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At least 271 records · Page 15

A deep learning approach to identify missing is-a relations in SNOMED CT

Abstract Objective SNOMED CT is the largest clinical terminology worldwide. Quality assurance of SNOMED CT is of utmost importance to ensure that it provides accurate domain knowledge to various SNOMED CT-based applications. In this work, we introduce a deep learning-based approach to uncover missing is-a relations in SNOMED CT. Materials and Methods Our focus is to identify missing is-a relations between concept-pairs exhibiting a containment pattern (ie, the set of words of one concept being a proper subset of that of the other concept). We use hierarchically related containment concept-pairs as positive instances and hierarchically unrelated containment concept-pairs as negative instances to train a model predicting whether an is-a relation exists between 2 concepts with containment pattern. The model is a binary classifier leveraging concept name features, hierarchical features, enriched lexical attribute features, and logical definition features. We introduce a cross-validation inspired approach to identify missing is-a relations among all hierarchically unrelated containment concept-pairs. Results We trained and applied our model on the Clinical finding subhierarchy of SNOMED CT (September 2019 US edition). Our model (based on the validation sets) achieved a precision of 0.8164, recall of 0.8397, and F1 score of 0.8279. Applying the model to predict actual missing is-a relations, we obtained a total of 1661 potential candidates. Domain experts performed evaluation on randomly selected 230 samples and verified that 192 (83.48%) are valid. Conclusions The results showed that our deep learning approach is effective in uncovering missing is-a relations between containment concept-pairs in SNOMED CT.

97 MATHEMATICS AND COMPUTING↗

Advancing representations of equity and justice in climate mitigation futures

THIS PAPER WAS PRIMARILY COMPLETED PRIOR TO THE AUTHOR JOINING PNNL AND NO DOE FUNDING WAS USED FOR THIS PAPER. In this work, we review how equity and justice issues in global climate mitigation scenarios are addressed within Integrated Assessment Models (IAMs) and propose a new research agenda to strengthen their integration in model development and application. We begin by examining prominent concerns at the science-policy interface. We introduce a typology of equity and justice limitations in climate mitigation scenarios, distinguishing among structural, methodological, and epistemological biases that shape what integrated assessment models can reveal at policy-relevant scales. Reflecting on these concerns, we propose a research agenda that describes new avenues of work and draws together distinct emerging initiatives. This agenda is based on the feasibility and depth of required interventions, from incremental improvements to structural reforms and alternative participatory approaches. Drawing on reflexive insights from integrated assessment practitioners, it addresses the operational challenges of translating justice concepts into metrics, including risks of reductionism, tokenism, and narrow definitions. Underlying this research agenda is a recognition that modeling communities must engage more critically with implicit assumptions in model design and use that have equity and justice implications. Achieving equitable climate futures will require transformative actions that integrate diverse justice concerns, advance sustainable development goals, and confront systemic inequities across both human and ecological dimensions. Although models will never capture all these aspects, they can be significantly enhanced to support more informed discussion and practical application. Our contribution proposes a way forward to achieving this goal.

Pachauri, Shonali↗

A taxonomy of constraints in black-box simulation-based optimization

The types of constraints encountered in black-box simulation-based optimization problems differ significantly from those addressed in nonlinear programming. Here, we introduce a characterization of constraints to address this situation. We provide formal definitions for several constraint classes and present illustrative examples in the context of the resulting taxonomy. This taxonomy, denoted KARQ, is useful for modeling and problem formulation, as well as optimization software development and deployment. It can also be used as the basis for a dialog with practitioners in moving problems to increasingly solvable branches of optimization.

