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DOE OSTI2018

Two-dimensional models for the optical response of thin films

Here, we present a systematic study of 2D optical models for the response of thin layers of material under excitation by normally incident light. The treatment, within the framework of classical optics, analyzes a thin film supported by a semi-infinite substrate, with both the thin layer and the substrate assumed to exhibit local, isotropic linear response. Starting from the conventional three-dimensional (3D) slab model of the system, we derive a two-dimensional (2D) sheet model for the thin film in which the optical response is described by a sheet optical conductivity. We develop criteria for the applicability of this 2D sheet model for a layer with an optical thickness far smaller than the wavelength of the light. We examine in detail atomically thin semi-metallic and semiconductor van-der-Waals layers and ultrathin metal films as representative examples. Excellent agreement of the 2D sheet model with the 3D slab model is demonstrated over a broad spectral range from the radio frequency limit to the near ultraviolet. A linearized version of system response for the 2D model is also presented for the case where the influence of the optically thin layer is sufficiently weak. Analytical expressions for the applicability and accuracy of the different optical models are derived, and the appropriateness of the linearized treatment for the materials is considered. We discuss the advantages, as well as limitations, of these models for the purpose of deducing the optical response function of the thin layer from experiment. We generalize the theory to take into account in-plane anisotropy, layered thin film structures, and more general substrates. Implications of the 2D model for the transmission of light by the thin film and for the implementation of half- and totally absorbing layers are discussed.

2D materials↗

NASA NTRS2018

Analysis of Simulated and Experimental Noise Sources of Boeing 777 Main Gear Model via CLEAN in 3D

Previously obtained experimental and simulated phased microphone array data for the NASA 26%-scale model of a six-wheel main landing gear, with and without a toboggan-shaped noise reduction fairing, were analyzed using the CLEAN technique in three dimensions. The model is a high-fidelity representation of the Boeing 777-200 aircraft main landing gear. The reprocessing of the acoustic data was undertaken to address the deficiencies encountered in the source localization (beamform) maps and the integrated farfield spectra at mid to high frequencies in our previous study, where conventional array processing techniques were applied to the same data sets. Application of the CLEAN approach resulted in higher quality beamform maps with many of the previously observed side lobes either eliminated or suppressed significantly. As a result, integration of the experimentally and computationally based maps showed substantial improvement in the quality of the high-frequency spectral content relative to the corresponding spectra generated via conventional array processing, thus extending the good agreement achieved between the measured and predicted farfield spectra from 8 kHz to 14 kHz in model-scale frequencies. In addition, an examination of the simulated surface pressure fluctuations, off-surface flow field, and three-dimensionally constructed noise sources was conducted to determine the cause of the subtle discrepancies between measured and predicted sound pressure levels that occur in the 1,800 Hz to 4,000 Hz model-scale frequency range.

Ravetta, Patricio↗

DOE OSTI2015

DREAM3D simulations of inner-belt dynamics

A 1973 paper by Lyons and Thorne explains the two-belt structure for electrons in the inner magnetosphere as a balance between inward radial diffusion and loss to the atmosphere, where the loss to the atmosphere is enabled by pitch-angle scattering from Coulomb and wave-particle interactions. In the 1973 paper, equilibrium solutions to a decoupled set of 1D radial diffusion equations, one for each value of the first invariant of motion, μ, were computed to produce the equilibrium two-belt structure. Each 1D radial diffusion equation incorporated an L-and μ-dependent `lifetime' due to the Coulomb and wave-particle interactions. This decoupling of the problem is appropriate under the assumption that radial diffusion is slow in comparison to pitch-angle scattering. However, for some values of μ and L the lifetime associated with pitch-angle scattering is comparable to the timescale associated with radial diffusion, suggesting that the true equilibrium solutions might reflect `coupled modes' involving pitch-angle scattering and radial diffusion and thus requiring a 3D diffusion model. In the work we show here, we have computed the equilibrium solutions using our 3D diffusion model, DREAM3D, that allows for such coupling. We find that the 3D equilibrium solutions are quite similar to the solutions shown in the 1973 paper when we use the same physical models for radial diffusion and pitch-angle scattering from hiss. However, we show that the equilibrium solutions are quite sensitive to various aspects of the physics model employed in the 1973 paper that can be improved, suggesting that additional work needs to be done to understand the two-belt structure.

