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DOE OSTI2021

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Demonstration of Vertical 2T-nC FeRAM Hybrid Cell and Its Scalability for High-Density 3-D Ferroelectric Capacitor Memory

In this work, we present a comprehensive experimental and modeling study on the scaling of vertical 2T-nC ferroelectric random access memory (FeRAM) hybrid cells, comprising n metal-ferroelectric–metal (MFM) capacitors, to demonstrate a high-performance and high-density 3-D capacitor memory. Our contributions include: 1) successful process integration of vertical 2T-3C FeRAM cells by stacking MFM structures on top of Si CMOS transistors; 2) experimental validation of memory cell functionality, confirming the feasibility of the vertical 2T-nC FeRAM architecture; 3) an analysis of scaling effects on parasitic capacitance in densely integrated 3-D arrays, using 3-D technology computer-aided design (TCAD) simulations; 4) exploration of aggressive stacking of write bitlines (WBLs) to enhance memory density, where ferroelectric linear capacitance ( C FE ) enables self-boosted inhibition under the V W /2 scheme, but renders the V W /3 scheme ineffective due to intolerable write disturbances; and 5) assessment of horizontal scaling, revealing significant increases in read disturbances caused by interplane capacitance between adjacent WBLs ( C Z ). This work represents an early exploration into the potential of 2T-nC FeRAM as a scalable and efficient 3-D memory solution.

42 ENGINEERING↗

DOE OSTI2024

ParaStell: parametric modeling and neutronics support for stellarator fusion power plants

The three-dimensional variation inherent to stellarator geometries and fusion sources motivates three-dimensional modeling to obtain accurate results from computational modeling in support of design and analysis of first wall, blanket, and shield (FWBS) systems. Manually constructing stellarator fusion power plant geometries in computer-aided design (CAD) and defining the corresponding fusion source can be cumbersome and challenging. The open-source parametric modeling toolset ParaStell has been developed to automate construction of such geometries in low-fidelity. Low-fidelity modeling is useful during the conceptual phase of engineering design as a means of rapidly exploring the design space of a given device. The modeling capability of ParaStell includes in-vessel components and magnets, for any given stellarator configuration, using a parametric definition and plasma equilibrium data. Furthermore, the toolset automates the generation of detailed, tetrahedral neutron source definitions and DAGMC geometries for use in neutronics modeling. ParaStell assists rapid design iteration, parametric study, and design optimization of stellarator fusion cores. As a demonstration of the design iteration capability, the effect of the three-dimensional parameter space on tritium breeding and magnet shielding is investigated, using the WISTELL-D configuration as a design basis. Blanket and shield thicknesses are varied in three dimensions, using the space available between the plasma edge and magnet coils as a constraint. The corresponding effects on tritium breeding ratio and magnet heating are tallied using the open-source Monte Carlo particle transport code OpenMC. The inclusion of additional and higher-fidelity modeling capabilities is planned for ParaStell’s future, as well as its implementation in machine-driven optimization.

Moreno, Connor↗

DOE OSTI2022

Machine learning in nuclear materials research

Nuclear materials are often demanded to function for extended time in extreme environments, including high radiation fluxes with associated transmutations, high temperature and temperature gradients, mechanical stresses, and corrosive coolants. They also have a wide range of microstructural and chemical makeups, resulting in multifaceted and often out-of-equilibrium interactions. Machine learning (ML) is increasingly being used to tackle these complex time-dependent interactions and aid researchers in developing models and making predictions, sometimes with better accuracy than traditional modeling that focuses on one or two parameters at a time. Conventional practices of acquiring new experimental data in nuclear materials research are often slow and expensive, limiting the opportunity for data-centric ML, but new methods are changing that paradigm. Here we review high-throughput computational and experimental data approaches, especially robotic experimentation and active learning that is based on Gaussian process and Bayesian optimization. We show ML examples in structural materials (e.g., reactor pressure vessel (RPV) alloys and radiation detecting scintillating materials) and highlight new techniques of high-throughput sample preparation and characterizations, and automated radiation/environmental exposures and real-time online diagnostics. Herein, this review suggests that ML models of material constitutive relations in plasticity, damage, and even electronic and optical responses to radiation are likely to become powerful tools as they develop. Finally, we speculate on how the recent trends of using natural language processing (NLP) to aid the collection and analysis of literature data, interpretable artificial intelligence (AI), and the use of streamlined scripting, database, workflow management, and cloud computing platforms that will soon make the utilization of ML techniques as commonplace as the spreadsheet curve-fitting practices of today.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Machine-Learning-aided Approach for Predicting the Thermal Expansion Behaviors in Advanced Test Reactor Capsules (NURETH-20 full paper)

