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DOE OSTI2024

NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study

Abstract Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model: Modeling Archive

This archive contains the data and Python scripts required to reproduce the analyses and figures in the study: Gomez-Velez, J. D., Rathore, S. S., Cohen, M. J., & Painter, S. L. (2025). Hyporheic-zone Processes and Stream Oxygen Dynamics: Insights from a Multiscale Reactive Transport Model. Submitted to Water Resources Research. The analysis utilizes the subgrid model Advection Dispersion Equation with Lagrangian Subgrids (ADELS) implemented in the Advanced Terrestrial Simulator (ATS; https://amanzi.github.io/ats/stable/). In this case, the ATS and Amanzi versions are (1) ATS version 1.5.1_f5ba18f8 and (2) Amanzi version 1.6-dev_53444cca4. The repository includes a Jupyter Notebook and the necessary data (Pandas DataFrames stored as pickle files) to generate the figures for the manuscript. Additionally, it contains Python scripts to create ATS input files, run the ATS simulations, and post-process the results. Finally, it provides routines for parameter estimation using the Single-Station Metabolism (SSM) model with the Differential Evolution Adaptive Metropolis (DREAM) Markov Chain Monte Carlo (MCMC) algorithm with ZS enhancements (DREAM-ZS).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

MCNP modelling of the Thermo SPA3 with Tungsten (Rees model) collimator

A Thermo Model SPA3 2”x2” NaI probe fitted with a Tungsten collimator has been modelled using MCNP6. The collimator was assumed to be machinable Tungsten which typically includes Ni and Fe. Various ratios of these additives are used in industry and for the purposes of these calculations the collimator was assumed to contain 7% Ni and 3% Fe with a density of 17.0 g/cm 3 . The dimensions of the collimator were based on measurements taken by Mike Fanning. The above detector model was used, in a manner similar to the approach described in LA-UR-19-32358, to calculate photopeak count rates per unit activity per unit area (i.e. cpm per pCi/cm 2 ) conversion factors for various contamination scenarios.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2020

Comparison of Modeled to Measured Spectra using MCNP and GADRAS to Benchmark and Contrast Modeling Limitations

The desire to improve nuclear material detection through portal monitors and other low resolution detectors has led to interest in benchmarking the performance of radiation transport codes. These codes can be used to generate a variety and quantity of spectra that may be cost prohibitive to measure directly. Particular characteristics of typical detection scenarios were isolated to compare the performance of radiation transport codes to laboratory experiments. These benchmark experiments were performed to validate simulations in a number of key areas. These experiments included high areal density configurations in both one- and three-dimensional configurations. In addition, off-angle measurements were conducted to investigate the impact of detector response assumptions on complex geometries, for example where an unknown source is not physically collocated with an apparent hot spot. Furthermore, by examining both simple shielding and backscatter configurations, isolation of the scatter emanating from the object and environmental background scatter contributions to the spectra could be elucidated. A series of experiments were performed in which the order of shielding layers and the thickness were evaluated to examine the ability of the simulations to address these variables. Experiments with increasing thickness of polyethylene around a neutron source also allows for examinations of the ability of the transport simulations to properly model n,γ reactions. Finally, depleted uranium (DU) measurements have more complicated spectra than the cobalt-60 and consequently allow for investigations into the ability of transport simulations to model self-shielding. In each case, the results of the experiments were compared to MCNP simulations to judge the performance of the code, as was done previously with GADRAS 18.7.9 simulations [7]. All of the benchmark measurements were taken with a liquid nitrogen cooled 140% high purity germanium (HPGe) detector with a bismuth collimator that had the front tin filter removed. The measurement location and detector configuration were subsequently used for all experimental configurations. The remainder of this report details the experimental measurements, Section 2 and the MCNP model, Section 3. Comparisons between the experimental results and MCNP-generated spectra are performed, Section 4. Section 5 compares the results obtained with MCNP with the previously reported results obtained with GADRAS [2]. Finally, Section 6 presents the conclusions.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2020

SNL will be able to provide well-calibrated models to weapons systems analysts by integrating an engine for constitutive model calibration with the GRANTA materials database

Researchers at Sandia National Laboratories have integrated the GRANTA materials database with the MatCal calibration engine to calibrate material models from characterization data. GRANTA is gaining acceptance across the NNSA Tri-lab complex and is being populated with weapons-specific test data by Sandia experimentalists. To use that data to create material models for use by weapons systems analysts, MatCal has been enabled import calibration data and test conditions from GRANTA to quickly and reproducibly produce a calibrated set of parameters for a given constitutive model. The team is currently working to store the parameters characterizing material behavior in GRANTA to make them accessible by all weapons analysts.