42 ENGINEERING↗

Co-optimized machine-learned manifold models for large eddy simulation of turbulent combustion

Many modeling approaches in large eddy simulation (LES) of turbulent combustion employ a projection of the thermochemical state onto a low-dimensional manifold within state space to reduce the number of transported variables and hence computational cost. Flamelet-generated manifolds (FGM) is an example of a well-established, physics-based approach, but increasingly, principal component analysis (PCA) is being used as a data-driven method for generating manifold models. For both approaches, the nonlinear relationship between the location on the predefined manifold and the outputs of interest, such as reaction rates, can be tabulated or encoded in a neural network. This work proposes a new approach for manifold modeling that extends these existing approaches. A modified neural network structure simultaneously encodes the definition of the manifold variables, the nonlinear mapping, and the subfilter closure for LES. This allows all three of these aspects of the model to be co-optimized, generating a model from any source of combustion thermochemical state data. The manifold parameterizing variables are constrained to be linear combinations of species, as in FGM and PCA-based models, to aid in interpretability and implementation. For LES, subfilter variances of the manifold variables are also included as inputs. Two types of a priori analysis are performed to evaluate the new approach. In the first, the model is trained on data from one-dimensional premixed flames. In this case, the approach recovers the behavior of flamelet-based manifold approaches, and in fact slightly improves performance by identifying an optimized progress variable. The approach is also applied to data from direct numerical simulations of spherical ignition kernels in isotropic turbulence. For any specified manifold dimensionality, the new approach provides substantially lower prediction errors than a PCA-based model developed from the same data set. Additionally, the LES formulation of the new approach can provide accurate predictions for filtered reaction rates across a variety of filter widths.

97 MATHEMATICS AND COMPUTING↗

A Comprehensive X-Ray Absorption Model for Atomic Oxygen

An analytical formula is developed to accurately represent the photoabsorption cross section of atomic Oxygen for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.

supernova remnants↗

Towards philosophical reasoning with agentic LLMs: Socratic method for scientific assistance

As large language models (LLMs) become central tools in science, improving their reasoning capabilities is critical for meaningful and trustworthy applications. We introduce a Socratic agent for scientific reasoning, implemented through a structured system prompt that guides LLMs via classical principles of inquiry. Unlike typical prompt engineering or retrieval-based methods, our approach leverages definition, analogy, hypothesis elimination, and other Socratic techniques to generate more coherent, critical, and domain-aware responses. We evaluate the agent across diverse scientific domains and benchmark it on the abstraction and reasoning corpus challenge dataset, achieving 97.15% under a fixed prompting protocol and without fine-tuning or external tools. Expert evaluation shows improved reasoning depth, clarity, and adaptability over conventional LLM outputs, suggesting that structured prompting rooted in philosophical reasoning can improve the scientific utility of language models.

LLM reasoning↗

Application of Powder Diffraction Methods to the Analysis of the Atomic Structure of Nanocrystals: The Concept of the Apparent Lattice Parameter (ALP)

The applicability of standard methods of elaboration of powder diffraction data for determination of the structure of nano-size crystallites is analysed. Based on our theoretical calculations of powder diffraction data we show, that the assumption of the infinite crystal lattice for nanocrystals smaller than 20 nm in size is not justified. Application of conventional tools developed for elaboration of powder diffraction data, like the Rietveld method, may lead to erroneous interpretation of the experimental results. An alternate evaluation of diffraction data of nanoparticles, based on the so-called 'apparent lattice parameter' (alp) is introduced. We assume a model of nanocrystal having a grain core with well-defined crystal structure, surrounded by a surface shell with the atomic structure similar to that of the core but being under a strain (compressive or tensile). The two structural components, the core and the shell, form essentially a composite crystal with interfering, inseparable diffraction properties. Because the structure of such a nanocrystal is not uniform, it defies the basic definitions of an unambiguous crystallographic phase. Consequently, a set of lattice parameters used for characterization of simple crystal phases is insufficient for a proper description of the complex structure of nanocrystals. We developed a method of evaluation of powder diffraction data of nanocrystals, which refers to a core-shell model and is based on the 'apparent lattice parameter' methodology. For a given diffraction pattem, the alp values are calculated for every individual Bragg reflection. For nanocrystals the alp values depend on the diffraction vector Q. By modeling different a0tomic structures of nanocrystals and calculating theoretically corresponding diffraction patterns using the Debye functions we showed, that alp-Q plots show characteristic shapes which can be used for evaluation of the atomic structure of the core-shell system. We show, that using a simple model of a nanocrystal with spherical shape and centro-symmetric strain at the surface shell we obtain theoretical alp-Q values which match very well the alp-Q plots determined experimentally for Sic, GaN, and diamond nanopowders. The theoretical models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the surface shell. According to our calculations, the part of the diffraction pattern measured at relatively low diffraction vectors Q (below 10/angstrom) provides information on the surface strain, whle determination of the lattice parameters in the grain core requires measurements at large Q-values (above 15 - 20/angstrom).

