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DOE OSTI2023

Evaluating Retention Index Score Assumptions to Refine GC–MS Metabolite Identification

As metabolomics grows into a high-throughput and high demand research field, current metrics for the identification of small molecules in gas chromatography–mass spectrometry (GC–MS) still require manual verification. Though steps have been taken to improve scoring metrics by combining spectral similarity (SS) and retention index (RI), the problem persists. A large body of literature has analyzed and refined SS scores, but few studies have explicitly studied improvements to RI scores. Here, in this study, we examined whether uninvestigated assumptions of the RI score are valid and propose ways to improve them. Query RIs were matched to library RI with a generous window of ±35 to avoid unintentional removal of valid compound identifications. Each match was manually verified as a true positive (TP), true negative, or unknown. Metabolites with at least 30 TP identifications were included in downstream analyses, resulting in a total of 87 metabolites from samples of varying complexity and type (e.g., amino acid mixtures, human urine, fungal species, and so on.). Our results showed that the RI score assumptions of normality, consistent variance across metabolites, and a mean error centered at 0 are often violated. We demonstrated through a cross-validation analysis that modifying these underlying assumptions according to empirical metabolite-specific distributions improved the TP and negative rankings. Further, we statistically determined the minimum number of samples required to estimate distributional parameters for scoring metrics. Overall, this work proposes a robust statistical pipeline to reduce the time bottleneck of metabolite identification by improving RI scores and thus minimize the effort to complete manual verification.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Evaluating Shallow Convection Parameterization Assumptions With a q t – w Quadrant Analysis

Abstract Uncertainties associated with the response of shallow clouds to global warming remain a great challenge for climate projection. Due to the small size of these clouds, parameterizations are required to represent them in both current‐ and next‐generation climate models. We present a quantitative evaluation of several important assumptions used in both mass‐flux and Assumed‐PDF Higher‐Order Closure parameterizations of shallow convection. We use large‐eddy simulations (LESs) of four different shallow convection regimes as benchmarks and apply a q t (total moisture)– w (vertical velocity) quadrant analysis technique to identify the “coherent structures” of moist and dry up/down‐drafts. The statistics of these coherent structures and the environment are then used to evaluate commonly used assumptions in mass‐flux parameterizations related to (a) the convective downdrafts and (b) the subplume variability of convective updrafts. For quantitative evaluation of the PDF closure used in AP‐HOCs, we perform offline calculations with the PDF closure used in the Cloud Layers Unified By Bi‐normals and the Simplified Higher‐Order Closure schemes by supplying the closure with statistical quantities directly calculated from the LESs. Then, the impact of parameterization assumptions embedded in the PDF closure in the same two categories is analyzed and understood through comparisons of the output from the closure with the statistics of the moist and dry up/down‐drafts from the LESs.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Impact of microkinetic modeling assumptions on predicted kinetics and mechanisms over undercoordinated sites

Accurate modeling of catalytic reactions on undercoordinated sites requires accounting for the structural and ensemble-specific nature of the active sites. This study examines how common microkinetic modeling (MKM) assumptions affect predicted kinetics and mechanisms on the stepped Pt(211) facet for the ethane dehydrogenation (EDH) and the ethane hydrogenolysis (EH). Six (211) MKMs were developed, differing in (i) the number of active sites represented, (ii) adsorbate site occupancy treatment, and (iii) inclusion of cross-facet interactions. These models are benchmarked against a particle-based microkinetic model (PB-MKM), which best represents step-edge behavior. MKM assumptions caused deviations in turnover frequencies exceeding ten orders of magnitude and led to contrasting mechanistic and selectivity predictions. Multi-site MKMs overestimate activity by inflating free site availability, single-site models underestimate activity, and uniform occupancy models overpredict coverage of multi-dentate intermediates, leading to reaction-specific artifacts. Overall, the Combined Site Edge Model (CSEM), a single-site MKM accounting for site occupancy and cross-facet interactions, most closely approximates PB-MKM predictions. All models predict similar kinetics when surfaces are clean or primarily occupied by monodentate species. This work provides practical guidance for selecting MKM frameworks for undercoordinated catalytic surfaces and highlights the critical role of modeling assumptions in catalytic predictions.

