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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The kinetics of SARS-CoV-2 infection based on a human challenge study

Studying the early events that occur after viral infection in humans is difficult unless one intentionally infects volunteers in a human challenge study. Here, we use data about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in such a study in combination with mathematical modeling to gain insights into the relationship between the amount of virus in the upper respiratory tract and the immune response it generates. We propose a set of dynamic models of increasing complexity to dissect the roles of target cell limitation, innate immunity, and adaptive immunity in determining the observed viral kinetics. We introduce an approach for modeling the effect of humoral immunity that describes a decline in infectious virus after immune activation. We fit our models to viral load and infectious titer data from all the untreated infected participants in the study simultaneously. We found that a power-law with a power h < 1 describes the relationship between infectious virus and viral load. Viral replication at the early stage of infection is rapid, with a doubling time of ~2 h for viral RNA and ~3 h for infectious virus. We estimate that adaptive immunity is initiated ~7 to 10 d postinfection and appears to contribute to a multiphasic viral decline experienced by some participants; the viral rebound experienced by other participants is consistent with a decline in the interferon response. Altogether, we quantified the kinetics of SARS-CoV-2 infection, shedding light on the early dynamics of the virus and the potential role of innate and adaptive immunity in promoting viral decline during infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Using PyBioNetFit to leverage qualitative and quantitative data in biological model parameterization and uncertainty quantification

Data generated in studies of cellular regulatory systems are often qualitative. For example, measurements of signaling readouts in the presence and absence of mutations may reveal a rank ordering of responses across conditions but not the precise extents of mutation-induced differences. Qualitative data are often ignored by mathematical modelers or are considered in an ad hoc manner, as in the study of Kocieniewski and Lipniacki (2013) [Phys Biol 10: 035006], which was focused on the roles of MEK isoforms in ERK activation. In this earlier study, model parameter values were tuned manually to obtain consistency with a combination of qualitative and quantitative data. This approach is not reproducible, nor does it provide insights into parametric or prediction uncertainties. Here, starting from the same data and the same ordinary differential equation (ODE) model structure, we generate formalized statements of qualitative observations, making these observations more reusable, and we improve the model parameterization procedure by applying a systematic and automated approach enabled by the software package PyBioNetFit. We also demonstrate uncertainty quantification (UQ), which was absent in the original study. Our results show that PyBioNetFit enables qualitative data to be leveraged, together with quantitative data, in parameterization of systems biology models and facilitates UQ. These capabilities are important for reliable estimation of model parameters and model analyses in studies of cellular regulatory systems and reproducibility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A consensus mathematical model of vaccine-induced antibody dynamics for multiple vaccine platforms and pathogens

Introduction: Vaccine platforms used in successful, licensed vaccines have varied among pathogens. However, antibody level is still the main clinical correlate of protection in most approved vaccines. Decisions as to the best vaccine platform to pursue for a given pathogen may be informed through improved understanding of the process of antibody generation and its temporal dynamics, as well as the relationship between these processes and the type of vaccine. Methods: We have analyzed the dynamics of antibody generation for different vaccine platforms against diverse pathogens, and developed a consensus mathematical model that captures antibody dynamics across these diverse systems. Initially, the model was fitted to a rich dataset of antibody and immune cell concentrations in a SARS-CoV-2 vaccine experiment. We then used concepts from machine learning, such as transfer learning, to apply the same model to a variety of systems, involving different pathogens, vaccine platforms, and booster dose use/timing, fixing most parameter values relating to the dynamics of the immune system. Results: The model includes B cell proliferation and differentiation, as well as the generation of plasma cells, which secrete large amounts of antibody, and memory B cells. Overall, the model describes antibody generation in all systems tested well and shows that the main differences across platforms are related to the dynamics of antigen presentation. Discussion: This model can be used to predict antibody generation in pairs of vaccine platform/pathogen, allowing for the use of in silico results to narrow down experimental burden in vaccine development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Computational flow modeling of triply periodic minimal surfaces as feed channel spacers in ultra-high pressure reverse osmosis applications

