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At least 181 records · Page 10

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↗

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↗

Impacts of irrigation expansion on moist-heat stress based on IRRMIP results

Irrigation rapidly expanded during the 20 th century, affecting climate via water, energy, and biogeochemical changes. Previous assessments of these effects predominantly relied on a single Earth System Model, and therefore suffered from structural model uncertainties. Here we quantify the impacts of historical irrigation expansion on climate by analysing simulation results from six Earth system models participating in the Irrigation Model Intercomparison Project (IRRMIP). Results show that irrigation expansion causes a rapid increase in irrigation water withdrawal, which leads to less frequent 2-meter air temperature heat extremes across heavily irrigated areas (≥4 times less likely). However, due to the irrigation-induced increase in air humidity, the cooling effect of irrigation expansion on moist-heat stress is less pronounced or even reversed, depending on the heat stress metric. In summary, this study indicates that irrigation deployment is not an efficient adaptation measure to escalating human heat stress under climate change, calling for carefully dealing with the increased exposure of local people to moist-heat stress.

54 ENVIRONMENTAL SCIENCES↗

Ultrahigh-pressure crystallographic passage towards metallic hydrogen

The structural evolution of molecular hydrogen H 2 under multi-megabar compression and its relation to atomic metallic hydrogen is a key unsolved problem in condensed-matter physics. Although dozens of crystal structures have been proposed by theory, only one, the simple hexagonal-close-packed (hcp) structure of only spherical disordered H 2 , has been previously confirmed in experiments. Through advancing nano-focused synchrotron X-ray probes, here we report the observation of the transition from hcp H 2 to a post-hcp structure with a six-fold larger supercell at pressures above 212 GPa, indicating the change of spherical H 2 to various ordered configurations. Theoretical calculations based on our XRD results found a time-averaged structure model in the space group $P\bar{6}2c$ with alternating layers of spherically disordered H 2 and new graphene-like layers consisting of H 2 trimers (H 6 ) formed by the association of three H 2 molecules. Here, this supercell has not been reported by any previous theoretical study for the post-hcp phase, but is close to a number of theoretical models with mixed-layer structures. The evidence of a structural transition beyond hcp establishes the trend of H 2 molecular association towards polymerization at extreme pressures, giving clues about the nature of the molecular-to-atomic transition of metallic hydrogen. Considering the spectroscopic behaviours that show strong vibrational and bending peaks of H 2 up to 400 GPa, it would be prudent to speculate the continuation of hydrogen molecular polymerization up to its metallization.

Ji, Cheng [Center for High Pressure Science and Te↗

Dark matter halo mass functions and density profiles from mass and energy cascade

Abstract Halo abundance and structure play a central role for modeling structure formation and evolution. Without relying on a spherical or ellipsoidal collapse model, we analytically derive the halo mass function and cuspy halo density (inner slope of −4/3) based on the mass and energy cascade theory in dark matter flow. The hierarchical halo structure formation leads to halo or particle random walk with a position-dependent waiting time $$\tau _g$$ τ g . First, the inverse mass cascade from small to large scales leads to the halo random walk in mass space with $$\tau _g\propto m_h^{-\lambda }$$ τ g ∝ m h - λ , where $$m_h$$ m h is the halo mass and $$\lambda$$ λ is a halo geometry parameter with predicted value of 2/3. The corresponding Fokker-Planck solution for halo random walk in mass space gives rise to the halo mass function with a power-law behavior on small scale and exponential decay on large scale. This can be further improved by considering two different $$\lambda$$ λ for haloes below and above a critical mass scale $$m_h^*$$ m h ∗ , i.e. a double- $$\lambda$$ λ halo mass function. Second, a double- $$\gamma$$ γ density profile can be derived based on the particle random walk in 3D space with a position-dependent waiting time $$\tau _g \propto \Phi (r)^{-1} \propto r^{-\gamma }$$ τ g ∝ Φ ( r ) - 1 ∝ r - γ , where $$\Phi$$ Φ is the gravitational potential and r is the particle distance to halo center. Theory predicts $$\gamma =2/3$$ γ = 2 / 3 that leads to a cuspy density profile with an inner slope of −4/3, consistent with the predicted scaling laws from energy cascade. The Press-Schechter mass function and Einasto density profile are just special cases of proposed models. The small scale permanence can be identified due to the scale-independent rate of mass and energy cascade, where density profiles of different halo masses and redshifts converge to the $$-4/3$$ - 4 / 3 scaling law ( $$\rho _h \propto r^{-4/3}$$ ρ h ∝ r - 4 / 3 ) on small scales. Theory predicts the halo number density scales with halo mass as $$\propto m_h^{-1.9}$$ ∝ m h - 1.9 , while the halo mass density scales as $$\propto m_h^{4/9}$$ ∝ m h 4 / 9 . Results were compared against the Illustris simulations. This new perspective provides a theory for nearly universal halo mass functions and density profiles.

