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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Dosage optimization for reducing tumor burden using a phenotype-structured population model with a drug-resistance continuum

Abstract Drug resistance is a significant obstacle to effective cancer treatment. To gain insights into how drug resistance develops, we adopted a concept called fitness landscape and employed a phenotype-structured population model by fitting to a set of experimental data on a drug used for ovarian cancer, olaparib. Our modeling approach allowed us to understand how a drug affects the fitness landscape and track the evolution of a population of cancer cells structured with a spectrum of drug resistance. We also incorporated pharmacokinetic (PK) modeling to identify the optimal dosages of the drug that could lead to long-term tumor reduction. We derived a formula that indicates that maximizing variation in plasma drug concentration over a dosing interval could be important in reducing drug resistance. Our findings suggest that it may be possible to achieve better treatment outcomes with a drug dose lower than the levels recommended by the drug label. Acknowledging the current limitations of our work, we believe that our approach, which combines modeling of both PK and drug resistance evolution, could contribute to a new direction for better designing drug treatment regimens to improve cancer treatment.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2023

A Level Set Model for Structured Mesh Representation of Fibrous Preforms used in Composites Manufacturing

Here, a model for implicit representation of fibrous and woven preforms used for composites manufacturing is described. The method is based on a level set function defined on a structured mesh to implicitly capture the complex fiber and weave geometries. Since most software packages used to model woven preforms are based on unstructured mesh, a numerical model for transforming a discretized surface to a structured mesh representation and vice-a-versa is presented. Specific emphasis is on scalable computation of a level set function for large and complex 3D woven structures from a triangulated surface of the smallest unit (yarn). The model is applied to capture a periodic 3D layered 5-harness satin (5HS) weave geometry on a structured mesh. Geometric transformations needed to efficiently compute the level set function for the 3D structure on a high resolution mesh are described. Effects of mesh resolution on the geometric features such as number of resolved fibers, effective fiber size, and the surface area to volume ratio of the iso-surface are analyzed. Using the distance property of the level set function, an approach to evaluate the structure function resulting from transient evolving topology representing densification due to matrix phase depositions is also presented. The approach captures transition of the geometric characteristic from fiber governed at early stages of densification to yarn governed at the terminal stage.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A structural equation modeling approach to leveraging the power of extant sentiment analysis tools

Machine-derived sentiment analysis has become a pervasive and useful tool to address a wide array of issues in natural language processing. Leading technology companies such as Google now provide sentiment analysis tools (SATs) as readily accessible online products. Academic researchers develop and make available SATs to support the research enterprise. One of the major challenges with SATs is the inconsistencies in results among the various SATs. Consequently, the selection of a SAT for a specific purpose may significantly impact the application. This study addresses the foregoing problem by utilizing structural equation modeling to merge the outputs of SATs to develop a combined sentiment metric without the need for a labeled training dataset. This method is applicable to a wide range of text-based problems, is data-driven, and replicable. It was tested using three publicly available datasets and compared against seven different SATs. The results indicate that as a continous measure, the proposed method outperformed other SATs in the movie reviews and SemEval datasets, and achieved a tie for first place with IBM Watson on the Sentiment 140 dataset. Also, compared to the published major alternatives, the arithmetic mean solution, this approach performed better across these three datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Since the 14th Critical Assessment of Techniques for Protein Structure Prediction (CASP14), AlphaFold2 has become the standard method for protein tertiary structure prediction. One remaining challenge is to further improve its prediction. We developed a new version of the MULTICOM system to sample diverse multiple sequence alignments (MSAs) and structural templates to improve the input for AlphaFold2 to generate structural models. The models are then ranked by both the pairwise model similarity and AlphaFold2 self-reported model quality score. The top ranked models are refined by a novel structure alignment-based refinement method powered by Foldseek. Moreover, for a monomer target that is a subunit of a protein assembly (complex), MULTICOM integrates tertiary and quaternary structure predictions to account for tertiary structural changes induced by protein-protein interaction. The system participated in the tertiary structure prediction in 2022 CASP15 experiment. Our server predictor MULTICOM_refine ranked 3rd among 47 CASP15 server predictors and our human predictor MULTICOM ranked 7th among all 132 human and server predictors. The average GDT-TS score and TM-score of the first structural models that MULTICOM_refine predicted for 94 CASP15 domains are ~0.80 and ~0.92, 9.6% and 8.2% higher than ~0.73 and 0.85 of the standard AlphaFold2 predictor respectively.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Structural coherence model for predicting molten salt thermal conductivity informed by the pair distribution function