(211) facet↗

DOE OSTI2024

Exploring poly-crystallization in semiconductors through assumption-less growth simulations: CdTe/CdS case study

Crystal growth is a complex process with far-reaching implications for high-performance materials across various fields. Recent advancements in structural analysis methods such as polyhedral template matching, which allows semiconductor-specific analysis, coupled with simulation technology, have enabled the comprehensive study of crystallization dynamics in semiconductors. However, the exploration of polycrystalline semiconductors created with minimal external intervention of the crystallization processes is relatively uncharted in comparison with metals. In this study, we employ molecular dynamics to simulate the growth of polycrystalline CdTe/CdS with the assumptions of classical mechanics, a Stillinger–Weber potential, an amorphous substrate, and common vapor growth conditions to allow the polycrystalline structures to evolve naturally. Post-simulation, we identify and analyze impactful structures and events, comparing them to theory and experiment to gain insight into various modes of crystallization dynamics. Two research questions guided the study: (1) How realistic are assumption-less simulated polycrystalline semiconductor structures? (2) To what extent can the approach provide insight into crystallization? The simulations, performed with minimal external control, yield polycrystalline structures mirroring experimental findings. The analysis reveals key crystallization insights, such as the role of amorphous atoms in the transition from nucleation to grain growth and the transformative impact of single events, such as dislocations, on crystallization dynamics. The method paves the way for reproducing and analyzing realistic polycrystalline semiconductor structures with minimal simulation assumptions across various growth modes.

Abdullah, Sharmin↗

DOE OSTI2022

Impact of Storage Dispatch Assumptions on Resource Adequacy and Capacity Credit

Representing energy-limited resources in power system probabilistic resource adequacy assessment introduces new considerations that invalidate classical modeling assumptions. In particular, such resources have multi-period operating objectives and constraints that in real systems are addressed via a sequence of rolling intertemporal optimizations. Ideally, adequacy models would develop dispatch decisions by solving a similar sequence of problems, but this approach has historically been too computationally intensive for practical use in Monte Carlo simulations, with studies making use of simplifying approximations instead. These simplifications have the potential to distort the assessed value of energy-limited resources on the system.This work describes three classes of storage dispatch assumptions in current use and discusses their theoretical differences. It then provides an empirical analysis of their differences on test systems with different levels of storage, assessing the potential for a study's modeling assumptions to influence the perceived contribution of energy-limited resources.

capacity credit↗

DOE OSTI2020

Heavy and wet: The consequences of violating assumptions of measuring soil microbial growth efficiency using the 18O water method

Soils store more carbon than the biosphere and atmosphere combined, and the efficiency to which soil microorganisms allocate carbon to growth rather than respiration is increasingly considered a proxy for the soil capacity to store carbon. This carbon use efficiency (CUE) is measured via different methods, and more recently, the 18O-H2O method has been embraced as a significant improvement for measuring CUE of soil microbial communities. Based on extrapolating 18O incorporation into DNA to new biomass, this measurement makes various implicit assumptions about the microbial community at hand. Here we conducted a literature review to evaluate how viable these assumptions are and then developed a mathematical model to test how violating them affects estimates of the growth component of CUE in soil. We applied this model to previously collected data from two kinds of soil microbial communities. By changing one parameter at a time, we confirmed our previous observation that CUE was reduced by fungal removal. Our results also show that depending on the microbial community composition, there can be substantial discrepancies between estimated and true microbial growth. Of the numerous implicit assumptions that might be violated, not accounting for the contribution of sources of oxygen other than extracellular water to DNA leads to a consistent underestimation of CUE. We present a framework that allows researchers to evaluate how their experimental conditions may influence their 18O-H2O-based CUE measurements and suggest the parameters that need further constraining to more accurately quantify growth and CUE.