Triply periodic minimal surfaces (TPMS) are a special class of mathematical surfaces characterized by a high surface area-to-volume ratio. They have generated considerable interest in fields such as acoustics, heat transfer, and membrane-based filtration processes. This study evaluates the performance of four different TPMS designs—Schoen Gyroid, Schoen Crossed Layers of Parallels (CLP), Schoen Transverse Crossed Layers of Parallels (tCLP), and Schwarz-Primitive—when used as feed channel spacers under ultra-high pressure reverse osmosis (UHPRO) conditions, at approximately 200 bar. Our experimentally validated computational fluid dynamics model reveal different flow patterns within the feed channels for each of the four TPMS designs, leading to varying hydrodynamic and permeation properties. Under the simulated UHPRO conditions, the Gyroid and tCLP designs yield up to a 23% increase in average permeate velocity and a 14% reduction in average membrane-surface concentration relative to a non-woven spacer of the same porosity. Furthermore, the enhanced performance comes with an increased feed channel pressure drop, although it only constitutes less than 4% of the operating pressure when extrapolated for a meter-long membrane module. Additionally, the study analyzes the effects of varying inlet velocity and spacer porosity on membrane performance. Overall, this research provides valuable insights into the potential use of TPMS spacers in UHPRO applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Discovering Strong Gravitational Lenses in the Dark Energy Survey with Interactive Machine Learning and Crowd-sourced Inspection with Space Warps

We conduct a search for strong gravitational lenses in the Dark Energy Survey (DES) Year 6 imaging data. We implement a pre-trained Vision Transformer (ViT) for our machine learning (ML) architecture and adopt interactive machine learning to construct a training sample with multiple classes to address common types of false positives. Our ML model reduces ∼236 million DES cutout images to 22,564 targets of interest, including ∼85% of previously reported galaxy–galaxy lens candidates discovered in DES. These targets were visually inspected by citizen scientists, who ruled out ∼90% as false positives. Of the remaining 2618 candidates, 149 were expert-classified as “definite” lenses and 516 as “probable” lenses, for a total of 665 systems, with 147 of these candidates being newly identified. Additionally, we trained a second ViT to find double-source plane lens systems, finding at least one double-source system. Our main ViT excels at identifying galaxy–galaxy lenses, consistently assigning high scores to candidates with high expert assessments. The top 800 ViT-scored images include ∼100 of our “definite” lens candidates. This selection is an order of magnitude higher in purity than previous convolutional neural-network-based lens searches and demonstrates the feasibility of applying our methodology for discovering large samples of lenses in future surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A Corrected Score Function Framework for Modelling Circadian Gene Expression

Many biological processes display oscillatory behaviour based on an approximately 24 h internal timing system specific to each individual. One process of particular interest is gene expression, for which several circadian transcriptomic studies have identified associations between gene expression during a 24 h period and an individual's health. A challenge with analysing data from these studies is that each individual's internal timing system is offset relative to the 24 h day-night cycle, where day–night cycle time is recorded for each collected sample. Laboratory procedures can accurately determine each individual's offset and determine the internal time of sample collection. However, these laboratory procedures are labour-intensive and expensive. Here, in this paper, we propose a corrected score function framework to obtain a regression model of gene expression given internal time when the offset of each individual is too burdensome to determine. A feature of this framework is that it does not require the probability distribution generating offsets to be symmetric with a mean of zero. Simulation studies validate the use of this corrected score function framework for cosinor regression, which is prevalent in circadian transcriptomic studies. Illustrations with data from three circadian transcriptomic studies further demonstrate that the proposed framework consistently mitigates bias relative to using a score function that does not account for this offset.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

PDE-constrained high-order mesh optimization

Here, we present a novel framework for PDE-constrained r-adaptivity of high-order meshes. The proposed method formulates mesh movement as an optimization problem, with an objective function defined as a convex combination of a mesh quality metric and a measure of the accuracy of the PDE solution obtained via finite element discretization. The proposed formulation achieves optimized, well-defined high-order meshes by integrating mesh quality control, PDE solution accuracy, and robust gradient regularization. We adopt the Target-Matrix Optimization Paradigm to control geometric properties across the mesh, independent of the PDE of interest. To incorporate the accuracy of the PDE solution, we introduce error measures that control the finite element discretization error. The implicit dependence of these error measures on the mesh nodal positions is accurately captured by adjoint sensitivity analysis. Additionally, a convolution-based gradient regularization strategy is used to ensure stable and effective adaptation of high-order meshes. We demonstrate that the proposed framework can improve mesh quality and reduce the error by up to 10 times for the solution of Poisson and linear elasto-static problems. The approach is general with respect to the dimensionality, the order of the mesh, the types of mesh elements, and can be applied to any PDE that admits well-defined adjoint operators.