To enable thermal behavior prediction and design optimization of molten salt reactors, thermal conductivity of molten salts must be characterized in terms of salt composition and temperature. Current theoretical models fail to provide consistent approximations for all halide mixtures, particularly actinide-bearing melts. This study aims to link the short-range order structure of molten salts to the mean free path of energy carriers through a simple structural coherence model informed by the partial pair distribution function. The proposed method is used to predict the thermal conductivity of 33 alkali and alkaline earth halide salts. Predictions approximate experimental measurements with a mean absolute error of 15.7% for dissociating, complexing, and actinide salts, including unary LiCl, NaCl, and MgCl 2 as well as mixtures LiF–NaF–KF (FLiNaK), LiF–BeF 2 (FLiBe), and NaCl–UCl 3 . The work provides evidence for the validity of energy carrier descriptions of molecular-level heat transfer in molten salts, with implications for improved theories of liquid energy transport in general.

Actinide mixtures↗
DOE OSTI2023

Bridging Time-series Image Phenotyping and Functional–Structural Plant Modeling to Predict Adventitious Root System Architecture

Root system architecture (RSA) is an important measure of how plants navigate and interact with the soil environment. However, current methods in studying RSA must make tradeoffs between precision of data and proximity to natural conditions, with root growth in germination papers providing accessibility and high data resolution. Functional–structural plant models (FSPMs) can overcome this tradeoff, though parameterization and evaluation of FSPMs are traditionally based in manual measurements and visual comparison. Here, we applied a germination paper system to study the adventitious RSA and root phenology of Populus trichocarpa stem cuttings using time-series image-based phenotyping augmented by FSPM. We found a significant correlation between timing of root initiation and thermal time at cutting collection (P value = 0.0061, R 2 = 0.875), but little correlation with RSA. We also present a use of RhizoVision [1] for automatically extracting FSPM parameters from time series images and evaluating FSPM simulations. A high accuracy of the parameterization was achieved in predicting 2D growth with a sensitivity rate of 83.5%. This accuracy was lost when predicting 3D growth with sensitivity rates of 38.5% to 48.7%, while overall accuracy varied with phenotyping methods. Despite this loss in accuracy, the new method is amenable to high throughput FSPM parameterization and bridges the gap between advances in time-series phenotyping and FSPMs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Strategies for solving the excited-state self-consistent-field problem for highly excited and multiply ionized states

The dynamics of molecules exposed to intense x-ray radiation involve a large number of multiply ionized and highly excited electronic configurations. To model these dynamics a reliable and efficient electronic structure model is imperative. Employing the Hartree-Fock-Slater electronic structure model in combination with the maximum overlap method, we quantify the associated convergence failures when calculating electronic states of carbon monoxide with multiple vacancies in the core and valence levels. Here, we characterize these cases and describe strategies to overcome the convergence problems. The described techniques not only eliminate all convergence issues for CO but also result in a significant reduction of convergence failures for simulations of the x-ray-induced multiple ionization dynamics of the phenol molecule.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Environment-sensitivity functions for gross primary productivity in light use efficiency models

The sensitivity of photosynthesis to environmental changes is essential for understanding carbon cycle responses to global climate change and for the development of modeling approaches that explains its spatial and temporal variability. We collected a large variety of published sensitivity functions of gross primary productivity (GPP) to different forcing variables to assess the response of GPP to environmental factors. These include the responses of GPP to temperature; vapor pressure deficit, some of which include the response to atmospheric CO 2 concentrations; soil water availability (W); light intensity; and cloudiness. These functions were combined in a full factorial light use efficiency (LUE) model structure, leading to a collection of 5600 distinct LUE models. Each model was optimized against daily GPP and evapotranspiration fluxes from 196 FLUXNET sites and ranked across sites based on a bootstrap approach. The GPP sensitivity to each environmental factor, including CO 2 fertilization, was shown to be significant, and that none of the previously published model structures performed as well as the best model selected. From daily and weekly to monthly scales, the best model's median Nash-Sutcliffe model efficiency across sites was 0.73, 0.79 and 0.82, respectively, but poorer at annual scales (0.23), emphasizing the common limitation of current models in describing the interannual variability of GPP. Although the best global model did not match the local best model at each site, the selection was robust across ecosystem types. The contribution of light saturation and cloudiness to GPP was observed across all biomes (from 23% to 43%). Temperature and W dominates GPP and LUE but responses of GPP to temperature and W are lagged in cold and arid ecosystems, respectively. The findings of this study provide a foundation towards more robust LUE-based estimates of global GPP and may provide a benchmark for other empirical GPP products.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Efficient Modeling of Structural, Electronic, and Optical Properties of Silver and Gold Metal Nanoclusters and Alloys Using Optimized SCC-DFTB Parameters