Instrumented experiments at test reactors are essential to deploying new advanced reactor systems. Designing new experiments and generating data on specific conditions require both time and cost investment. A high-fidelity model of the experiment environment can be created using finite element analysis software to support the actual experiments, but computation time is still a concern in applying outcomes to real-time usage (e.g., a digital twin). This research proposes a machine-learning-aided approach to temperature and displacement predictions, based on the thickness of the outer gas gap on the experimental capsule used for the in-pile demonstration of a novel thermal conductivity probe in the Advanced Test Reactor. The capsule consisted of U10Zr fuel, a rodlet, sodium, and inner and outer capsules. There were gas gaps between the fuel and rodlet and between the inner and outer capsule. The learning data consisted of an experimental capsule’s radial distributions of temperature and displacement, as obtained from Abaqus and the physical features. For the first step, temperature was predicted using three positional parameters. Then the displacement was predicted using six different positional parameters. Each physical feature was normalized to be both nondimensional and standardized. The temperature and displacement predictions showed good agreement in all cases involving interpolation and extrapolation. Also, data similarity enhancement increased the similarity between training and target data increasing the predictive accuracy of machine-learning models. In some cases of extrapolation, the accuracy of the machine-learning model showed limited performance, but still data similarity enhancement improved the accuracy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2023

Hybrid Particle Method for Computational Shock Physics

A long-standing area of research for Eulerian shock wave physics codes has been the treatment of strength and damage for materials. Here we present a method that will aid in the analysis of strength and failure in shock physics applications where excessive diffusion of critical variables can occur and control the solution outcome. Eulerian methods excel for large deformation simulations in general but are inaccurate in capturing structural behavior. Lagrangian methods provide better structural response, but finite element meshes can become tangled. Therefore, a technique for merging Lagrangian and Eulerian treatments of material response, within a single numerical framework, was implemented in the Multiple Component computational shock physics hydrocode. The capability is a Lagrangian/Eulerian Particle Method (LEPM) that uses particles to interface a Lagrangian treatment of material strength with a more traditional Eulerian treatment of the Equation of State (EOS). Lagrangian numerical methods avoid the advection diffusion found in Eulerian methods, which typically strongly affects strength constitutive law internal variables, such as equivalent plastic strain, porosity and/or damage. The Lagrangian capability enhances existing capabilities and permits accurate predictions of high rate, large deformation and/or shock of mechanical structures.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Reproducibility and Replication of Experimental Particle Physics Results

Recently, much attention has been focused on the replicability of scientific results, causing scientists, statisticians, and journal editors to examine closely their methodologies and publishing criteria. Experimental particle physicists have been aware of the precursors of non-replicable research for many decades and have many safeguards to ensure that the published results are as reliable as possible. The experiments require large investments of time and effort to design, construct, and operate. Large collaborations produce and check the results, and many papers are signed by more than three thousand authors. This paper gives an introduction to what experimental particle physics is and to some of the tools that are used to analyze the data. It describes the procedures used to ensure that results can be computationally reproduced, both by collaborators and by non-collaborators. It describes the status of publicly available data sets and analysis tools that aid in reproduction and recasting of experimental results. It also describes methods particle physicists use to maximize the reliability of the results, which increases the probability that they can be replicated by other collaborations or even the same collaborations with more data and new personnel. Examples of results that were later found to be false are given, both with failed replication attempts and one with alarmingly successful replications. While some of the characteristics of particle physics experiments are unique, many of the procedures and techniques can be and are used in other fields.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Integrated Biophysical Modeling and Image Analysis: Application to Neuro-Oncology

