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DOE OSTI2023

Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining

Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Rapid discovery and evolution of nanosensors containing fluorogenic amino acids

Binding-activated optical sensors are powerful tools for imaging, diagnostics, and biomolecular sensing. However, biosensor discovery is slow and requires tedious steps in rational design, screening, and characterization. Here we report on a platform that streamlines biosensor discovery and unlocks directed nanosensor evolution through genetically encodable fluorogenic amino acids (FgAAs). Building on the classical knowledge-based semisynthetic approach, we engineer ~15 kDa nanosensors that recognize specific proteins, peptides, and small molecules with up to 100-fold fluorescence increases and subsecond kinetics, allowing real-time and wash-free target sensing and live-cell bioimaging. An optimized genetic code expansion chemistry with FgAAs further enables rapid (~3 h) ribosomal nanosensor discovery via the cell-free translation of hundreds of candidates in parallel and directed nanosensor evolution with improved variant-specific sensitivities (up to ~250-fold) for SARS-CoV-2 antigens. Altogether, this platform could accelerate the discovery of fluorogenic nanosensors and pave the way to modify proteins with other non-standard functionalities for diverse applications.

Biosensors↗

DOE OSTI2021

Precipitation of dopants on acceptor-doped LaMnO3±δ revealed by defect chemistry from first principles

Perovskite oxides degrade at elevated temperatures while precipitating dopant-rich particles on the surface. A knowledge-based improvement of surface stability requires a fundamental and quantitative understanding of the dopant precipitation mechanism on these materials. We propose that dopant precipitation is a consequence of the variation of dopant solubility between calcination and operating conditions in solid oxide fuel cells (SOFCs) and electrolyzer cells (SOECs). To study dopant precipitation, we use 20% (D = Ca, Sr, Ba)-doped LaMnO3+δ (LDM20) as a model system. We employ a defect model taking input from density functional theory calculations. The defect model considers the equilibration of LDM20 with a reservoir consisting of dopant oxide (DO), peroxide (DO2), and O2 in the gas phase. The equilibrated non-stoichiometry of the A-site and B-site as a function of temperature, T, and oxygen partial pressure, p(O2), reveals three regimes for LDM20: A-site deficient (oxidizing conditions), A-site rich (atmospheric conditions), and near-stoichiometric (reducing conditions). Assuming an initial A/B non-stoichiometry, we compute the dopant precipitation boundaries in a p–T phase diagram. Our model predicts precipitation both under reducing (DO) and under highly oxidizing conditions (DO2). We found precipitation under anodic, SOEC conditions to be promoted by large dopant size, while under cathodic, SOFC conditions precipitation is promoted by initial A-site excess. The main driving forces for precipitation are oxygen uptake by the condensed phase under oxidizing conditions and oxygen release assisted by B-site vacancies under reducing conditions. Possible strategies for mitigating dopant precipitation under in electrolytic and fuel cell conditions are discussed.

Hess, Franziska (ORCID:000000024460643X)↗

DOE OSTI2023

Machine learning guided optimal composition selection of niobium alloys for high temperature applications

Nickel- and cobalt-based superalloys are commonly used as turbine materials for high-temperature applications. However, their maximum operating temperature is limited to about 1100 °C. Therefore, to improve turbine efficiency, current research is focused on designing materials that can withstand higher temperatures. Niobium-based alloys can be considered as promising candidates because of their exceptional properties at elevated temperatures. The conventional approach to alloy design relies on phase diagrams and structure–property data of limited alloys and extrapolates this information into unexplored compositional space. In this work, we harness machine learning and provide an efficient design strategy for finding promising niobium-based alloy compositions with high yield and ultimate tensile strength. Unlike standard composition-based features, we use domain knowledge-based custom features and achieve higher prediction accuracy. We apply Bayesian optimization to screen out novel Nb-based quaternary and quinary alloy compositions and find these compositions have superior predicted strength over a range of temperatures. We develop a detailed design flow and include Python programming code, which could be helpful for accelerating alloy design in a limited alloy data regime.