58 GEOSCIENCES↗

DOE OSTI2024

RELAP5-3D validation studies based on the High Temperature Test facility

In the spring and summer of 2019, experiments were conducted at the High Temperature Test Facility (HTTF) that form the basis of an upcoming high-temperature gas-cooled reactor (HTGR) thermal hydraulics (T/H) benchmark. HTTF is an integral effects test facility for HTGR T/H modeling validation. This paper presents RELAP5-3D models of two of those experiments: PG-27, a pressurized conduction cooldown (PCC); and PG-29, a depressurized conduction cooldown (DCC). These models used the RELAP5-3D model of HTTF originally developed by Paul Bayless as a starting point. The sensitivity analysis and uncertainty quantification code, RAVEN was used to perform calibration studies for the steady-state portion of PG-27. Here we developed four PG-27 calibrations based on steady-state conditions. These calibrations all used an effective thermal conductivity equal to 36 % of the measured thermal conductivity, but they differed with respect to the frictional pressure drops and radial conduction models. These models all captured the trends in steady-state temperature distributions and transient temperature behavior well. All four calibrations show room for improvement in predicting the transient temperature rise. The smallest error in temperature rise during the transient was a 21 % underprediction, and the largest was a 48 % underprediction. The errors in transient temperature rise are largely a result of a mismatch in power density between the RELAP5-3D model and the experiment due to the location of active heater rods along the boundary between heat structures in the model. The best of these calibrations was applied to PG-29 to model the DCC. Once again, temperatures during the transient were underpredicted but trends in temperature were captured. The RELAP5-3D model captured trends in the data but could not reproduce measured temperatures exactly. This result is not attributed to deficiencies in the experimental data or to RELAP5–3D itself. Rather, this result likely arises due to the some of the assumptions and decisions made when the RELAP5-3D model was first developed, prior to the execution of HTTF experiments. An agreement in prediction of temperature trends but challenges reproducing HTTF temperatures within measurement uncertainty is consistent with previous analyses of HTTF in the literature. Future RELAP5-3D validation activities centered around HTTF may be able to provide greater insight into the code’s capabilities for HTGR modeling with a more finely nodalized model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Simulation of the High Temperature Test Facility (HTTF) Core Using the 2D Ring Model with SAM

A two-dimensional ring model is developed with SAM to model the core of the High Temperature Test Facility (HTTF) at the system level. The ring model simplifies the complex structure of the HTTF core by converting the hexagonal rows of heaters and flow channels into layers of concentric annular rings. The ring model is first compared against a 3D-1D model where the solid structures are fully resolved in three dimensions while the fluid structures are modeled as one-dimensional flows. Comparison between the 3D-1D and the ring models shows that the latter can predict major parameters reasonably well under steady-state normal operating condition, but the heater temperatures are underpredicted. Adjustment is made to the effective thermal conductivity of the ceramic core of the ring model to improve the heater temperature predictions. Furthermore, the ring model is also used to simulate a transient Pressurized Conduction Cooldown (PCC) condition and is benchmarked with the experimental data from the HTTF Test PG-27. Good agreement is obtained between the experimental data and the predictions by the ring model.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2017

Floorspace.js

Floorspace.js is a 2D geometry editor. Users can define an explicit floor plan for each story of a building. A story-by-story interface makes it easy to develop space geometry and assign properties. Referencing satellite imagery or floor plan images, when available, speeds up geometry entry. Conversion of 2D to 3D geometry is currently out of scope for Floorspace.js, a reference implementation is available in the OpenStudio® SDK. Explicit floor plans allow more building-specific information than parameterized shoe-boxes but less information than a full 3D BIM model. Sloped walls, complex roofs, detailed shading structures, and other complex 3D structures are out of FloorspaceJS's scope. In general, if users have a 3D BIM model in a tool that can export a useful BEM representation then it is better to use that export than to recreate a new model using FloorspaceJS. Re-usability and minimal dependencies were key design considerations for software developers. Web technologies can be used in both online and desktop applications. The editor was written in pure JavaScript for maximum portability and re-usability. A custom JavaScript Object Notation (JSON) file format was developed to ease integration with other applications. Custom JSON schema design was a key part of FloorspaceJS development.