Palosz, B.↗

Selective mass scaling for single-layer thick shell elements in DYNA3D

Hexahedral elements can be adapted to model thin and moderately thick structures by neglecting the coupling of through-thickness stress, resulting in a fully three-dimensional, but simplified, state of stress. These specialized elements, often referred to as “thick” or “solid” shells, are generally employed to model thin-walled structures using continuum mechanics-based material models. In explicit dynamics simulations, where computational speed is important, these elements are integrated with a single quadrature point and a set of anti-hourglassing (stabilizing) forces. Thick shells, by definition, have a thickness dimension smaller than their in-plane dimensions, and this small thickness often determines the stable time step size in simulations, despite the mechanics being approximated. To alleviate this limitation while retaining the relevant dynamics of thin-walled structures, selective mass scaling (SMS), or selective mass “augmentation,” has been proposed in the literature. In this technical report, we explore the application of SMS to single-layer thick shells in the simulation software DYNA3D.

42 ENGINEERING↗

Development of Comprehensive Reduced Kinetic Models for Supersonic Reacting Shear Layer Simulations

Large-scale simulations of multi-dimensional unsteady turbulent reacting flows with detailed chemistry and transport can be computationally extremely intensive even on distributed computing architectures. With the development of suitable reduced chemical kinetic models, the number of scalar variables to be integrated can be decreased, leading to a significant reduction in the computational time required for the simulation with limited loss of accuracy in the results. A general MATLAB-based automated mechanism reduction procedure is presented to reduce any complex starting mechanism (detailed or skeletal) with minimal human intervention. Based on the application of the quasi steady-state (QSS) approximation for certain chemical species and on the elimination of the fast reaction rates in the mechanism, several comprehensive reduced models, capable of handling different fuels such as C2H4, CH4 and H2, have been developed and thoroughly tested for several combustion problems (ignition, propagation and extinction) and physical conditions (reactant compositions, temperatures, and pressures). A key feature of the present reduction procedure is the explicit solution of the concentrations of the QSS species, needed for the evaluation of the elementary reaction rates. In contrast, previous approaches relied on an implicit solution due to the strong coupling between QSS species, requiring computationally expensive inner iterations. A novel algorithm, based on the definition of a QSS species coupling matrix, is presented to (i) introduce appropriate truncations to the QSS algebraic relations and (ii) identify the optimal sequence for the explicit solution of the concentration of the QSS species. With the automatic generation of the relevant source code, the resulting reduced models can be readily implemented into numerical codes.

Zambon, A. C.↗

Enhancements to NURBS-Based FEA Airfoil Modeler: SABER

NURBS (Non-Uniform Rational B-Splines) have become a common way for CAD programs to fit a smooth surface to discrete geometric data. This concept has been extended to allow for the fitting of analysis data in a similar manner and "attaching" the analysis data to the geometric definition of the structure. The "attaching" of analysis data to the geometric definition allows for a more seamless sharing of data between analysis disciplines. NURBS have become a useful tool in the modeling of airfoils. The use of NURBS has allowed for the development of software that easily and consistently generates plate finite element models of the midcamber surface of a given airfoil. The resulting displacements can then be applied to the original airfoil surface and the deformed shape calculated.

