnesses, and modal damping are presented. Matrix equations relating changes in element parameters to dynamic sensitivities are summarized. The sensitivity equations for the entire dynamical system are rearranged as a system of algebraic equations with unknowns of stiffness losses at selected locations. The feasibility of the formulation is numerically demonstrated on a simply-supported Euler-Bernouilli beam with simulated construction defects. The method is next extended to large space structures modelled as equivalent continua with simulated construction defects.

Stubbs, Norris↗

Knowledge Graph for End-to-End Traceability of an Integrated Human-Earth System Model

Integrated human-Earth system models inform energy-water-land system dynamics and policies, yet their results are difficult to trace through input-data, model structure, scenario configurations, and solved outputs. Because this information is siloed across disconnected artifacts, process-based IAMs have historically lacked a unified, queryable representation. Such lack of traceability prevents researchers from systematically isolating the multi-sector drivers of complex outcomes (such as tracing water-scarcity results back to distant energy-system dynamics) or conducting holistic uncertainty attribution across hundreds of interacting parameters. To address this concern, our work documents the software engineering process of a knowledge graph that unifies these four layers for the Global Change Analysis Model (GCAM-USA_Reference scenario, GCAM v9.1). The graph was built as a relational property graph in DuckDB from the run’s own artifacts: the input-preparation dependency map (gcamdata chunk map), the model’s XML input files, the run configuration, and the results database (BaseX), successfully mapping the model’s declared structure. The resulting graph comprises 204,321 nodes and 1,687,814 edges across 16 node types and 15 edge types, with approximately 16.3 million time-series values stored separately to maintain structural efficiency. To ensure representation fidelity, every edge carries an epistemic-status annotation recording the warrant for the relationship (structural, provenance, dependency, or model-derived), and a machine-readable provenance ledger classifying the origin of every schema element. Evaluation against a fixed five-benchmark suite with locked baselines reports zero structural orphans, zero dangling edge endpoints, and 100% of output-producing technologies traceable to raw input files. Two interactive interfaces present the graph, including a serverless browser application built on DuckDB-Wasm. By establishing the first end-to-end provenance framework for an IAM, this work enables researchers and scientists to systematically audit complex policy scenarios, debug model structures, and trace policy-relevant outputs to their data origins in real time.

Artifical Intelligence↗

Study of beyond nearest-neighbor environment and intermediate-range order in a sodium aluminosilicate geopolymer using Reverse Monte Carlo modeling

A large scale three-dimensional structural model of a geopolymer with an approximate composition of NaAlSi 2 O 6 .5.5H 2 O obtained by Reverse Monte Carlo (RMC) modeling based on experimental high-energy x-ray diffraction is presented for the first time in order to obtain information regarding beyond nearest-neighbor environment and intermediate-range order (IRO). RMC model exhibits a three-dimensional network consisting of randomly cross-linked AlO 4 and SiO 4 tetrahedral units with uniformly distributed Na atoms and H 2 O molecules. The bond angle distributions, i.e. T-O-T, O-T-O and Na-O-Na angles, are somewhat distorted with lower values compared to analogous crystal systems. The origin of the first peak in the structure factor indicating IRO is investigated using the partial structure factors; Na-Na, Si-Na, Al-Si, O-H, and H-H atom pairs are found to be the main contributors. Ring size distribution analysis demonstrates that the structure mainly involves 6-, 7- and 8-membered rings. Finally, the coherence length of these IRO characteristics is ~10.3 Å.

36 MATERIALS SCIENCE↗

Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks

Cryogenic electron microscopy (CryoEM) produces structures of macromolecules at near-atomic resolution. However, building molecular models with good stereochemical geometry from those structures can be challenging and time-consuming, especially when many structures are obtained from datasets with conformational heterogeneity. Here we present a model refinement protocol that automatically generates series of molecular models from CryoEM datasets, which describe the dynamics of the macromolecular system and have near-perfect geometry scores. This method makes it easier to interpret the movement of the protein complex from heterogeneity analysis and to compare the structural dynamics observed from CryoEM data with results from other experimental and simulation techniques.

59 BASIC BIOLOGICAL SCIENCES↗

Combining Structural and Substructural Mathematical Models

Automation reduces input length and potential data-entry errors. Matrix Automated Reduction and Coupling (MARC) program used for combining NASTRAN substructural models with primary structural model MARC also constructs job-control language (JCL) stream for NASTRAN batch job that utilizes previously-written user library of dynamic models. Minimizes lengthy input and reduces potential data-entry errors. MARC procedure used in assembling Space Shuttle orbiter dynamic models since 1983 and reduced NASTRAN modeling input time by as much as 50 percent. MARC program written in FORTRAN IV for interactive execution.