Noland, Katie↗

NASA NTRS1995

Modeling the Properties of 3D Woven Composites

An extensive study has been completed of the internal geometry, the mechanisms of failure, and the micromechanics of local failure events in graphite/epoxy composites with three dimensional (3D) woven reinforcement. This work has led to the development of models for predicting elastic constants, strength, notch sensitivity, and fatigue life. A summary is presented here.

Cox, Brian N.↗

NASA NTRS2010

High-Fidelity Roadway Modeling and Simulation

Roads are an essential feature in our daily lives. With the advances in computing technologies, 2D and 3D road models are employed in many applications, such as computer games and virtual environments. Traditional road models were generated by professional artists manually using modeling software tools such as Maya and 3ds Max. This approach requires both highly specialized and sophisticated skills and massive manual labor. Automatic road generation based on procedural modeling can create road models using specially designed computer algorithms or procedures, reducing the tedious manual editing needed for road modeling dramatically. But most existing procedural modeling methods for road generation put emphasis on the visual effects of the generated roads, not the geometrical and architectural fidelity. This limitation seriously restricts the applicability of the generated road models. To address this problem, this paper proposes a high-fidelity roadway generation method that takes into account road design principles practiced by civil engineering professionals, and as a result, the generated roads can support not only general applications such as games and simulations in which roads are used as 3D assets, but also demanding civil engineering applications, which requires accurate geometrical models of roads. The inputs to the proposed method include road specifications, civil engineering road design rules, terrain information, and surrounding environment. Then the proposed method generates in real time 3D roads that have both high visual and geometrical fidelities. This paper discusses in details the procedures that convert 2D roads specified in shape files into 3D roads and civil engineering road design principles. The proposed method can be used in many applications that have stringent requirements on high precision 3D models, such as driving simulations and road design prototyping. Preliminary results demonstrate the effectiveness of the proposed method.

Wang, Jie↗

DOE OSTI2018

Modelling DC responses of 3D complex fracture networks

Here, the determination of the geometrical properties of fractures plays a critical role in many engineering problems to assess the current hydrological and mechanical states of geological media and to predict their future states. However, numerical modeling of geoelectrical responses in realistic fractured media has been challenging due to the explosive computational cost imposed by the explicit discretizations of fractures at multiple length scales, which often brings about a tradeoff between computational efficiency and geologic realism. Here, we use the hierarchical finite element method to model electrostatic response of realistically complex 3D conductive fracture networks with minimal computational cost.

58 GEOSCIENCES↗

DOE OSTI2016

Postoperative 3D spine reconstruction by navigating partitioning manifolds

Purpose: The postoperative evaluation of scoliosis patients undergoing corrective treatment is an important task to assess the strategy of the spinal surgery. Using accurate 3D geometric models of the patient’s spine is essential to measure longitudinal changes in the patient’s anatomy. On the other hand, reconstructing the spine in 3D from postoperative radiographs is a challenging problem due to the presence of instrumentation (metallic rods and screws) occluding vertebrae on the spine. Methods: This paper describes the reconstruction problem by searching for the optimal model within a manifold space of articulated spines learned from a training dataset of pathological cases who underwent surgery. The manifold structure is implemented based on a multilevel manifold ensemble to structure the data, incorporating connections between nodes within a single manifold, in addition to connections between different multilevel manifolds, representing subregions with similar characteristics. Results: The reconstruction pipeline was evaluated on x-ray datasets from both preoperative patients and patients with spinal surgery. By comparing the method to ground-truth models, a 3D reconstruction accuracy of 2.24 ± 0.90 mm was obtained from 30 postoperative scoliotic patients, while handling patients with highly deformed spines. Conclusions: This paper illustrates how this manifold model can accurately identify similar spine models by navigating in the low-dimensional space, as well as computing nonlinear charts within local neighborhoods of the embedded space during the testing phase. This technique allows postoperative follow-ups of spinal surgery using personalized 3D spine models and assess surgical strategies for spinal deformities.