Mohanty, Trupti (ORCID:0000000342701430)↗

DOE OSTI2024

Designing workflows for materials characterization

Experimental science is enabled by the combination of synthesis, imaging, and functional characterization organized into evolving discovery loop. Synthesis of new material is typically followed by a set of characterization steps aiming to provide feedback for optimization or discover fundamental mechanisms. However, the sequence of synthesis and characterization methods and their interpretation, or research workflow, has traditionally been driven by human intuition and is highly domain specific. Here, we explore concepts of scientific workflows that emerge at the interface between theory, characterization, and imaging. In this study, we discuss the criteria by which these workflows can be constructed for special cases of multiresolution structural imaging and functional characterization, as a part of more general material synthesis workflows. Some considerations for theory–experiment workflows are provided. We further pose that the emergence of user facilities and cloud labs disrupts the classical progression from ideation, orchestration, and execution stages of workflow development. To accelerate this transition, we propose the framework for workflow design, including universal hyperlanguages describing laboratory operation, ontological domain matching, reward functions and their integration between domains, and policy development for workflow optimization. These tools will enable knowledge-based workflow optimization; enable lateral instrumental networks, sequential and parallel orchestration of characterization between dissimilar facilities; and empower distributed research.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Summary report of the 4th IAEA Technical Meeting on Fusion Data Processing, Validation and Analysis (FDPVA)

The objective of the Fourth Technical Meeting on Fusion Data Processing, Validation and Analysis was to provide a platform during which a set of topics relevant to fusion data processing, validation and analysis are discussed with the view of extrapolating needs to next step fusion devices such as ITER. The validation and analysis of experimental data obtained from diagnostics used to characterize fusion plasmas are crucial for a knowledge-based understanding of the physical processes governing the dynamics of these plasmas. This paper presents the recent progress and achievements in the domain of plasma diagnostics and synthetic diagnostics data analysis (including image processing, regression analysis, inverse problems, deep learning, machine learning, big data and physics-based models for control) reported at the meeting. The progress in these areas highlight trends observed in current major fusion confinement devices. A special focus is dedicated on data analysis requirements for ITER and DEMO with a particular attention paid to artificial intelligence for automatization and improving reliability of control processes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Summary of the 5th IAEA technical meeting on fusion data processing, validation and analysis (FDPVA)

The purpose of the 5th International Atomic Energy Agency technical meeting on fusion data processing, validation and analysis (FDPVA) (Ghent University, Ghent, Belgium, 12–15 June 2023) was to provide a platform during which a set of topics relevant to FDPVA were discussed with the view of meeting the needs of next step fusion devices such as ITER. The validation and analysis of experimental data obtained from diagnostics used to characterize fusion plasmas are crucial for a knowledge-based understanding of the physical processes governing the dynamics of these plasmas. This paper presents the recent progress and achievements in the domain of plasma diagnostics data analysis and synthetic diagnostics reported at the meeting, including concept description of new devices; fusion databases; integrated data analysis; inverse problems; uncertainty propagation, verification and validation; probabilistic methods and machine learning. The relevant results underline trends observed in the current major fusion confinement devices.

fusion databases↗

DOE OSTI2024

Evaluating the impact of peat soils and snow schemes on simulated active layer thickness at pan-Arctic permafrost sites