Choa, V. K.↗

Structure Based Prediction of Neoantigen Immunogenicity

The development of immunological therapies that incorporate peptide antigens presented to T cells by MHC proteins is a long sought-after goal, particularly for cancer, where mutated neoantigens are being explored as personalized cancer vaccines. Although neoantigens can be identified through sequencing, bioinformatics and mass spectrometry, identifying those which are immunogenic and able to promote tumor rejection remains a significant challenge. Here we examined the potential of high-resolution structural modeling followed by energetic scoring of structural features for predicting neoantigen immunogenicity. After developing a strategy to rapidly and accurately model nonameric peptides bound to the common class I MHC protein HLA-A2, we trained a neural network on structural features that influence T cell receptor (TCR) and peptide binding energies. The resulting structurally-parameterized neural network outperformed methods that do not incorporate explicit structural or energetic properties in predicting CD8 + T cell responses of HLA-A2 presented nonameric peptides, while also providing insight into the underlying structural and biophysical mechanisms governing immunogenicity. Our proof-of-concept study demonstrates the potential for structure-based immunogenicity predictions in the development of personalized peptide-based vaccines.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling Deformable Linear Objects for Autonomous Robotic Outfitting of Lunar Surface Systems

This paper presents structural models of deformable linear objects (DLOs). DLOs are a subclass of deformable objects that encompasses common outfitting elements such as cables and ropes. Models are validated through hardware experiments, and integration in a robotic autonomy architecture for space environments is discussed. A persistent human presence on the lunar surface is one of the next major milestones in space exploration. This requires the development of robust extraplanetary construction technologies including structures and materials modeling and robotic systems. Previous robotic construction technology development has primarily focused on structural assembly, with significantly less focus on robotically performed outfitting tasks to instantiate subsystems providing power, data, life support, etc. These tasks involve manipulation of highly flexible elements, which are difficult to model, such as cable harnesses, ropes, and hoses. Robotic manipulation of DLOs, especially cable harnesses, is an active area of research as cable harnesses are essential for providing power and data to space assets. DLO models that can be used for robot manipulator trajectory generation are necessary for autonomous operation of lunar infrastructure. There are many proposed methods for modeling DLOs, and they primarily fall into three types: 1) discrete model-based, 2) continuum model-based, and 3) Neural Network-based. These types each have pros and cons, and the tradeoff between model accuracy and computational speed informs which type should be used. An understanding of this trade-off is imperative for real-time control of autonomous systems. High computational requirements reduce the speed of the model, making real-time control difficult, while accuracy is critical to preventing collisions. Discrete models, such as a mass-spring multibody representation, require relatively few calculations, and accuracy is directly tied to the step size of the discretization. Continuum models, such as a B-spline representation or a Cosserat rod model (a mix of continuous and discrete), are more informed of the structural properties of the cable and are much more accurate than a rigid body mass-spring model, but at significant computational cost. A Neural Network approach can provide an online solution with very few computational steps, but properly generating training data can be difficult and validation for an in-space application is not trivial. This paper explores the trade-off between different modeling approaches and compares accuracy and computational speed/complexity of the three types mentioned above. Model accuracy is evaluated using a cable in a static configuration. True cable shape is obtained using a depth camera for RGB images and point-cloud segmentation. The purpose of this experiment is to evaluate the trade-offs of different approaches to the DLO modeling problem. Understanding the tradeoffs between different cable modeling techniques paves the way for developing robotic control and planning architectures necessary for real-time manipulation of DLOs for lunar infrastructure outfitting. Real-time control is required for robotic systems to be able to actively manipulate a cable in a harsh environment where model and sensor errors compound, and environmental conditions can cause significant disturbances. Cable routing must be performed in areas with high density of objects/obstacles: through truss structures, near solar panels or mirror arrays, next to bundles of electrical equipment. Understanding the best way to plan and manipulate a cable without disrupting the environment or damaging the cable is imperative to robotic outfitting operations on the lunar surface.

Amy M Quartaro↗

Shock-wave structure using nonlinear model Boltzmann equations.