61 RADIATION PROTECTION AND DOSIMETRY↗

DOE OSTI2022

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

While deep learning models have seen increasing applications in protein science, few have been implemented for protein backbone generation—an important task in structure-based problems such as active site and interface design. We present a new approach to building class-specific backbones, using a variational auto-encoder to directly generate the 3D coordinates of immunoglobulins. Our model is torsion- and distance-aware, learns a high-resolution embedding of the dataset, and generates novel, high-quality structures compatible with existing design tools. We show that the Ig-VAE can be used with Rosetta to create a computational model of a SARS-CoV2-RBD binder via latent space sampling. We further demonstrate that the model’s generative prior is a powerful tool for guiding computational protein design, motivating a new paradigm under which backbone design is solved as constrained optimization problem in the latent space of a generative model.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2003

A New Look into the Effect of Large Drops on Radiative Transfer Process

Recent studies indicate that a cloudy atmosphere absorbs more solar radiation than any current 1D or 3D radiation model can predict. The excess absorption is not large, perhaps 10-15 W/sq m or less, but any such systematic bias is of concern since radiative transfer models are assumed to be sufficiently accurate for remote sensing applications and climate modeling. The most natural explanation would be that models do not capture real 3D cloud structure and, as a consequence, their photon path lengths are too short. However, extensive calculations, using increasingly realistic 3D cloud structures, failed to produce photon paths long enough to explain the excess absorption. Other possible explanations have also been unsuccessful so, at this point, conventional models seem to offer no solution to this puzzle. The weakest link in conventional models is the way a size distribution of cloud particles is mathematically handled. Basically, real particles are replaced with a single average particle. This "ensemble assumption" assumes that all particle sizes are well represented in any given elementary volume. But the concentration of larger particles can be so low that this assumption is significantly violated. We show how a different mathematical route, using the concept of a cumulative distribution, avoids the ensemble assumption. The cumulative distribution has jumps, or steps, corresponding to the rarer sizes. These jumps result in an additional term, a kind of Green's function, in the solution of the radiative transfer equation. Solving the cloud radiative transfer equation with the measured particle distributions, described in a cumulative rather than an ensemble fashion, may lead to increased cloud absorption of the magnitude observed.

Marshak, Alexander↗

DOE OSTI2020

Modular high temperature gas reactor core modeling with RELAP5-3D/PHISICS – Optimization schemes for load following

The objective of this study is to develop a 3D/NK model to study the load following operation of a Modular High-Temperature Gas-Cooled Reactor (MHTGR). The selected design is the 350 MW prismatic, graphite moderated, helium cooled thermal reactor based on the MHTGR-350 transient benchmark led by the High-Temperature Gas-Cooled Reactor (HTGR) Methods Core Simulation Group at Idaho National Laboratory (INL) in the framework of the Organization for Economic Cooperation and Development Nuclear Energy Agency (OECD/NEA). This kind of reactor usually reacts very slowly to the perturbation of the core parameters due to the large amount of graphite in the core. This kind of behavior promotes the reactor stability but on the other hand limits the reactor load-following operability. Recently advances in gas reactor designs have made load-following in gas reactors a feasible and achievable goal. Modern nuclear reactors (such as the MHTGR-350) are designed to withstand the structural stresses associated with load-following. Operating the reactor in load-following mode will inevitably reduce the load factor. Although a higher load factor means more revenue and the best usage of the fuel, following the variable energy demand will increase the maximum achievable fraction of generated nuclear power, being no more limited to the base load power generation. In general, if low impact on material aging and the safe operability are demonstrated the plant economics will be minimally affected. In order to ensure that the system can be safely operated in a load-following mode an extensively study has been carried out. Some tests with linear coolant mass flow rate change demonstrated that the reactor behavior is suitable for operation in load following mode. This assumption has been confirmed by a 4 days load following transient test in which the reactor supplied the requested power with a negligible error.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2018