36 MATERIALS SCIENCE↗

DOE OSTI2020

FY19 Status Report on the Computing Systems for the Yucca Mountain Project TSPA-LA Models and Preliminary Testing of a Selected Process Model

Sandia National Laboratories continued evaluation of total system performance assessment (TSPA) computing systems for the previously considered Yucca Mountain Project. This was done to maintain the operational readiness of the computing infrastructure (computer hardware and software) and knowledge capability for total system performance assessment) type analysis, as directed by the National Nuclear Security Administration (NNSA), DOE 2010. The FY19 task included continued operation of the cluster; maintenance of the TSPA-LA models (with Gold Sim 9.60.300); preliminary assessment of the status of the Infiltration Model (a process model that feeds the TSPA-LA). In addition, precautionary actions were needed to extend the life of the cluster hardware. To do that, three new nodes were added to the cluster. In the event any of the original nodes fail they will be replaced with the new nodes, thereby maintaining the core capability. The 2014 cluster and supporting software systems are currently fully operational to support TSPA-LA type analysis.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Mesoscale modeling to inform Bison models of accident tolerant fuel concepts

U 3 Si 2 and doped UO 2 have been under investigation in recent years as potential accident-tolerant fuel concepts. In this report, lower-length scale studies of these fuel concepts carried out during Fiscal Year 2020 are detailed. U 3 Si 2 is a potential accident-tolerant fuel that shows promise due to its high thermal conductivity and higher uranium density relative to UO 2 . However, its swelling and fission gas release behavior in light water reactor (LWR) conditions is relatively unknown. To provide mechanistic insight and determine parameters for engineering-scale fuel performance modeling of pellet-form U 3 Si 2 , phase-field simulations of the growth, interconnection, and venting of intergranular fission gas bubbles were performed. The fractional coverage of the grain boundary and the fraction of bubble area that is vented were calculated as a function of time. From the simulation data, the fractional grain boundary coverage at saturation, an important parameter needed in engineering-scale modeling of swelling and fission gas release, was determined. Multiple simulations were run to determine the uncertainty in the calculated value. The effect of model assumptions and input parameters that are not well known was evaluated. Simulation results are compared to related theoretical and computational work. Based on the simulation results, a value of 0.60 for the fractional grain boundary coverage at saturation is recommended for U 3 Si 2 fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Geochemical Modeling Using OLI Systems Mixed Solvent Electrolyte Model in Support of the Waste Isolation Pilot Plant

Aqueous electrolyte thermodynamic models were developed for synthetic Salado (GWB) and Castile (ERDA-6) brines to inform the experimental design and to facilitate laboratory data interpretation in geochemical studies supporting disposal in the Waste Isolation Pilot Plant (WIPP). The thermodynamic models, which include the relevant vapor-liquid-solid equilibria for the oxidation-reduction conditions of interest, enable computation of system parameters such as activity-based pH, E h [vs. standard hydrogen electrode (SHE)], ionic strength, total dissolved solids, and solution density; the chemical speciation of all phases; saturation tendencies for thermodynamically feasible solids; and changes in brine chemistry because of the addition of H 2 (g), argon, MgO, Fe(0), and other waste form components. The impacts of oxidation-reduction potential (ORP) and pH on aqueous speciation and dominant solid phases were also assessed with the aid of real-solution Pourbaix diagrams for key elements of interest. In addition to the OLI modeling results, limited measurement data for pH and ORP standards are provided, analyzed, and discussed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2025

Implementation of a turbine farm model into the Energy Exascale Earth System Model for investigation and quantification of global climate impacts