The structure of strong plane shock waves in a perfect monatomic gas was studied using four nonlinear models of the Boltzmann equation. The models involved the use of a simplified collision operator with velocity-independent collision frequency, in place of the complicated Boltzmann collision operator. The models employed were the BGK and ellipsoidal models developed by earlier authors, and the polynomial and trimodal gain function models developed during the work. An exact set of moment equations was derived for the density, velocity, temperature, viscous stress, and heat flux within the shock. This set was reduced to a pair of coupled nonlinear integral equations and solved using specially adapted numerical techniques. A new and simple Gauss-Seidel iteration was developed during the work and found to be as efficient as the best earlier iteration methods.

Segal, B. M.↗

Renewable Energy and Efficiency Technologies in Scenarios of U.S. Decarbonization in Two Types of Models: Comparison of GCAM Modeling and Sector-Specific Modeling

Energy system projections from quantitative models inform actions ranging from short-term and local decisions, such as those about technology and infrastructure deployment, and global and long-term negotiations and targets. Computational limits require model designers to balance coverage and resolution (i.e., breadth versus depth). Some models, such as the Global Change Analysis Model (GCAM), represent all energy sources and uses with less resolution than models that focus on a single sector's energy use. GCAM balances global supply and demand of all energy carriers projecting prices using internal calculations for energy sources and costs of greenhouse gas mitigation while capturing interlinkages between the energy system, water, agriculture and land use, the economy, and the climate. This globally comprehensive model was used to frame the Long-Term Strategy of the United States: Pathways to Net-Zero Greenhouse Gas Emissions by 2050, which the White House released in 2021 and has been used to inform national and global economy-wide climate change mitigation discussions and strategy development for decades. Unlike GCAM, sectoral models focus on a portion of the energy sector and with greater detail and resolution. The Regional Energy Deployment System (ReEDS) electricity-sector model, for example, projects electricity system capacity expansion and operation with high-fidelity representation of emerging technologies for deep decarbonization, such as variable renewable energy and energy storage, and integration of these technologies into the electric grid. The Transportation Energy and Mobility Pathway Options (TEMPO) transportation-sector model enables analysis of household choices, with a focus on adoption, charging, and use of electric vehicles. The Scout buildings-sector model supports detailed consideration of the policies and markets that can accelerate the adoption of electrification and energy conservation measures in buildings. Such sector-specific models are instrumental in informing technology research, sectoral planning strategies, and sector-specific aspects of greenhouse gas mitigation strategies in the United States. The integrated multisector and sector-specific modeling approaches represented by GCAM and these sectoral models are complementary. The integrated multisector approach calculates energy pricing and resource allocation within the model, which is important for consistency when future conditions substantially diverge from current conditions in transformative scenarios. The sector-specific approach facilitates representation of granular details across spatial, temporal, technological, and market dimensions that enable exploration of particular interactions and trade-offs. This report presents the results of recent work to explore the differences and trade-offs between these approaches by comparing GCAM with the sector-specific ReEDS, TEMPO, and Scout models. The report compares both model structures and results, and it addresses their potential relevance and applications.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Enumeration as a Tool for Structure Solution: A Materials Genomic Approach to Solving the Cation-Ordered Structure of Na 3 V 2 (PO 4 ) 2 F 3

While powder diffraction methods are routinely utilized to optimize structural models for compounds whose crystal structures are known, the determination of unknown structures is far more challenging. When the unknown structure is large, structure solution can become a virtually intractable problem using standard structure solution methodologies, especially when the space group cannot be unambiguously resolved. One such system is the promising Na-ion battery cathode material Na 3 V 2 (PO 4 ) 2 F 3 whose high temperature and room temperature structures were previously solved, but whose more complex low-temperature structure could not be determined. Here, a novel materials genomic approach is demonstrated for the solution of the unknown 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 in which enumeration methods are first used to generate a large number (~3,000) of trial structures based on plausible orderings of Na ions and then automated Rietveld refinements are carried out to optimize each of these trial structures. Based on both the analysis of the ensemble of optimized trial structures and the density functional theory energy minimization of selected trial structures, the 100 K structure of Na 3 V 2 (PO 4 ) 2 F 3 is best described as belonging to the space group A2 1 am with unit cell dimensions of a = 9.01928(4), b = 27.1379(1), c = 10.73307(5). The 100 K unit cell has a large volume of 2627.07(2) Å 3 with Z = 12 and 33 independent crystallographic sites (9 Na, 3 V, 3 P, 12 O, and 6 F) that is 3x and 6x larger than the room- and high-temperature polymorphs of this phase, respectively. Finally, the novel methods described here will be generally applicable for the solution of the complex cation-ordered structures that commonly occur for battery materials.

36 MATERIALS SCIENCE↗