Abstract Permafrost stability is significantly influenced by the thermal buffering effects of snow and active-layer peat soils. In the warm season, peat soils act as a barrier to downward heat transfer mainly due to their low thermal conductivity. In the cold season, the snowpack serves as a thermal insulator, retarding the release of heat from the soil to the atmosphere. Currently, many global land models overestimate permafrost soil temperature and active layer thickness (ALT), partially due to inaccurate representations of soil organic matter (SOM) density profiles and snow thermal insulation. In this study, we evaluated the impacts of SOM and snow schemes on ALT simulations at pan-Arctic permafrost sites using the Energy Exascale Earth System Model (E3SM) land model (ELM). We conducted simulations at the Circumpolar Active Layer Monitoring (CALM) sites across the pan-Arctic domain. We improved ELM-simulated site-level ALT using a knowledge-based hierarchical optimization procedure and examined the effects of precipitation-phase partitioning methods (PPMs), snow compaction schemes, and snow thermal conductivity schemes on simulated snow depth, soil temperature, ALT, and CO 2 fluxes. Results showed that the optimized ELM significantly improved agreement with observed ALT (e.g. RMSE decreased from 0.83 m to 0.15 m). Our sensitivity analysis revealed that snow-related schemes significantly impact simulated snow thermal insulation levels, soil temperature, and ALT. For example, one of the commonly used snow thermal conductivity schemes (quadratic Sturm or SturmQua) generally produced warmer soil temperatures and larger ALT compared to the other two tested schemes. The SturmQua scheme also amplified the model’s sensitivity to PPMs and predicted deeper ALTs than the other two snow schemes under both current and future climates. The study highlights the importance of accurately representing snow-related processes and peat soils in land models to enhance permafrost dynamics simulations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Quantum Computing for AI-based Design and Optimization of Electric Motors

Knowledge-based artificial intelligence and hierarchical fuzzy logic offer an interpretable framework for electricvehicle motor preliminary design, but their computational burden grows with linguistic granularity and coupled design-space size. This paper presents a reduced quantum reformulation of the hierarchical fuzzy inference of air-gap flux density, a representative level-one motor-design parameter. Starting from the published electric-vehicle motor-design framework, a three-term fuzzy prototype is constructed from the original inference structure. The reduced model is then reformulated as a modular quantum register-oracle system, in which each hierarchical subrelation is encoded as a block oracle and evaluated through superpositionbased candidate-label testing. The proposed modular quantum formulation reproduces the reduced classical prototype after block fusion. A resource analysis shows that the reduced modular system requires seven qubits per block and twenty-two qubits in a straightforward four-block implementation. Finally, a crossovercomplexity model is derived to identify the regime in which quantum candidate search may become favorable relative to hierarchical fuzzy inference. The results show that no quantum advantage should be claimed for the present one-output reduced benchmark, but that a plausible crossover emerges for larger joint candidate spaces and higher linguistic granularity. The work therefore establishes a technically consistent starting point for future quantum-assisted electric-vehicle motor-design optimization.

Kumar, Praveen [ORNL] (ORCID:0000000291877857)↗

DOE OSTI2024

Physics-Guided, Physics-Informed, and Physics-Encoded Neural Networks and Operators in Scientific Computing: Fluid and Solid Mechanics

Abstract Advancements in computing power have recently made it possible to utilize machine learning and deep learning to push scientific computing forward in a range of disciplines, such as fluid mechanics, solid mechanics, materials science, etc. The incorporation of neural networks is particularly crucial in this hybridization process. Due to their intrinsic architecture, conventional neural networks cannot be successfully trained and scoped when data are sparse, which is the case in many scientific and engineering domains. Nonetheless, neural networks provide a solid foundation to respect physics-driven or knowledge-based constraints during training. Generally speaking, there are three distinct neural network frameworks to enforce the underlying physics: (i) physics-guided neural networks (PgNNs), (ii) physics-informed neural networks (PiNNs), and (iii) physics-encoded neural networks (PeNNs). These methods provide distinct advantages for accelerating the numerical modeling of complex multiscale multiphysics phenomena. In addition, the recent developments in neural operators (NOs) add another dimension to these new simulation paradigms, especially when the real-time prediction of complex multiphysics systems is required. All these models also come with their own unique drawbacks and limitations that call for further fundamental research. This study aims to present a review of the four neural network frameworks (i.e., PgNNs, PiNNs, PeNNs, and NOs) used in scientific computing research. The state-of-the-art architectures and their applications are reviewed, limitations are discussed, and future research opportunities are presented in terms of improving algorithms, considering causalities, expanding applications, and coupling scientific and deep learning solvers.