Central nervous system (CNS) tumors come with vastly heterogeneous histologic, molecular, and radiographic landscapes, rendering their precise characterization challenging. The rapidly growing fields of biophysical modeling and radiomics have shown promise in better characterizing the molecular, spatial, and temporal heterogeneity of tumors. Integrative analysis of CNS tumors, including clinically acquired multi-parametric magnetic resonance imaging (mpMRI) and the inverse problem of calibrating biophysical models to mpMRI data, assists in identifying macroscopic quantifiable tumor patterns of invasion and proliferation, potentially leading to improved (a) detection/segmentation of tumor subregions and (b) computer-aided diagnostic/prognostic/predictive modeling. This article presents a summary of (a) biophysical growth modeling and simulation,(b) inverse problems for model calibration, (c) these models' integration with imaging workflows, and (d) their application to clinically relevant studies. We anticipate that such quantitative integrative analysis may even be beneficial in a future revision of the World Health Organization (WHO) classification for CNS tumors, ultimately improving patient survival prospects.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Taylor-Expansion-Based Robust Power Flow in Unbalanced Distribution Systems: A Hybrid Data-Aided Method

Traditional power flow methods often adopt certain assumptions designed for passive balanced distribution systems, thus lacking practicality for unbalanced operation. moreover, their computation accuracy and efficiency are heavily subject to unknown errors and bad data in measurements or prediction data of distributed energy resources (ders). to address these issues, this paper proposes a hybrid data-aided robust power flow algorithm in unbalanced distribution systems, which combines taylor series expansion knowledge with a data-driven regression technique. the proposed method initiates a linearization power flow model to derive an explicitly analytical solution by modified taylor expansion. to mitigate the approximation loss that surges due to the der integration and bad data, we further develop a data-aided robust support vector regression approach to estimate the errors efficiently. comparative analysis in the 13-bus and 123-bus ieee unbalanced feeders shows that the proposed hybrid algorithm achieves superior computational efficiency, with guaranteed accuracy and robustness against outliers.

data-driven↗

DOE OSTI2023

Exploration of Potential Superconducting Multi-Mode Cavity Architectures for Quantum Computing

This thesis describes the investigation of superconducting multi-mode cavity architecture for superconducting transmon-based quantum computing. The dissertation highlights useful features of radio-frequency cavities used for quantum computing, with a brief discussion on the advantages of superconducting cavities. In the subsequent section, the concept of transmon is introduced and the mechanism of coupling with a cavity is analyzed. Once the foundations of the topic are laid down, the thesis focuses on optimizing a multi-mode superconducting rf cavity design originally developed for high-energy physics applications. Such section articulates in two main parts, the first part concerning the "bare" cavity remake via finite-elements eigenmode simulations using a computer-aided design software called CST Studio Suite®. In the second part, a transmon qubit is physically inserted into the modified cavity to assess the qubit-cavity coupling of the new design. In evaluating said coupling, two distinct analysis methods are used, namely the black-box quantization method and the energy participation ratio method, both implemented using Ansys® High-Frequency Electromagnetic-Field Simulator, or HFSS™. Results from the two evaluations, compared together, show that the optimized design meets the requisites to be used for quantum computing purposes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Computational Risk Analysis of Propane Releases in Maintenance Facilities

Liquefied petroleum gas (LPG) is a viable, cleaner alternative to traditional diesel fuel used in busses and other heavy-duty vehicles and could play a role in helping the US meet its lower emission goals. While the LPG industry has focused efforts on developing vehicles and fueling infrastructure, we must also establish safe parameters for maintenance facilities which are servicing LPG fueled vehicles. Current safety standards aid in the design of maintenance facilities, but additional quantitative analysis is needed to prove safeguards are adequate and suggest improvements where needed. In this report we aim to quantify the amount of flammable mass associated with propane releases from vehicle mounted fuel vessels within enclosed garages. Furthermore, we seek to qualify harm mitigation with variable ventilations and facility layout. To accomplish this we leverage validated computational resources at Sandia National Laboratories to simulate various release scenarios representative of real world vehicles and maintenance facilities. Flow solvers are used to predict the dynamics of fuel systems as well as the evolution of propane during release events. From our simulated results we observe that both inflow and outflow ventilation locations play a critical role in reducing flammable cloud size and potential overpressure values during a possible combustion event.