Although there has been widespread deployment of wind farms in the United States, and plans to continue deployment into the future, the complete effects of wind farms on Earth systems are not well understood. The work performed here has incorporated wind farm models into the Energy Exascale Earth System Model (E3SM) capable of simulating the effects of extracting momentum from the atmospheric flow field using power generating wind farms. This new capability will allow scientists to quantify the impacts of wind farm induced changes on Earth systems by exploiting E3SM’s ability to couple atmospheric, oceanic, and biogeochemical (BGC) models on a global scale and monitor precipitation levels, extreme weather events, soil moisture content and jet stream location over decades-long time periods. This tool will be used to inform decision making on wind farm citing and will contribute to the Lab’s ability to assess energy technology impacts on the environment and evaluate the trade-offs between energy infrastructure investments and their impacts on natural systems.

17 WIND ENERGY↗

DOE OSTI2026

Modeling Material Interfaces with the Six-Equation Model in FLEXO

FLEXO is a multiphysics code developed at Sandia National Laboratories for predictive simulation of pulsed power target physics with extended magnetohydrodynamics modeling. Given this application space, FLEXO must be able to perform high-fidelity simulations of pulsed-power systems that include multiple materials. This work presents the augmentation of FLEXO with a six-equation model for multimaterial flow. We design and analyze discretizations of the six-equation model, emphasizing desirable properties for robust multimaterial simulation. We also present solution limiting, bounds preservation, and pressure equilibration/relaxation techniques that enhance the robustness of the overall multimaterial scheme. We present a suite of test problems to document these new capabilities of the FLEXO code.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Core Mass Estimates in Strong Lensing Galaxy Clusters: A Comparison between Masses Obtained from Detailed Lens Models, Single-halo Lens Models, and Einstein Radii

The core mass of galaxy clusters is both an important anchor of the radial mass distribution profile and probe of structure formation. With thousands of strong lensing galaxy clusters being discovered by current and upcoming surveys, timely, efficient, and accurate core mass estimates are needed. Here, we assess the results of two efficient methods to estimate the core mass of strong lensing clusters: the mass enclosed by the Einstein radius (M(<θ E ) where θ E is approximated from arc positions; Remolina González et al. 2020), and single-halo lens model (M SHM ; Remolina González et al. 2021), against measurements from publicly available detailed lens models (M DLM ) of the same clusters. We use data from the Sloan Giant Arc Survey, the Reionization Lensing Cluster Survey, the Hubble Frontier Fields, and the Cluster Lensing and Supernova Survey with Hubble. We find a scatter of 18.2% (8.2%) with a bias of -7.1% (1.0%) between M corr (<θ arcs ) (M SHM ) and M DLM . Last, we compare the statistical uncertainties measured in this work to those from simulations. This work demonstrates the successful application of these methods to observational data. As the effort to efficiently model the mass distribution of strong lensing galaxy clusters continues, we need fast, reliable methods to advance the field.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Disentangling atmospheric, hydrological, and coupling uncertainties in compound flood modeling within a coupled Earth system model

Compound riverine and coastal flooding is usually driven by complex interactions among meteorological, hydrological, and ocean extremes. However, existing efforts to model this phenomenon often do not integrate hydrological processes across atmosphere–land–river–ocean systems, leading to substantial uncertainties that have not been fully examined. To bridge this gap, we leverage the new capabilities of the Energy Exascale Earth System Model (E3SM) that enable a multi-component framework that integrates coastally refined atmospheric, terrestrial, and oceanic components. We evaluate compound uncertainties arising from two-way land–river–ocean coupling in E3SM and track the cascading meteorological and hydrological uncertainties through ensemble simulations over the Delaware River basin and estuary during Hurricane Irene (2011). Our findings highlight the importance of two-way river–ocean coupling to compound flood modeling and demonstrate E3SM's capability in capturing compound flood extent near the coast, with a hit rate over 0.75. Our study shows the growing uncertainties that transition from atmospheric forcings to flood distribution and severity. Furthermore, an analysis based on artificial neural networks is used to assess the roles of hydrological drivers, such as infiltration and soil moisture, in the generation of compound flooding. The response of compound floods to tropical cyclones (TCs) is found to be susceptible to these often overlooked drivers. For instance, the flooded area could increase more than 2-fold (∼2.4) if Hurricane Irene were preceded by an extreme antecedent soil moisture condition (AMC). The results not only support the use of a multi-component framework for interactive flooding processes, but also underscore the necessity of broader definitions of compound flooding that encompass the simultaneous occurrence of intense precipitation, storm surge, and high AMC during TCs.