Computer science↗
DOE OSTI2026

Prediction of Creep-Induced Strain Using a Symbolic Regression-Based Model

Material creep under high-temperature conditions limits the lifetime and safety of structural systems such as advanced nuclear reactors. Conventional creep testing is slow and often produces inconsistent results across nominally identical experiments, making lifetime prediction uncertain. Here, to address these challenges, this work develops a data-driven symbolic regression (SR) model that consolidates results from duplicate creep tests and predicts the remaining strain-time curve of an ongoing experiment. The method uses piece-wise multi-objective SR with physical constraints to generate analytic, interpretable functions describing transient creep strain. Applied to Inconel Alloy 617 data, the approach achieved relative mean absolute errors of 1.0–9.5%, providing closed-form predictions of strain evolution. These results demonstrate a first step toward reducing the duration and cost of long-term creep testing while retaining physically interpretable model forms.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models

Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the design, the effect of the experiment and prior knowledge about the effect. Estimation of the precision matrix is a fundamental task to infer biological graphical structures like microbial networks. We compare the marginal posterior precision of the precision matrix under four priors: flat, conjugate Normal-Wishart, Normal-MGIG and a general independent. Under the flat and conjugate priors, the Laplace-approximated posterior precision is not a function of the design matrix rendering useless any efforts to find an optimal experimental design to infer the precision matrix. In contrast, the Normal-MGIG and general independent priors do allow for the search of optimal experimental designs, yet there is a sharp upper bound on the information that can be extracted from a given experiment. We confirm our theoretical findings via a simulation study comparing (i) the KL divergence between prior and posterior and (ii) the Stein’s loss difference of MAPs between random and no experiment. Our findings provide practical advice for domain scientists conducting experiments to better infer the precision matrix as a representation of a biological network.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Scaling microstructural processes in the sintering of ionic ceramics

A multi-scale framework, combining a multiphase field formulation and large deformation mechanics, was developed as a stepping stone to perform the data analytics of the microstructural level kinetics of a sintering solid. Relevant microstructural information from this framework, such as grain, stress, and porosity statistics, was scaled up to describe the macroscopic level sintering kinetics. Here, the developed formulation was applied to describe the electric field assisted sintering of Y 2 O 3 . Microstructural inhomogeneities in a multi-granular solid result in the formation of a field of compressive stress networks, which interleave with low compression and weakly tensile regions, defining a scaffolding for sintering concentration regions to develop. A Poisson effect-induced lateral stress network is also naturally self-induced as a result of the mechanical constraints imposed by the sintering apparatus. For long sintering times, localized shear stresses enhancing mass flow along grain boundaries and internal surfaces develop. Three-sided pores are removed by either vacancy transport to the surrounding pores, or move towards the external surfaces through grain boundary diffusion. Four- and higher order-sided pores stabilize because an equal amount of vacancies are gained and lost through the connecting grain boundaries. Grain dewetting contributes to pore coalescence, suggesting that pore kinetics and grain growth are coupled and should be analyzed in concert. The combined sintering and grain growth kinetics define six regimes of sintering behavior: (1) T, the transient regime; (2) E$_Υ$, the surface energy dominated, early sintering regime, where the grain growth exponent, p = 1, and the stress concentration factor, $f$ ~ $1/\hat{ρ}^{4.6}$; (3) E S , the stress dominated, early sintering regime, where p = 1 and $f$ ~ $1/\hat{ρ}^{4}$; (4) I$_Υ$, the surface energy dominated, intermediate sintering regime, where p = 2 and $f$ ~ $1/\hat{ρ}^{4.6}$; (5) I S , the stress dominated, intermediate sintering regime, where p = 2 and $f$ ~ $1/\hat{ρ}^{4}$; and (6) L, the late sintering regime, where p = 3 and $f$ ~ 1. At the macroscopic level, the rapid densification and suppression of grain growth observed in the electric field assisted sintering process is a consequence of the compounding effects of the underlying stress-, transport-, and interfacial-energy-induced energy minimization kinetics, as predicted by the multi-scale framework.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Microgrid design and multi-year dispatch optimization under climate-informed load and renewable resource uncertainty