Computation of optical properties using conventional time-dependent density functional theory (TD-DFT) is time-consuming and memory-intensive. In this study, we investigate the accuracy and efficiency of the density functional tight binding (DFTB) framework with newly optimized Slater–Koster (SK) parameters for modeling the structural, electronic properties, and absorption spectra of silver and gold nanoclusters and their alloys. Our investigation of the ground state (GS) properties demonstrates that the newly developed GS-SK parameters enable DFTB to closely approximate DFT-calculated bond lengths for octahedron, tetrahedron, icosahedra, and truncated octahedron with sizes Ag n /Au n (n = 19, 20, 38, 55), nanoclusters and Ag 20 /Au 20 nanoalloys, with a maximum deviation of approximately 0.15 Å. Formation energy results indicate that the GS-SK parameters can closely estimate changes in formation energies with alloy composition, and the comparison of electronic structures for Ag 20 , Au 20 , and AgAu alloy nanoclusters using the DFTB approximation reveals good agreement in the projected density of states (DOS) profiles and energy levels. A second set of SK parameters, ES-SK, has been developed to describe excited state (ES) properties, including the absorption spectra of silver octahedron Ag 19 , tetrahedral Ag n (n = 20, 56, 84), truncated octahedron Ag 38 , and icosahedra Ag 55 closed-shell clusters and their gold and alloy counterparts over a broad range of alloy compositions. This parametrization uses TD-DFTB calculations and fine-tunes the d and p eigenvalues by comparing them to reference absorption spectra from first-principles TD-DFT. This enables the generation of absorption spectra that closely match the reference spectra when plasmon excitation is dominant, as demonstrated by studying the plasmonic properties of icosahedral Ag n and Au n (n = 309 and 561) nanoparticles. This includes the rapid loss in plasmon quality when Au partially replaces Ag in alloy clusters. Furthermore, these results provide a foundation for addressing computational bottlenecks in plasmonics and with new prospects for applications in the quantum plasmonics for bimetallic alloys.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Deep convolutional autoencoders as generic feature extractors in seismological applications

The idea of using a deep autoencoder to encode seismic waveform features and then use them in different seismological applications is appealing. In this paper, we designed tests to evaluate this idea of using autoencoders as feature extractors for different seismological applications, such as event discrimination (i.e., earthquake vs. noise waveforms, earthquake vs. explosion waveforms), and phase picking. These tests involve training an autoencoder, either undercomplete or overcomplete, on a large amount of earthquake waveforms, and then using the trained encoder as a feature extractor with subsequent application layers (either a fully connected layer, or a convolutional layer plus a fully connected layer) to make the decision. By comparing the performance of these newly designed models against the baseline models trained from scratch, we conclude that the autoencoder feature extractor approach may only outperform the baseline under certain conditions, such as when the target problems require features that are similar to the autoencoder encoded features, when a relatively small amount of training data is available, and when certain model structures and training strategies are utilized. The model structure that works best in all these tests is an overcomplete autoencoder with a convolutional layer and a fully connected layer to make the estimation.

58 GEOSCIENCES↗
DOE OSTI2020

Summary of Structural Material Modeling Development for the NEAMS Program in Fiscal Year 2020

This report summarizes work performed during Fiscal Year (FY) 2020 at Idaho National Laboratory (INL) for the U.S. Department of Energy?s Nuclear Engineering Advanced Modeling and Simulation (NEAMS) program for the Structural Materials and Chemistry Technical Area in the work package entitled "MS- 20IN050104 - Structural Materials - INL." The Structural Materials and Chemistry Technical Area is a relatively new component of the NEAMS program, and is currently focusing on developing simulation capabilities to support the deployment of nuclear energy in the areas of molten salt reactor chemistry, light water reactor (LWR) structural material degradation, and structural material behavior for advanced reactor applications. INL performed work for to advance capabilities for simulation of structural material behavior in both LWR and advanced reactor applications in the work described here.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2021

Radiation effects on atherosclerosis in atomic bomb survivors: a cross-sectional study using structural equation modeling

Past reports indicated that total-body irradiation at low to moderate doses could be responsible for cardiovascular disease risks, but the mechanism remains unclear. The purpose of this study was to investigate the association between radiation exposure and atherosclerosis, an underlying pathology of cardiovascular diseases, in the Japanese atomic bomb survivors. We performed a cross-sectional study measuring 14 clinical-physiological atherosclerosis indicators during clinical exams from 2010 to 2014 in 3274 participants of the Adult Health Study cohort. Multivariable analyses were performed by using a structural equation model with latent factors representing underlying atherosclerotic pathologies: (1) arterial stiffness, (2) calcification, and (3) plaque as measured with indicators chosen a priori on the basis of clinical-physiological knowledge. Radiation was linearly associated with calcification (standardized coefficient per Gy 0.15, 95 % confidence interval: CI [0.070, 0.23]) and plaque (0.11, 95 % CI [0.029, 0.20]), small associations that were comparable to about 2 years of aging per Gy of radiation exposure, but not with arterial stiffness (0.036, 95 % CI [-0.025, 0.095]). The model fitted better and had narrower confidence intervals than separate ordinary regression models explaining individual indicators independently. The associations were less evident when the dose range was restricted to a maximum of 2 or 1 Gy. By combining individual clinical-physiological indicators that are correlated because of common, underlying atherosclerotic pathologies, we found a small, but significant association of radiation with atherosclerosis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Modelica-based system modeling for studying control-related faults in chiller plants and boiler plants serving large office buildings