The Role of Dimensionality in Understanding Granuloma Formation

Within the first 2–3 months of a Mycobacterium tuberculosis (Mtb) infection, 2–4 mm spherical structures called granulomas develop in the lungs of the infected hosts. These are the hallmark of tuberculosis (TB) infection in humans and non-human primates. A cascade of immunological events occurs in the first 3 months of granuloma formation that likely shapes the outcome of the infection. Understanding the main mechanisms driving granuloma development and function is key to generating treatments and vaccines. In vitro, in vivo, and in silico studies have been performed in the past decades to address the complexity of granuloma dynamics. This study builds on our previous 2D spatio-temporal hybrid computational model of granuloma formation in TB (GranSim) and presents for the first time a more realistic 3D implementation. We use uncertainty and sensitivity analysis techniques to calibrate the new 3D resolution to non-human primate (NHP) experimental data on bacterial levels per granuloma during the first 100 days post infection. Due to the large computational cost associated with running a 3D agent-based model, our major goal is to assess to what extent 2D and 3D simulations differ in predictions for TB granulomas and what can be learned in the context of 3D that is missed in 2D. Our findings suggest that in terms of major mechanisms driving bacterial burden, 2D and 3D models return very similar results. For example, Mtb growth rates and molecular regulation mechanisms are very important both in 2D and 3D, as are cellular movement and modulation of cell recruitment. The main difference we found was that the 3D model is less affected by crowding when cellular recruitment and movement of cells are increased. Overall, we conclude that the use of a 2D resolution in GranSim is warranted when large scale pilot runs are to be performed and if the goal is to determine major mechanisms driving infection outcome (e.g., bacterial load). To comprehensively compare the roles of model dimensionality, further tests and experimental data will be needed to expand our conclusions to molecular scale dynamics and multi-scale resolutions.

2D vs. 3D↗

DOE OSTI2022

-Omics potential of in vitro skin models for radiation exposure

There is a growing need to uncover biomarkers of ionizing radiation exposure that leads to a better understanding of how exposures take place, including dose type, rate, and time since exposure. As one of the first organs to be exposed to external sources of ionizing radiation, skin is uniquely positioned in terms of model systems for radiation exposure study. The simultaneous evolution of both MS-based -omics studies, as well as in vitro 3D skin models, has created the ability to develop a far more holistic understanding of how ionizing radiation affects the many interconnected biomolecular processes that occur in human skin. However, there are a limited number of studies describing the biomolecular consequences of low-dose ionizing radiation to the skin. As a result, this review will seek to explore the current state-of-the-art technology in terms of in vitro 3D skin models, as well as track the trajectory of MS-based -omics techniques and their application to ionizing radiation research, specifically, the search for biomarkers within the low-dose range.

3D tissue model↗

DOE OSTI2023

HPC-Enabled Optimization of High Temperature Heat Exchangers (CRADA Final Report)

This project was a collaborative effort between Lawrence Livermore National Security, LLC (LLNS) as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Materials Sciences, LLC, to develop a technology for design and optimization of heat exchangers using powerful desktop and laptop computers. The project was originally designated as a 12-month project, and consisted of 3# major tasks and the following 8# major deliverables: 1) CFD models of 3D heat exchangers based on existing and new geometry. 2) Validation against experimental data provided by MSC and published in the literature. 3) CFD models of 3D unit cells based on TPMS. 4) Surrogate models capable of delivering the gradients of the homogenized properties with respect to the parametrization. 5) 3D design methodology using TO algorithms. 6) Conventional reference and topology optimized designs. 7) 3D optimized designs stored in a 3D printer build format. 8) Verification of the improved performance. All of the deliverables for this project were successfully completed with two no-cost time extensions.

36 MATERIALS SCIENCE↗

DOE OSTI2026

HPC-Enabled Optimization of High Temperature Heat Exchangers (CRADA Final Report)

13 HYDRO ENERGY↗

NASA NTRS1992

Simulation of the zonal mean climatology of the middle atmosphere with a three-dimensional spectral model for solstice and equinox conditions

A 3D spectral model was used to simulate the zonal mean state of the middle atmosphere for solstice and equinox conditions. The model incorporates realistic parameterizations of atmospheric infrared cooling and a gravity wave formulation based on a combination of Lindzen's (1981) and Matsuno's (1982) approaches. The temperature distributions for both seasons and the zonal wind distribution for solstice are found to be in satisfactory agreement with the empirical model of Fleming et al. (1988). Net vertical fluxes of horizontal momentum are in good agreement with systematic observations of gravity waves in the middle atmosphere.

Akmaev, R. A.↗