Microgrids are an increasingly popular solution to provide energy resilience in response to increasing grid dependency and the growing impacts of climate change on grid operations. However, existing microgrid models do not currently consider the uncertain and long-term impacts of climate change when determining a set of design and operational decisions to minimize long-term costs or meet a resilience threshold. In this paper, we develop a novel scenario generation method that accounts for the uncertain effects of (i) climate change on variable renewable energy availability, (ii) extreme heat events on site load, and (iii) population and electrification trends on load growth. Additionally, we develop a two-stage stochastic programming extension of an existing microgrid design and dispatch optimization model to obtain uncertainty-informed and climate-resilient energy system decisions that minimizes long-term costs. Use of sample average approximation to validate our two case studies illustrates that the proposed methodology produces high-quality solutions that add resilience to systems with existing backup generation while reducing expected long-term costs.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Extending SLUSCHI for Automated Diffusion Calculations

We present an extension of the SLUSCHI package (Solid and Liquid in Ultra Small Coexistence with Hovering Interfaces) to enable automated diffusion calculations from first-principles molecular dynamics. While the original SLUSCHI workflow was designed for melting temperature estimation via solid-liquid coexistence, we adapt its input and output handling to isolate the volume search stage and generate one production trajectory suitable for diffusion analysis. Post-processing tools parse VASP outputs, compute mean-square displacements (MSD), and extract tracer diffusivities using the Einstein relation with robust error estimates through block averaging. Diagnostic plots, including MSD curves, running slopes, and velocity autocorrelations, are produced automatically to help identify diffusive regimes. The method has been validated through representative case studies: self-diffusion in Al-Cu liquid alloys, sublattice melting in Li7La3Zr2O12 and Er2O3, interstitial oxygen transport in bcc and fcc Fe, and oxygen diffusivity in Fe-O liquids with variable Si and Al contents. Viscosity and diffusivity are linked through the Stokes-Einstein relation, with composition dependence assessed via simple linear mixing. This capability broadens SLUSCHI from melting-point predictions to transport property evaluation, enabling high-throughput, fully first-principles datasets of diffusion coefficients and viscosities across metals and oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Uncertainty quantification of graph convolution neural network models of evolving processes

The application of neural network models to scientific machine learning tasks has proliferated in recent years. In particular, neural networks have proved to be adept at modeling processes with spatial–temporal complexity. Nevertheless, these highly parameterized models have garnered skepticism in their ability to produce outputs with quantified error bounds over the regimes of interest. Hence there is a need to find uncertainty quantification methods that are suitable for neural networks. In this work we present comparisons of the parametric uncertainty quantification of neural networks modeling complex spatial–temporal processes with Hamiltonian Monte Carlo and Stein variational gradient descent and its projected variant. Specifically we apply these methods to graph convolutional neural network models of evolving systems modeled with recurrent neural network and neural ordinary differential equations architectures. We show that Stein variational inference is a viable alternative to Monte Carlo methods with some clear advantages for complex neural network models. For our exemplars, Stein variational interference gave similar pushed forward uncertainty profiles through time compared to Hamiltonian Monte Carlo, albeit with generally more generous variance. As a result, projected Stein variational gradient descent also produced similar uncertainty profiles to the non-projected counterpart, but large reductions in the active weight space were confounded by the stability of the neural network predictions and the convoluted likelihood landscape.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A MPET 2 -mPBPK model for subcutaneous injection of biotherapeutics with different molecular weights: From local scale to whole-body scale