79 ASTRONOMY AND ASTROPHYSICS↗

The crystal structure of a new calcium aluminate phase containing formate

A new calcium aluminate phase containing formate ions was synthesized and its crystal structure determined. This new phase is indicated as M-phase and was firstly observed in Portland cement pastes hydrated in presence of Ca-formate and in excess of water. The crystal structure of the M-phase was successfully solved in the R-3 space group of the trigonal system on the basis of synchrotron X-ray single crystal diffraction data. The structural model was confirmed by Rietveld refinement of the powder diffraction data acquired on the synthesized pure sample. The crystal structure of the M-phase is similar to that of ettringite, being characterized by columns of AlO{sub 6} octahedra alternating with groups of three edge-sharing CaO{sub 7} polyhedra. The formate ions (HCOO){sup −} share two oxygens with Ca polyhedra and are located in the interspace between the columns. The crystal structure of the M-phase testifies the strong interaction occurring between small organic molecules as formate and the calcium aluminate components of Portland cement.

36 MATERIALS SCIENCE↗

Modification of Quark-Gluon Distributions in Nuclei by Correlated Nucleon Pairs

We extend the QCD Parton Model analysis using a factorized nuclear structure model incorporating individual nucleons and pairs of correlated nucleons. Our analysis of high-energy data from lepton deep-inelastic scattering, Drell-Yan, and W and Z boson production simultaneously extracts the universal effective distribution of quarks and gluons inside correlated nucleon pairs, and their nucleus-specific fractions. Such successful extraction of these universal distributions marks a significant advance in our understanding of nuclear structure properties connecting nucleon- and parton-level quantities. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Determining the ballistic threshold velocity for a composite structure using multiple failure models

A composite structure, such as a laminated composite panel, for example, comprises one or more layers or “plies” embedded in a matrix material or otherwise fixed together in an arrangement, commonly referred to as a “stack up.” Each material in the structure has a corresponding material failure model (MFM) defining the physical characteristics of that material. A ballistic threshold velocity computing device obtains the MFMs for each material in the composite structure, generates a predicted ballistic velocity threshold velocity for each MFM, and then generates a parametric model to compute a composite ballistic velocity threshold velocity for the composite structure.

36 MATERIALS SCIENCE↗

Combining Experimental and Theoretical Techniques to Gain an Atomic Level Understanding of the Defect Binding Mechanism in Hard Carbon Anodes for Sodium Ion Batteries