System modeling is critical when studying operation faults in chiller plants and boiler plants. However, current fault models have difficulties faithfully representing the operation of chiller plants and boiler plants under the effects of those faults, especially the control-related ones. In this study, we present a systematic method to develop high-fidelity models for approximating the behaviors of chiller plants and boiler plants under faulty conditions. Compared to existing ones, the resulting fault models have two advantages: first, they better characterize the dynamic patterns in the system operation. In those models, control architecture and control logic are faithfully implemented. Thus, they can be used to study control-related faults, such as incorrect staging control due to sensor bias and mistuned feedback control. Second, they are readily extensible and can support large-scale investigations to explore different faulty conditions/scenarios. Those models are established in a hierarchical structure while modules in each layer can be redeclared and parameterized at upper layers. In such a case, modifications to the models can be realized through model modifiers and the process can be easily streamlined with scripts. We applied the proposed models in a comprehensive fault impact evaluation of the 13 control-related faults of chiller and boiler plants. In this evaluation, the proposed plant model is coupled with the EnergyPlus thermal load model to study the impact of various faulty scenarios. Based on the evaluation results, we identified the faults that have the most significant impacts on the operation of the chiller and boiler plants, respectively. We also found that the relationship between the impacts of the studied faults and the severity level of the faults are highly non-linear

Huang, Sen↗
DOE OSTI2023

Reducing uncertainty of high-latitude ecosystem models through identification of key parameters

Abstract Climate change is having significant impacts on Earth’s ecosystems and carbon budgets, and in the Arctic may drive a shift from an historic carbon sink to a source. Large uncertainties in terrestrial biosphere models (TBMs) used to forecast Arctic changes demonstrate the challenges of determining the timing and extent of this possible switch. This spread in model predictions can limit the ability of TBMs to guide management and policy decisions. One of the most influential sources of model uncertainty is model parameterization. Parameter uncertainty results in part from a mismatch between available data in databases and model needs. We identify that mismatch for three TBMs, DVM-DOS-TEM, SIPNET and ED2, and four databases with information on Arctic and boreal above- and belowground traits that may be applied to model parametrization. However, focusing solely on such data gaps can introduce biases towards simple models and ignores structural model uncertainty, another main source for model uncertainty. Therefore, we develop a causal loop diagram (CLD) of the Arctic and boreal ecosystem that includes unquantified, and thus unmodeled, processes. We map model parameters to processes in the CLD and assess parameter vulnerability via the internal network structure. One important substructure, feed forward loops (FFLs), describe processes that are linked both directly and indirectly. When the model parameters are data-informed, these indirect processes might be implicitly included in the model, but if not, they have the potential to introduce significant model uncertainty. We find that the parameters describing the impact of local temperature on microbial activity are associated with a particularly high number of FFLs but are not constrained well by existing data. By employing ecological models of varying complexity, databases, and network methods, we identify the key parameters responsible for limited model accuracy. They should be prioritized for future data sampling to reduce model uncertainty.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

A Novel Method to Train Classification Models for Structure Detection in In Situ Spacecraft Data

We present a method for creating spacecraft-like data which can be used to train Machine Learning (ML) models to detect and classify structures in in situ spacecraft data. First, we use the Grad-Shafranov equation to numerically solve for several magnetohydrostatic equilibria which are variations on a known analytic equilibrium. These equilibria are then used as the initial conditions for Particle-In-Cell simulations in which the structures of interest are observed and labeled. We then take one-dimensional slices through the simulations to replicate what a spacecraft collecting data from the simulation would observe. This sliced data then can be used as training data for the initial training of ML models intended for use on spacecraft data. We demonstrate the method applied to the problem of detecting small-scale plasmoids in the magnetotail, which is important for understanding complex magnetotail reconnection dynamics. The simple 1D classifier we train is able to detect more than 70% of the plasmoid points in the data set but also produces a large number of false positives. Our further work on this example problem is detailed, and further potential uses of the method are discussed.

79 ASTRONOMY AND ASTROPHYSICS↗