Environmental Sciences & Ecology↗

DOE OSTI2026

Hofmann Stability Charts Revisited for PIP-II: From Classical Theory to Assumption-Free and ML-Driven Maps

The Hofmann stability chart remains a standard for visualizing parametric resonances in space-charge–dominated linacs, but its use typically relies on non-oscillatory Vlasov dispersion relations with simplifying assumptions (continuous focusing, KV phase space, linear optics, limited transverse–longitudinal coupling). We revisit the chart for the PIP-II linac along three tracks. (1) We reproduce the conventional maps in the (νz/νx, νx/ν0x) plane for relevant εz/εx, providing a validated reference. (2) We remove key assumptions by deriving stability surfaces directly from multi-particle tracking with realistic lattice discreteness, RF defocusing, solenoid/quad optics, and bunched-beam dynamics; local tunes and early-time growth rates are estimated from envelope oscillations and projected to the same coordinates. These assumption-reduced maps recover the canonical stopbands while revealing shifts and broadenings driven by tune modulation, non-KV distributions, and transverse–longitudinal coupling at PIP-II intensities. (3) We train a compact machine-learning surrogate that emulates the growth surface from zero-current optics, tune depression, emittance ratio, bunching factor, and selected lattice descriptors, enabling rapid scans and online working-point selection. We compare the three representations on representative PIP-II sections and discuss implications for commissioning guard bands, resonance avoidance, and routine operations.

Pathak, Abhishek [Fermilab] (ORCID:000000021704208↗

DOE OSTI2023

Impact of Aerodynamic Modeling Assumptions on Flutter Speeds of Vertical-Axis Wind Turbines

Theodorsen’s unsteady aerodynamic theory has been used extensively in flutter speed prediction of wind turbine blades. In this study, three key assumptions of Theodorsen theory (thin airfoil, flat wake, and small angle of attack) have been revisited, and all three assumptions have been addressed in combination to obtain new lift and moment equations that are subsequently applied in flutter calculations for full-scale vertical-axis wind turbine (VAWT) rotors, not just of an individual airfoil or blade. Furthermore, edgewise aerodynamics terms are added to the lift and moment equations to include their effects on flutter speeds. The newly obtained equations were implemented in the OWENS (Offshore Wind ENergy Simulation) toolkit, which is an FEM (Finite Element Method)-based toolkit for aeroelastic analysis of VAWTs. The effect of modifying each of these assumptions has been studied for the flutter RPM prediction of three primary modes of flutter of VAWTs: propeller, butterfly, and tower modes. For the land-based case, the most change was observed for the flutter RPM of the propeller mode, with a maximum increase of 2.62% for the two-bladed UTD 5 MW VAWT case. For the floating offshore case, the primary flutter modes (tower and platform pitch) were not significantly affected.

Engineering↗

NASA NTRS1977

A note on the assumption of quasiequilibrium in semiconductor junction devices

It is shown that the quasi-equilibrium theory for p-n junctions, as originally proposed by Shockley (1949), does not apply under conditions involving an application of comparatively low external voltages. A numerical example indicates that the quasi-equilibrium assumption must be discarded as soon as the voltage is increased beyond a certain critical value, although the system may still be in a low-level injection regime. It is currently not known which set of simplifying assumptions may replace the quasi-equilibrium assumptions. Possible analytic simplification relations applicable to moderate or high injection levels can, perhaps, be based on an approach considered by Mari (1968) and Choo (1971, 1972).

Von Roos, O.↗

NASA NTRS1980

Effects of various assumptions on the calculated liquid fraction in isentropic saturated equilibrium expansions

The saturated equilibrium expansion approximation for two phase flow often involves ideal-gas and latent-heat assumptions to simplify the solution procedure. This approach is well documented by Wegener and Mack and works best at low pressures where deviations from ideal-gas behavior are small. A thermodynamic expression for liquid mass fraction that is decoupled from the equations of fluid mechanics is used to compare the effects of the various assumptions on nitrogen-gas saturated equilibrium expansion flow starting at 8.81 atm, 2.99 atm, and 0.45 atm, which are conditions representative of transonic cryogenic wind tunnels. For the highest pressure case, the entire set of ideal-gas and latent-heat assumptions are shown to be in error by 62 percent for the values of heat capacity and latent heat. An approximation of the exact, real-gas expression is also developed using a constant, two phase isentropic expansion coefficient which results in an error of only 2 percent for the high pressure case.