Sodium ion batteries (NIBs) are an attractive alternative to lithium–ion batteries in applications that require large–scale energy storage due to sodium's high natural abundance and low cost. Hard carbon (HC) is the most promising anode material for NIBs; however, there is a knowledge gap in the understanding of the sodium binding mechanism that prevents a rational design of HC. This study tunes sucrose–derived HC via synthesis temperature then evaluates the structural, physical, and electrochemical properties. Neutron total scattering is used to generate structural models by fitting pair distribution functions (PDF) with a combination of molecular dynamics and reverse Monte Carlo methods. From this model, the number and type of structural features are identified, quantified, and correlated to the galvanostatic charge/discharge. A method of PDF “fingerprinting” binding sites using Na probe atoms is developed and analyzing these PDFs reveals an atomistic view of ion binding sites responsible for “defect” storage mechanisms. Combining these techniques results in an atomic–level study that provides a big picture of the Na–binding mechanism in NIBs, which allows for more precise tuning of the structure–property relationships in the future. Finally, the methodologies developed will also enable new strategies for the analysis of amorphous functional materials.

25 ENERGY STORAGE↗

Tools for analysis of optimization models

The software is code for analyzing, debugging, and solving optimization models. The code implements several algorithms and provides convenient APIs to apply these algorithms to optimization models. The algorithms are primarily based on graph theory. They compute well-known partitions of graphs, and use these partitions to provide the user information about their optimization model, including diagnosing certain types of structural modeling errors. Some algorithms may be used as a subroutine to solve an optimization problem, and may call an optimization solver to facilitate this. Well-known linear algebra routines are called to provide further diagnostics. The software contains no data and no models other than toy models used for testing.

Parker, Robert↗

Implementation of a self-consistent slab model of bilayer structure in the SasView suite

Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. Here, the use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.

36 MATERIALS SCIENCE↗

Unraveling the Molecular Origin of Prey-Wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR

Prey wrapping spider silk's unique mechanical properties are investigated confirming the silk's high degree of extensibility and superior toughness compared to other types of spider silk. For the first time, the pre-spinning dope phase is studied in isotope-enriched intact aciniform (AC) silk glands using solution NMR that reveals a combination of α-helical domains linked by disordered random coil chains consistent with previously proposed “beads-on-a-string” models. The model is further refined through the AlphaFold2 protein structure prediction tool. Finally, extensive magic angle spinning (MAS) solid-state (SS) NMR data for isotopically-enriched fibers is used to refine the structural model for AC silk from two species, A. aurantia and A. argentata. The SSNMR data shows that the AC silk fibers are highly α-helical, coiled-coil in structure but, also exhibit significant β-sheet components that can be traced back to the Gly-rich disordered linker regions in the pre-spinning dope phase that are converted to β-sheet structures during fiber formation. This combination of mechanical and structural characterization enhances the understanding of AC silk's liquid-to-solid transition and structure-mechanics relationship. In conclusion, these prey wrap silk results and models will provide the basis for the design of biomimetic materials inspired by the AC spider silk system.

36 MATERIALS SCIENCE↗

Mirror nucleon removal reactions in p-shell nuclei

Nucleon removal reactions have been shown to be an effective tool for studying the single particle structure of nuclei. This work continues efforts to experimentally probe and benchmark the reaction and structure models used to calculate the removal reaction cross sections when using microscopic nuclear structure inputs. Here, three different single nucleon removal reactions were performed, from p -shell nuclei with masses A = 7, 9, and 10. The residual nuclei from the reactions were detected in coincidence with γ rays to determine partial cross sections to individual final states. The eikonal direct-reaction model is combined with overlap functions and residual nucleus densities from microscopic, variational Monte Carlo calculations to provide consistent nuclear structure input to the partial cross section calculations. Comparisons of measured and calculated cross sections, including for mirror reactions, are presented. The analysis of the partial cross sections leading to the ground states shows a similar behavior to the one observed from analyses of inclusive cross sections using shell model nuclear structure input: the theoretical description of the removal process is in better agreement with the data when removing weakly bound nucleons, than when removing well-bound ones. The two mirror reaction pairs presented here show consistent results between the respective members of the pairs. The results obtained for the population of the excited states, however, show a systematically different trend that appears connected to the structure part of the calculation. Additional cases are needed to better understand the respective roles of structure and dynamical effects in the deviations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