03 NATURAL GAS↗

DOE OSTI2022

Operator Insights and Usability Evaluation of Machine Learning Assistance for Power Grid Contingency Analysis

Introducing machine learning (ML) assistance into any established process comes with adoption barriers, including entrenched procedures, technological and human readiness levels, human-machine trust, and work culture resistance to change. These barriers are even greater in critical operations such as operating a national or regional power grid, in which both regulatory frameworks and the importance of maintaining reliability levels causes additional resistance to the adoption of new computational support. Developers of future systems and job aides must consider not only technical aspects, but also whether new systems are usable by power system operators. This work presents the methodology and results of a study to evaluate the usability and readiness of a prototype recommender system for power grid contingency analysis. We explore operator cognitive load and evaluate operator performance when solving a collection of scenarios both with and without recommender assistance. We also examine operator trust in the system. We report insights gained on the readiness of the system using a collection of evaluation techniques.

Human-Machine Teaming, Power Systems, usability ev↗

DOE OSTI2021

Modeling Buried Object Brightness and Visibility for Ground Penetrating Radar

Comparing the observed brightness of various buried objects is a straightforward way to characterize the performance of a ground penetrating radar (GPR) system. However, a limitation arises. A simple comparison of buried object brightness values does not disentangle the effects of the GPR system itself from the system's operating environment and the objects being observed. Therefore, with brightness values exhibiting an unknown synthesis of systemic, environmental, and object factors, GPR system analysis becomes a convoluted affair. In this work, we use an experimentally collected dataset of over 25,000 object observations from five different multistatic radar arrays to develop models of buried object brightness and control for these various effects. Additionally, our modeling efforts provide a means for quantifying the relative brightness of GPR systems, the objects they detect, and the physical properties of those objects that influence observed brightness. To evaluate the models' performance on new object observations, we repeatedly simulate fitting them to half the dataset and predicting the observed brightness values of the unseen half. In addition, we introduce a method for estimating the probability that individual observations constitute a visible object, which aids in failure analysis, performance characterization, and dataset cleaning.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

A machine-learning-aided data recovery approach for predicting multi-material thermal behaviors in advanced test reactor capsules

Instrumented experiments conducted at test reactors are essential to the deployment of new advanced reactor systems. Designing new experiments and generating data on specific reactor conditions require significant investments in terms of both time and cost. Finite element analysis software can be used to create high-fidelity models of experiment environments in order to support the actual experiments, but computation time remains a concern in terms of applying outcomes to real-time usage of data (e.g., a digital twin [DT]). Here, the present research proposes a machine-learning (ML) aided approach to making temperature and displacement predictions based on the thickness of the outer gas gap on the experimental capsule used for in-pile demonstration of a novel new thermal conductivity probe in the Advanced Test Reactor (ATR). This capsule consisted of U10Zr fuel, a rodlet, sodium, and inner and outer capsules. Gas gaps existed between the fuel and the rodlet, and between the inner and the outer capsule. The learning data pertained to an experimental capsule's radial distributions of temperature and displacement, as obtained based on Abaqus and the physical features. For the first step of ML sequence, the temperature was predicted using three positional parameters. Next, the displacement was predicted using seven additional parameters. Each physical feature was normalized in order to be both nondimensional and standardized. The temperature and displacement predictions showed good agreement with the simulation results in all cases involving interpolation and extrapolation. Furthermore, data similarity enhancement increased the similarity between the training and the target data, thereby increasing the predictive accuracy of the ML models. In certain extrapolation cases involving limited original ML model accuracy, data similarity enhancement and data recovery was able to somewhat improve this accuracy.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2024

Stability optimization of energetic particle driven modes in nuclear fusion devices: the FAR3d gyro-fluid code