Subcutaneous injection of biotherapeutics has attracted considerable attention in the pharmaceutical industry. However, there is limited understanding of the mechanisms underlying the absorption of drugs with different molecular weights and the delivery of drugs from the injection site to the targeted tissue. Here, we propose the MPET 2 -mPBPK model to address this issue. This multiscale model couples the MPET 2 model, which describes subcutaneous injection at the local tissue scale from a biomechanical view, with a post-injection absorption model at injection site and a minimal physiologically-based pharmacokinetic (mPBPK) model at whole-body scale. Utilizing the principles of tissue biomechanics and fluid dynamics, the local MPET 2 model provides solutions that account for tissue deformation and drug absorption in local blood vessels and initial lymphatic vessels during injection. Additionally, we introduce a model accounting for the molecular weight effect on the absorption by blood vessels, and a nonlinear model accounting for the absorption in lymphatic vessels. The post-injection model predicts drug absorption in local blood vessels and initial lymphatic vessels, which are integrated into the whole-body mPBPK model to describe the pharmacokinetic behaviors of the absorbed drug in the circulatory and lymphatic system. We establish a numerical model which links the biomechanical process of subcutaneous injection at local tissue scale and the pharmacokinetic behaviors of injected biotherapeutics at whole-body scale. With the help of the model, we propose an explicit relationship between the reflection coefficient and the molecular weight and predict the bioavalibility of biotherapeutics with varying molecular weights via subcutaneous injection. The considered drug absorption mechanisms enable us to study the differences in local drug absorption and whole-body drug distribution with varying molecular weights. This model enhances the understanding of drug absorption mechanisms and transport routes in the circulatory system for drugs of different molecular weights, and holds the potential to facilitate the application of computational modeling to drug formulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

HTESP (High-throughput electronic structure package): A package for high-throughput ab initio calculations

High-throughput ab initio calculations are the indispensable parts of data-driven discovery of new materials with desirable properties, as reflected in the establishment of several online material databases. The accumulation of extensive theoretical data through computations enables data-driven discovery by constructing machine learning and artificial intelligence models to predict novel compounds and forecast their properties. Efficient usage and extraction of data from these existing online material databases can accelerate the next stage materials discovery that targets different and more advanced properties, such as electron–phonon coupling for phonon-mediated superconductivity. However, extracting data from these databases, generating tailored input files for different ab initio calculations, performing such calculations, and analyzing new results can be demanding tasks. Here, in this work, we introduce a software package named “HTESP” (High-Throughput Electronic Structure Package) written in Python and Bash languages, which automates the entire workflow including data extraction, input file generation, calculation submission, result collection and plotting. Our HTESP will help speed up future computational materials discovery processes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

A Finite Difference informed Random Walk solver for simulating radiation defect evolution in polycrystalline structures with strongly inhomogeneous diffusivity

Diffusivity of species and defects on grain boundaries is usually several orders of magnitude larger than that inside grains. Such strongly inhomogeneous diffusivity requires prohibitively high computational demands for modeling microstructural evolution. Here, this paper presents a highly-efficient numerical solver, combining the Finite Difference method and Random Walk model, designed for accurately modeling strongly inhomogeneous diffusion within polycrystalline structures. The proposed solver, termed Finite Difference informed Random Walk (FDiRW), integrates a customized Finite Difference (cFD) scheme tailored for fast diffusion along thin grain boundaries represented by a single-layer of nodes. Numerical experiments demonstrate that the FDiRW solver achieves an impressive efficiency gain of 1560x compared to traditional Finite Difference methods while maintaining accuracy, making it feasible for personal computer machines to handle diffusional systems with strongly inhomogeneous diffusivity across static polycrystalline microstructures. The model has been successfully applied to simulate radiation defect evolution, showcasing its scalability to engineering scales in both length and time dimensions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

SAM-I-Am: Semantic boosting for zero-shot atomic-scale electron micrograph segmentation

Image segmentation is a critical enabler for tasks ranging from medical diagnostics to autonomous driving. However, the correct segmentation semantics — where are boundaries located? what segments are logically similar? — change depending on the domain, such that state-of-the-art foundation models can generate meaningless and incorrect results. Moreover, in certain domains, fine-tuning and retraining techniques are infeasible: obtaining labels is costly and time-consuming; domain images (micrographs) can be exponentially diverse; and data sharing (for third-party retraining) is restricted. To enable rapid adaptation of the best segmentation technology, we propose the concept of semantic boosting: given a zero-shot foundation model, guide its segmentation and adjust results to match domain expectations. Here, we apply semantic boosting to the Segment Anything Model (SAM) to obtain microstructure segmentation for transmission electron microscopy. Our booster, SAM-I-Am, serves as a post-processing engine that extracts geometric and textural features of various intermediate masks to perform mask removal and mask merging operations. We demonstrate a zero-shot performance increase of (absolute) +21.35%, +12.6%, +5.27% in mean IoU, and a -9.91%, -18.42%, -4.06% drop in mean false positive masks across images of three difficulty classes over vanilla SAM (ViT-L).

36 MATERIALS SCIENCE↗