Saleeb, A. F.↗

Estimation of pipe failure frequencies in the absence of operational experience data: A pilot study

Probabilistic failure metrics such as leak frequency and rupture frequency are commonly used to characterize piping reliability. The methodologies for calculating the failure metrics rely on a complex set of input parameters. Operating experience data and experimental data play an important role in informing the different input parameters. The paper describes results and conclusions of a coordinated research project to benchmark three different reliability models using a four-step procedure: reference case definition of relevance to advanced reactor designs, input parameter calibration, validation of results, and application of different methodologies upon completion of the calibration and validation steps. The reference case is a weld consisting of nickel-base alloy 152/52 and located within a primary pressure boundary of an advanced reactor. This alloy is a class of structural materials known to be highly resistant to stress corrosion cracking. Synergies between the different methods are noted and the importance of a multi-disciplinary approach to input parameter development is underscored. A key conclusion is that the three methods are equally suitable for estimating failure frequencies. In any specific application, a selection of the most practical or effective computational tool can be considered. The comparison of alternative models confirms and helps to gain confidence in the computed failure frequency estimates. The study was part of a coordinated research project organized by the International Atomic Energy Agency.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Particle configurations in the $NN\bar K$ system

Three-body AAB model for the $NN\bar K$(s NN = 0) kaonic cluster is considered based on the configuration space Faddeev equations. Within a single channel approach, the difference between masses of nucleons and kaons and the charge independence breaking of nucleon-nucleon interaction are taken into consideration. We definite the particle configurations in the system according to the particle masses and pair potentials. There are two sets of the particle configurations, ppK¯, npK¯ 0 and nnK¯ 0 , npK¯, charged and neutral. The three-body calculations are performed by applying NN and NK¯ phenomenological isospin-dependent potentials. The mass and energy spectra related to the particle configurations are presented. We evaluate the mass and energy uncertainties for the NNK¯ model. As a result, an analogy to NNN model for the 3 H and 3 He nuclei is proposed.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Spaceliner Class Operability Gains Via Combined Airbreathing/ Rocket Propulsion: Summarizing an Operational Assessment of Highly Reusable Space Transports

In discussing a new NASA initiative in advanced space transportation systems and technologies, the Director of the NASA Marshall Space Flight Center, Arthur G. Stephenson, noted that, "It would use new propulsion technology, air-breathing engine so you don't have to carry liquid oxygen, at least while your flying through the atmosphere. We are calling it Spaceliner 100 because it would be 100 times cheaper, costing $ 100 dollars a pound to orbit." While airbreathing propulsion is directly named, rocket propulsion is also implied by, "... while you are flying through the atmosphere." In-space final acceleration to orbital speed mandates rocket capabilities. Thus, in this informed view, Spaceliner 100 will be predicated on combined airbreathing/rocket propulsion, the technical subject of this paper. Interestingly, NASA's recently concluded Highly Reusable Space Transportation (HRST) study focused on the same affordability goal as that of the Spaceliner 100 initiative and reflected the decisive contribution of combined propulsion as a way of expanding operability and increasing the design robustness of future space transports, toward "aircraft like" capabilities. The HRST study built on the Access to Space Study and the Reusable Launch Vehicle (RLV) development activities to identify and characterize space transportation concepts, infrastructure and technologies that have the greatest potential for reducing delivery cost by another order of magnitude, from $1,000 to $100-$200 per pound for 20,000 lb. - 40.000 lb. payloads to low earth orbit (LEO). The HRST study investigated a number of near-term, far-term, and very far-term launch vehicle concepts including all-rocket single-stage-to-orbit (SSTO) concepts, two-stage-to-orbit (TSTO) concepts, concepts with launch assist, rocket-based combined cycle (RBCC) concepts, advanced expendable vehicles, and more far term ground-based laser powered launchers. The HRST study consisted of preliminary concept studies, assessments and analysis tool development for advanced space transportation systems, followed by end-to-end system concept definitions and trade analyses, specific system concept definition and analysis, specific key technology and topic analysis, system, operational and economics model development, analysis, and integrated assessments. The HRST Integration Task Force (HITF) was formed to synthesize study results in several specific topic areas and support the development of conclusions from the study: Systems Concepts Definitions, Technology Assessment, Operations Assessment, and Cost Assessment. This paper summarizes the work of the Operations Assessment Team: the six approaches used, the analytical tools and methodologies developed and employed, the issues and concerns, and the results of the assessment. The approaches were deliberately varied in measures of merit and procedure to compensate for the uncertainty inherent in operations data in this early phase of concept exploration. In general, rocket based combined cycle (RBCC) concepts appear to have significantly greater potential than all-rocket concepts for reducing operations costs.