Computer Science↗

DOE OSTI2025

Atomic layer deposition of nanofilms on porous polymer substrates: Strategies for success

Atomic layer deposition (ALD) is a versatile technique for engineering the surfaces of porous polymers, imbuing the flexible, high-surface-area substrates with inorganic and hybrid material properties. Previously reported enhancements include fouling resistance, electrical conductance, thermal stability, photocatalytic activity, hydrophilicity, and oleophilicity. However, there are many poorly understood phenomena that introduce challenges in applying ALD to porous polymers. In this paper, we address five common challenges and ways to overcome them: (1) entrapped precursor, (2) embrittlement, (3) film fracture, (4) deformation, and (5) pore collapse. These challenges are often interrelated and can exacerbate one another. To investigate these phenomena, we applied various ALD chemistries to porous polymers including polyethersulfone, polysulfone, polyvinylidene fluoride, and polycarbonate track-etched membranes. Reaction-diffusion modeling revealed why certain precursors and processing conditions result in embrittling subsurface material growth, entrapment of unreacted precursors, and nongrowth. We quantify the limits of ALD processing temperatures that are dictated by thermal expansion mismatch and can lead to fractured ALD films. The results herein allow us to make recommendations to avoid, mitigate, or overcome the difficulties encountered when performing ALD and plasma-enhanced ALD on porous polymers. We intend this article to serve as a “lessons learned” guide informed by previous experience to provide a better understanding of the difficulties and limitations of ALD on porous polymers and knowledge-based guidelines for successful depositions. This knowledge can accelerate future research and help experimentalists navigate and troubleshoot as they expose porous polymers to reactive precursor vapors.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Artificial Reasoning System for Symptom-Based Conditional Failure Probability Estimation Using Bayesian Network

Advances in nuclear power technologies require enhanced capabilities for operator advice and autonomous control. One of the first tasks in the development of such capabilities is the formulation of symptom-based conditional failure probabilities for structures, systems, and components (SSCs) of interest, for which the primary goal is to aid plant personnel in deducing the probabilistic performance status of the monitored SSCs and in detecting impending faults/failure. The task of conditional failure probability estimation is a bidirectional inference problem and shall be logically tackled by the Bayesian network (BN) approach. As a knowledge-based artificial intelligence tool and a probabilistic graphical model, BN offers the capability of reasoning under uncertainty and graphical representation emulating the physical behavior of the target SSC. This paper provides a systematic overview of the BN technique and the software tools for handling implementation of BN models, along with the associated knowledge representation and reasoning paradigm. Both operational data and expert judgement can be readily incorporated into the knowledge base of a BN model. The challenges with data availability are highlighted, and the general approach to target SSC identification is presented. Our focus is upon failure-prone and risk-important balance of plant assets, especially cases having strong operator involvement. An exemplary case study on the failure of a motor-driven centrifugal pump is also conducted to demonstrate the usefulness and technical feasibility of the proposed artificial reasoning system using an expert system shell.

Zhao, Xingang↗

DOE OSTI2021

Software-defined Networking for Energy Delivery Systems (SDN4EDS): An Architectural Blueprint (Final Report)

This is the initial version of a reference for suppliers and energy companies of all sizes to deploy networks based on software-defined networking technology (SDN) to improve reliability, reduce cyber security attack surface, and facilitate mitigation of adversarial behavior. It is a living document and will progress over the life cycle of the Software-Defined Networking for Energy Delivery Systems (SDN4EDS) project. Version 2 of this report provides information on the Red Team tabletop assessment performed against the initial reference architecture. Version 3 of this report updates the reference architecture with lessons learned from the Red Team tabletop assessment, as well as provides additional details for the use cases. It also provides information on the decision process that could be used by an organization when considering deploying SDN in their environment. The final version of this report consolidates all the interim reports generated by the project into a final report. It also draws from PNNL’s experience in deploying SDN to make recommendations on how SDN could be deployed in a utility environment, and provides rationale for those decisions allowing individual utilities to make risk-based and knowledge-based decisions on how to best deploy SDN in their own environment