Bursik, J. W.↗

NASA NTRS1987

Closure assumptions in the cumulus parameterization problem

While concentrating on the thermodynamical aspects of parameterizing deep cumulus clouds, some of the existing schemes are reviewed with an emphasis on their closure assumptions. It is shown that the closure assumptions in these schemes are some combination of four types. It is emphasized that observations should be used more extensively than in the past to directly verify and improve closure assumptions and to assess the limit of parameterizability. As an example, results from an analysis of the macroscopic behavior of moist convection are presented. The results suggest that cumulus clouds are basically parameterizable, in spite of the existence of mesoscale organization.

Arakawa, Akio↗

NASA NTRS1986

Some implications of the isotropic momentarily frozen assumptions for the SPAN-MAT program

Potential tests using turbulence velocity histories measured in the SPAN-MAT Program are outlined to determine validity of the homogeneous, momentarily frozen assumptions for the vertical turbulence velocity component and the homogeneous, isotropic, momentarily frozen assumptions for the horizontal turbulence velocity components. In addition, methods are reviewed for prediction of the crosscorrelation function between any two spatially separated turbulence velocity components using the homogeneous, isotropic, momentarily frozen assumptions and measurements of the transverse and longitudinal turbulence velocity components.

Mark, W. D.↗

NASA NTRS2002

Influence of 2D Finite Element Modeling Assumptions on Debonding Prediction for Composite Skin-stiffener Specimens Subjected to Tension and Bending

The influence of two-dimensional finite element modeling assumptions on the debonding prediction for skin-stiffener specimens was investigated. Geometrically nonlinear finite element analyses using two-dimensional plane-stress and plane strain elements as well as three different generalized plane strain type approaches were performed. The computed deflections, skin and flange strains, transverse tensile stresses and energy release rates were compared to results obtained from three-dimensional simulations. The study showed that for strains and energy release rate computations the generalized plane strain assumptions yielded results closest to the full three-dimensional analysis. For computed transverse tensile stresses the plane stress assumption gave the best agreement. Based on this study it is recommended that results from plane stress and plane strain models be used as upper and lower bounds. The results from generalized plane strain models fall between the results obtained from plane stress and plane strain models. Two-dimensional models may also be used to qualitatively evaluate the stress distribution in a ply and the variation of energy release rates and mixed mode ratios with lamination length. For more accurate predictions, however, a three-dimensional analysis is required.

Krueger, Ronald↗

NASA NTRS2002

Learning Assumptions for Compositional Verification

Compositional verification is a promising approach to addressing the state explosion problem associated with model checking. One compositional technique advocates proving properties of a system by checking properties of its components in an assume-guarantee style. However, the application of this technique is difficult because it involves non-trivial human input. This paper presents a novel framework for performing assume-guarantee reasoning in an incremental and fully automated fashion. To check a component against a property, our approach generates assumptions that the environment needs to satisfy for the property to hold. These assumptions are then discharged on the rest of the system. Assumptions are computed by a learning algorithm. They are initially approximate, but become gradually more precise by means of counterexamples obtained by model checking the component and its environment, alternately. This iterative process may at any stage conclude that the property is either true or false in the system. We have implemented our approach in the LTSA tool and applied it to the analysis of a NASA system.

Cobleigh, Jamieson M.↗

NASA NTRS2004

Assume-Guarantee Verification of Source Code with Design-Level Assumptions

Model checking is an automated technique that can be used to determine whether a system satisfies certain required properties. To address the 'state explosion' problem associated with this technique, we propose to integrate assume-guarantee verification at different phases of system development. During design, developers build abstract behavioral models of the system components and use them to establish key properties of the system. To increase the scalability of model checking at this level, we have developed techniques that automatically decompose the verification task by generating component assumptions for the properties to hold. The design-level artifacts are subsequently used to guide the implementation of the system, but also to enable more efficient reasoning at the source code-level. In particular we propose to use design-level assumptions to similarly decompose the verification of the actual system implementation. We demonstrate our approach on a significant NASA application, where design-level models were used to identify; and correct a safety property violation, and design-level assumptions allowed us to check successfully that the property was presented by the implementation.