Feng, Dongyu [Pacific Northwest National Laborator↗

DOE OSTI2024

Metabolic model-based ecological modeling for probiotic design

The microbial community composition in the human gut has a profound effect on human health. This observation has lead to extensive use of microbiome therapies, including over-the-counter ‘probiotic’ treatments intended to alter the composition of the microbiome. Despite so much promise and commercial interest, the factors that contribute to the success or failure of microbiome-targeted treatments remain unclear. We investigate the biotic interactions that lead to successful engraftment of a novel bacterial strain introduced to the microbiome as in probiotic treatments. We use pairwise genome-scale metabolic modeling with a generalized resource allocation constraint to build a network of interactions between taxa that appear in an experimental engraftment study. We create induced sub-graphs using the taxa present in individual samples and assess the likelihood of invader engraftment based on network structure. To do so, we use a generalized Lotka-Volterra model, which we show has strong ability to predict if a particular invader or probiotic will successfully engraft into an individual’s microbiome. Furthermore, we show that the mechanistic nature of the model is useful for revealing which microbe-microbe interactions potentially drive engraftment.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1972

Model for energy transfer in the solar wind: Model results

A description is given of the results of solar wind flow in which the heating is due to (1) propagation and dissipation of hydromagnetic waves generated near the base of the wind, and (2) thermal conduction. A series of models is generated for fixed values of density, electron and proton temperature, and magnetic field at the base by varying the wave intensity at the base of the model. This series of models predicts the observed correlation between flow speed and proton temperature for a large range of velocities. The wave heating takes place in a shell about the sun greater than or approximately equal to 10 R thick. We conclude that large-scale variations observed in the solar wind are probably due mainly to variation in the hydromagnetic wave flux near the sun.

Barnes, A. A., Jr.↗

NASA NTRS1975

Hydrodynamic models of a Cepheid atmosphere. I - Deep envelope models

The implicit hydrodynamic code of Kutter and Sparks has been modified to include radiative transfer effects. This modified code has been used to compute deep envelope models of a classical Cepheid with a period of 12 days. It is shown that in this particular model the hydrogen ionization region plays only a small role in producing the observed phase lag between the light and velocity curves. The cause of the bumps on the model's light curve is examined, and a mechanism is presented to explain those Cepheids with two secondary features on their light curves. This mechanism is shown to be consistent with the Hertzsprung sequence only if the evolutionary mass-luminosity law is used.

Karp, A. H.↗

NASA NTRS1977

Atmospheric model development in support of SEASAT. Volume 4: Forecast model sensitivity study

Atmospheric analysis and prediction models of varying (grid) resolution were developed. The models were tested using real observational data for the purpose of assessing the impact of grid resolution on short range numerical weather prediction. The work statement was amended to include the performance of sensitivity tests using a coarse mesh (63 x 63 x 5 level) prediction model in order to identify and order factors which might mask or impair the utility of SEASAT data on short range weather prediction. Such factors included: initial conditions; topography; surface friction; latent heating; diffusion of momentum and temperature; and computational devices such as tendency truncators, pressure smoothers, and temporal filters.

Lewit, H. L.↗

NASA NTRS1979

Analytical model of an Annular Momentum Control Device (AMCD) laboratory test model magnetic bearing actuator

An analytical model of an Annular Momentum Control Device (AMCD) laboratory test model magnetic bearing actuator with permanent magnet fluxbiasing is presented. An AMCD consists of a spinning annular rim which is suspended by a noncontacting linear electromagnetic spin motor. The actuator is treated as a lumped-parameter electromechanical system in the development of the model.

Groom, N. J.↗