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Software-defined Networking for Energy Delivery Systems (SDN4EDS): An Architectural Blueprint (Final Summary Report)

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

LANL Fuel Cell Program [Slides]

Fuel Cell R&D programs are the longest running non-weapons programs at LANL, running since 1977. The current DOE HFTO program grew out of the Los Alamos program. It is primarily polymer electrolyte membrame (PEM) technology. The cost and durability are the biggest barriers to commercialization. The program focus is on obtaining fundamental understanding to enable "knowledge-based innovation," and subsequent materials and process development.

08 HYDROGEN↗

DOE OSTI2025

A Comparison of GPU-Accelerated Multiphase CFD Solvers on the Polaris Supercomputer: Part 1

This report is in support of the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program sponsored by the U.S. Department of Energy (USDOE). With INCITE-level resources, one project, titled BubblyFlow, was granted computational resources for the 2025 calendar year on the Polaris supercomputer at the Argonne Leadership Computing Facility (ALCF). The project aims to conduct simulations to understand the fundamental characteristics of turbulent bubbly flow phenomena in nature. Staff at the ALCF and Argonne’s Computational Science division, along with collaborators at the City College of New York and University of Illinois at Chicago, helped a summer student to assess the accuracy and performance of two high performance computing (HPC) codes. Both codes, ImExLBM and FluTAS, are fundamentally different in their mathematical and numerical modeling. However, both may be used to solve the same physical problem. The collaboration sought to better understand the differences between both codes in terms of accuracy and efficiency. This would ultimately help the BubblyFlow project better utilize resources and establish a knowledge-base of code capabilities in future simulation campaigns. We compare ImExLBM and FluTAS, two high-performance multiphase computational fluid dynamics (CFD) solvers, in terms of physical fidelity, time-to-solution, and parallel efficiency. We validate ImExLBM (Implicit-Explicit Lattice Boltzmann Method) against a canonical benchmark and assess it’s performance relative to FluTAS (Fluid Transport Accelerated Solver), a well-established open-source CFD code.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Why Terminology Matters for Successful Rollout of Carbon Dioxide Utilization Technologies

To realize their full sustainability potential, carbon dioxide utilization technologies (carbon capture and utilization/CCU) presently require policy support. Consequently, they require acceptance among a variety of stakeholders in industry, policy making, and in the public sphere alike. While CO 2 utilization is already a topic of discourse among these stakeholders, there is a lack of common terminology to describe such technologies. On the contrary: The present article shows that terminology in the field of CO 2 utilization technologies is currently used inconsistently, and that different designations such as CCU, CCUS, or CDR convey different meanings and contexts. These ambiguities may cause communication problems with regard to policy making, funding proposals, and especially in public discourse. In order to initiate and accompany a goal-oriented and knowledge-based debate on CO 2 utilization technologies in the future, actors in the field are asked to question their own choices of terminology and to assess its accuracy. Acronyms and technical abbreviations are the chief cause of potential misunderstandings, and so should be avoided whenever possible or else include a brief explanation. Consistent and precise use of terminology will facilitate transparent dialogue concerning CO 2 utilization in the future.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Physics-informed, empirically constrained machine learning for designing Fe-9Cr alloys

<span style="font-family: Calibri, sans-serif; font-size: 12pt;">Materials data analytics can be used to significantly shorten development time of specialized alloys needed for next generation energy applications. Incorporation of the domain knowledge into deep-learning graph structure via fuzzy pre-training and causal process imitation presents a viable approach to developing accurate data-driven models and reliable alloy design tools, with limited datasets. It was demonstrated that the domain knowledge-based empirical constraints not only inhibit overfitting but also allow training more accurate and reliable ML models with improved transparency of the output interpretation. In this study, alloy tensile properties were interpreted with three competing virtual-microstructure models.</span>

Romanov, Vyacheslav↗