The development of reduced models provide efficient methods that can be used to perform short term experimental data analysis or narrow down the parametric range of more sophisticated numerical approaches. Reduced models are derived by simplifying the physics description with the goal of retaining only the essential ingredients required to reproduce the phenomena under study. This is the role of the gyro-fluid code FAR3d, dedicated to analyze the linear and nonlinear stability of Alfvén Eigenmodes (AE), Energetic Particle Modes (EPM) and magnetic-hydrodynamic modes as pressure gradient driven mode (PGDM) and current driven modes (CDM) in nuclear fusion devices. Such analysis is valuable for improving the plasma heating efficiency and confinement; this can enhance the overall device performance. The present review is dedicated to a description of the most important contributions of the FAR3d code in the field of energetic particles (EP) and AE/EPM stability. FAR3d is used to model and characterize the AE/EPM activity measured in fusion devices as LHD, JET, DIII-D, EAST, TJ-II and Heliotron J. In addition, the computational efficiency of FAR3d facilitates performing massive parametric studies leading to the identification of optimization trends with respect to the AE/EPM stability. This can aid in identifying operational regimes where AE/EPM activity is avoided or minimized. This technique is applied to the analysis of optimized configurations with respect to the thermal plasma parameters, magnetic field configuration, external actuators and the effect of multiple EP populations. In addition, the AE/EPM saturation phase is analyzed, taking into account both steady-state phases and bursting activity observed in LHD and DIII-D devices. The nonlinear calculations provide: the induced EP transport, the generation of zonal structures as well as the energy transfer towards the thermal plasma and between different toroidal/helical families. Finally, FAR3d is used to forecast the AE/EPM stability in operational scenarios of future devices as ITER, CFETR, JT60SA and CFQS as well as possible approaches to optimization with respect to variations in the most important plasma parameters.

Alfv én Eigenmodes↗

DOE OSTI2021

A Hierarchical Feature-Based Methodology to Perform Cervical Cancer Classification

Prevention of cervical cancer could be performed using Pap smear image analysis. This test screens pre-neoplastic changes in the cervical epithelial cells; accurate screening can reduce deaths caused by the disease. Pap smear test analysis is exhaustive and repetitive work performed visually by a cytopathologist. This article proposes a workload-reducing algorithm for cervical cancer detection based on analysis of cell nuclei features within Pap smear images. We investigate eight traditional machine learning methods to perform a hierarchical classification. We propose a hierarchical classification methodology for computer-aided screening of cell lesions, which can recommend fields of view from the microscopy image based on the nuclei detection of cervical cells. We evaluate the performance of several algorithms against the Herlev and CRIC databases, using a varying number of classes during image classification. Results indicate that the hierarchical classification performed best when using Random Forest as the key classifier, particularly when compared with decision trees, k-NN, and the Ridge methods.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Watertight Tensor-Product Spline Reconstruction (KCNSC PDRD Technical Report)

The standard for representing geometric models in Computer Aided Design (CAD) systems is boundary representation with trimmed surfaces. However, the approximate nature of surface-surface intersections in CAD systems leaves many small gaps between mating surfaces. These gaps lead to problems for downstream analysis and manufacturing applications, requiring time consuming repair operations and further approximation of the geometry as polygonal meshes, which do not support design iteration. In this study, nVariate, Inc. evaluated its watertight reconstruction technology on a test part. The resulting watertight model has the same absolute model accuracy of the original model zero gaps, providing a representation that requires no repair and supports further design iterations in the CAD system.

42 ENGINEERING↗

DOE OSTI2025

Computational Analysis of the Energetic Stability of High-Entropy Structures of a Prototypical Lanthanide-Based Metal–Organic Framework

High-entropy materials are characterized by their complex compositions, typically comprising five or more elements in near-equiatomic proportions. Applying this concept to metal ions in metal−organic frameworks (MOFs) has paved the way for exploring a new class of high-entropy MOFs. While the compositional strategy of high-entropy materials leverages configurational entropy to aid thermodynamic stability, it also poses significant analytical challenges due to the vast compositional landscape and diverse phases that these materials can adopt. We present a computational study of several complexities associated with selecting potential high-entropy versions of a prototype lanthanidebased MOF. We compute the energetics of metal mixing of these heterometallic MOFs using density functional theory (DFT) and machine learning interatomic potential (MLIP) methods. The use of MLIP methods allows a systematic exploration of the convex hull of thermodynamically stable MOF structures containing up to 5 distinct metals.

Chemical structure↗