Giannakopoulou, Dimitra↗

NASA NTRS2004

Comparison of 2D Finite Element Modeling Assumptions with Results From 3D Analysis for Composite Skin-Stiffener Debonding

The influence of two-dimensional finite element modeling assumptions on the debonding prediction for skin-stiffener specimens was investigated. Geometrically nonlinear finite element analyses using two-dimensional plane-stress and plane-strain elements as well as three different generalized plane strain type approaches were performed. The computed skin and flange strains, transverse tensile stresses and energy release rates were compared to results obtained from three-dimensional simulations. The study showed that for strains and energy release rate computations the generalized plane strain assumptions yielded results closest to the full three-dimensional analysis. For computed transverse tensile stresses the plane stress assumption gave the best agreement. Based on this study it is recommended that results from plane stress and plane strain models be used as upper and lower bounds. The results from generalized plane strain models fall between the results obtained from plane stress and plane strain models. Two-dimensional models may also be used to qualitatively evaluate the stress distribution in a ply and the variation of energy release rates and mixed mode ratios with delamination length. For more accurate predictions, however, a three-dimensional analysis is required.

Krueger, Ronald↗

NASA NTRS2017

Evolution of Requirements and Assumptions for Future Exploration Missions

NASA programs are maturing technologies, systems, and architectures to enabling future exploration missions. To increase fidelity as technologies mature, developers must make assumptions that represent the requirements of a future program. Multiple efforts have begun to define these requirements, including team internal assumptions, planning system integration for early demonstrations, and discussions between international partners planning future collaborations. For many detailed life support system requirements, existing NASA documents set limits of acceptable values, but a future vehicle may be constrained in other ways, and select a limited range of conditions. Other requirements are effectively set by interfaces or operations, and may be different for the same technology depending on whether the hard-ware is a demonstration system on the International Space Station, or a critical component of a future vehicle. This paper highlights key assumptions representing potential life support requirements and explanations of the driving scenarios, constraints, or other issues that drive them.

Anderson, Molly↗

DOE OSTI2024

Challenging Common Assumptions of Thick-Wall Chamber Dynamics in Inertial Fusion Systems using MOOSE

As an increasing number of companies look toward commercial Inertial Fusion Energy (IFE) designs, there is a pressing need to understand the physics of thick-wall chamber gas dynamics. The thick liquid wall approach implements a renewable wall to mitigate the fusion target emissions, thereby reducing the radiation damage rate and significantly extending the lifetime of chamber structures, leading to increased plant availability and reduced waste streams in comparison to dry wall chamber designs. It is necessary, however, to assess the critical performance and safety aspects of these systems. For example, it is crucial to predict (1) where the mass ablated from the liquid walls will vent, which determines the placement of condensing surfaces; (2) debris propagation up the beam lines, which provides essential information for design and protection requirements; (3) peak pressures and impulse on chamber walls, which affect chamber structural design; and (4) momentum transfer to the liquid jets, which constrains the shape and positioning of the jets. In turn, the chamber design and its liquid walls affect shielding requirements, material activation, and tritium fuel cycle. Currently available simulation tools, however, are unable to accurately capture key thick-wall chamber dynamics. Significant assumptions are often made to simplify the system and reduce computational cost and modeling capability needs, but the impact of these assumptions on simulation predictions has not been evaluated. For example, no three-dimensional simulations can be found in the open literature to evaluate gas venting and momentum transfer to the jets with simulations using two-dimensional domains to represent complex three-dimensional geometries. Moreover, limited studies have been dedicated to jet breakup due to both turbulence and neutron heating, and no studies have been found that evaluate how jet breakup can impact shock-jet interaction. Furthermore, effects of radiative heat transfer have rarely been included for the hydrodynamic phase of shock propagation, and integration of proper equations of state in shock dynamics codes has been mostly exploratory. In this study, we use the flexible, high-fidelity Multiphysics Object-Oriented Simulation Environment (MOOSE) to model these complex phenomena and inform design and safety studies. Capabilities to model thick-wall chamber gas dynamics are being developed, and the impact of the assumptions listed above (i.e., two-dimensional vs three-dimensional, absence of jet breakout, no radiative heat transfer, and ideal gas behavior) are being quantified.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