Nix, Michael B.↗

Multi-species collisions for delta-f gyrokinetic simulations: Implementation and verification with GENE

we report a multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius (FLR) effects have also been implemented into the local version of the code. For the global version of the code, the collision operator has been developed to allow for block-structured velocity space grids, allowing for computationally tractable collisional global simulations. The validity of the collision operator has been demonstrated by relaxation and conservation tests, as well as appropriate benchmarks. The newly implemented operator shall be used in future simulations to study magnetically confined fusion plasma turbulence and transport in more extreme regions with higher collisionality.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Multi-species collisions for delta-f gyrokinetic simulations: Implementation and verification with GENE

A multi-species linearized collision operator based on the model developed by Sugama et al. has been implemented in the nonlinear gyrokinetic code, GENE. Such a model conserves particles, momentum, and energy to machine precision, and is shown to have negative definite free energy dissipation characteristics, satisfying Boltzmann’s H-theorem, including for realistic mass ratio. Finite Larmor Radius (FLR) effects have also been implemented into the local version of the code. For the global version of the code, the collision operator has been developed to allow for block-structured velocity space grids, allowing for computationally tractable collisional global simulations. The validity of the collision operator has been demonstrated by relaxation and conservation tests, as well as appropriate benchmarks. The newly implemented operator shall be used in future simulations to study magnetically confined fusion plasma turbulence and transport in more extreme regions with higher collisionality.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

High supersonic stability and control characteristics of a 0.015-scale (remotely controlled elevon) model 49-0 of the space shuttle orbiter tested in the NASA/LaRC 4-foot UPWT (LEG 2) (LA63B)

The model tested was a Langley-built 0.015-scale SSV Orbiter model with remote independently operated left and right elevon surfaces. The objective of the test was to generate a detailed aerodynamic data base for the current Shuttle Orbiter Configuration. Special attention was directed to definition of nonlinear aerodynamic characteristics by taking data at small increments, angle of attack, angle of sideslip, and elevon position. Six-component aerodynamic force and moment and elevon position data were recorded over an angle-of-attack range from -4 deg to 45 deg, at angles of sideslip of 0 deg, + or - 2 deg, and + or - 4 deg. Additional tests were made over an angle of sideslip range from -6 deg to 8 deg at selected angles of attack. The test Mach numbers were 2.86, 3.90, and 4.60 with Reynolds number held at a constant two million per foot.

Gamble, J. D.↗

Subsonic stability and control characteristics of a 0.015-scale (remotely controlled elevon) model 44-0 of the space shuttle orbiter tested in the NASA/ARC 12-foot pressure tunnel (LA66)

The investigation was conducted in the NASA/Ames Research Center 12-foot Pressure Tunnel. The model was a Langley-built 0.015-scale SSV orbiter model with remote independently operated left and right elevon surfaces. The objective of the test was to generate a detailed aerodynamic data base for the current shuttle orbiter configuration. Special attention was directed to definition of nonlinear aerodynamic characteristics by taking data at small increments in angle of attack, angle of sideslip, and elevon position. Six-component aerodynamic force and moment and elevon position data were recorded over an angle of attack range from -4 deg to 24 deg at angles of sideslip of 0 deg and + or - 4 deg. Additional tests were made over an angle of sideslip range from -6 deg to 6 deg at selected angles of attack. The test Mach numbers were 0.22 and 0.29 and the Reynolds number was varied from 2.0 to 8.5 million per foot.

Underwood, J. M.↗

Scattering of high-velocity Ar atoms by CO2, OCS, and CS2

Fast Ar beams have been scattered by room-temperature CO2, OCS, and CS2 to obtain average atom-molecule potentials. The results are consistent with other scattering measurements on similar systems, and are also in excellent agreement with available theoretical calculations based on an electron-gas model. Decomposition of the atom-molecule potentials into constituent atom-atom potentials shows that such a representation can be utilized with fair accuracy but that a definite discrepancy exists.

Amdur, I.↗