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DOE OSTI2023

Anticipating gelation and vitrification with medium amplitude parallel superposition (MAPS) rheology and artificial neural networks

Abstract Anticipating qualitative changes in the rheological response of complex fluids (e.g., a gelation or vitrification transition) is an important capability for processing operations that utilize such materials in real-world environments. One class of complex fluids that exhibits distinct rheological states are soft glassy materials such as colloidal gels and clay dispersions, which can be well characterized by the soft glassy rheology (SGR) model. We first solve the model equations for the time-dependent, weakly nonlinear response of the SGR model. With this analytical solution, we show that the weak nonlinearities measured via medium amplitude parallel superposition (MAPS) rheology can be used to anticipate the rheological aging transitions in the linear response of soft glassy materials. This is a rheological version of a technique called structural health monitoring used widely in civil and aerospace engineering. We design and train artificial neural networks (ANNs) that are capable of quickly inferring the parameters of the SGR model from the results of sequential MAPS experiments. The combination of these data-rich experiments and machine learning tools to provide a surrogate for computationally expensive viscoelastic constitutive equations allows for rapid experimental characterization of the rheological state of soft glassy materials. We apply this technique to an aging dispersion of Laponite ® clay particles approaching the gel point and demonstrate that a trained ANN can provide real-time detection of transitions in the nonlinear response well in advance of incipient changes in the linear viscoelastic response of the system.

Lennon, Kyle R. (ORCID:0000000212515461)↗

DOE OSTI2023

Benchmarking FFTF LOFWOS Test# 13 using SAM code: Baseline model development and uncertainty quantification

The development and deployment of advanced reactors, such as the sodium-cooled fast reactor (SFR), relies on sophisticated modeling tools to ensure the safety of the design under various transients. The predictive capability of these advanced modeling tools requires validation to garner trust in supporting the licensing of the advanced reactors. For this reason, the International Atomic Energy Agency (IAEA) initiated a coordinated research project (CRP) in 2018 for the analysis of the Fast Flux Test Facility (FFTF) Loss of Flow Without Scram (LOFWOS) Test #13.In this study, we present and discuss the benchmarking efforts of the modern system code SAM on the FFTF LOFWOS Test #13. Further, the SAM baseline model was developed according to the benchmark specification, which included a detailed core model with reactivity feedback. Generally, good agreement was observed between the baseline results and benchmark measurements; however, discrepancies persisted, particularly in predicted fuel assembly coolant outlet temperatures. Utilizing the baseline model, uncertainty quantification (UQ) and sensitivity analysis (SA) were conducted with the assistance of various statistical learning and machine learning methods, including kernel density estimation, Gaussian processes, and Sobol indices. Following the baseline model prediction and UQ and SA results, we discuss the reasons for the simulation discrepancies and propose further improvements to the model. This benchmarking effort adheres to the best-estimate plus uncertainty approach and can serve as a valuable example for supporting risk-informed licensing of advanced reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

TCF High Efficiency Anaerobic Electroporation (CRADA Final Report)

The Joint BioEnergy Institute (JBEI) researchers were co-inventors of the technology that will be used on this project and have developed a more current version of the chip and controller. JBEI will also assist with the design of the pathways and implementation of pathways on the chip. LanzaTech has developed novel gas fermentation technology that captures and utilizes greenhouse gases for production of fuels and chemicals. In contrast to traditional fermentation that uses sugars as substrate (and releases CO2 as a byproduct), gas fermentation utilizes C1 substrates carbon monoxide (CO) or CO2. This enables a diverse range of feedstock options including waste gases from industrial sources (e.g., steel mills and processing plants) or syngas generated from any biomass resource (e.g., agricultural waste, municipal solid waste, or organic industrial waste). Biomass is then gasified, allowing for maximum yields and complete carbon utilization including the recalcitrant lignocellulosic fraction that cannot be utilized in traditional sugar fermentation. To maximize the value that can be added to the array of gas resources that the LanzaTech process can use as an input, LanzaTech has pioneered genetic modification of acetogens and developed a comprehensive set of genetic tools to perform routine strain modification, including genome editing tools as CRISPR/Cas9 and libraries of validated genetic parts as promoters and terminators. Using this platform, production of over 50 new molecules have been demonstrated directly from gas. For a few selected molecules production rates and yields have been optimized and surpass production of native producers and engineered E. coli or yeast strains, but a higher throughput approach for combinatorial optimization of pathways is required to further advance synthesis of additional products in parallel.

09 BIOMASS FUELS↗

DOE OSTI2024

Interlaced Characterization and Calibration (ICC) for Improved Computational Simulation Credibility

Accurate material characterization and model calibration are pivotal for simulations used for high-consequence engineering decisions. Current characterization and calibration methods (1) use simplified test specimen geometries and global data, (2) cannot guarantee that sufficient characterization data is collected for a specific model of interest, (3) provide only mean parameter values with no uncertainty quantification, and (4) are sequential, inflexible, and time-consuming. This work developed a new paradigm—coined Interlaced Characterization and Calibration (ICC)—which drives forward the state-of-the-art in model calibration by bringing together recent advancements into one improved workflow. The ICC paradigm (1) employs tools to efficiently use full-field data to calibrate high-fidelity material models, (2) aligns the data needed with the data collected by adopting an optimal experimental design protocol, (3) provides uncertainty metrics on the calibrated model parameters, and (4) incorporates these advances into a quasi real-time feedback loop. The ICC framework was validated synthetically with both low-fidelity and high-fidelity simulations paired with several different elastoplastic material models, and was also demonstrated experimentally with an aluminum 6061 cruciform exemplar specimen. Results showed that the ICC framework—in which Bayesian optimal experimental design actively guided the experiment— resulted in calibrations with similar or better accuracy than predetermined experiments based on subject matter expertise. Moreover, the ICC framework produced a complete model calibration— with quantified uncertainties on model parameters—in 1 week, a 5 - 10× increase in efficiency over traditional approaches. Thus, the ICC paradigm improves both the calibration process and quality, by (1) improving efficiency, which increases agility of solid mechanics modeling and enables utilization of computational simulation (CompSim) at earlier stages of the design cycle and (2) providing quantified, and in some cases reduced, parameter uncertainties, which increases confidence in model predictions and supports credible decision making.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid

Agrobacterium is not only a costly plant pathogen but is also an essential tool for plant transformation. Though Agrobacterium-mediated transformation (AMT) has been heavily studied, its polygenic nature and complex transcriptional regulation make identification of the genetic basis of transformational efficiency difficult through traditional genetic and bioinformatic approaches. Here, we use a bottom-up synthetic approach to systematically engineer the tumor-inducing plasmid (pTi), wherein the majority of virulence machinery is encoded. Using a validated toolkit to control Agrobacterium gene expression in planta, we perform a quantitative dissection of AMT to investigate the contributions of critical vir-genes at different expression levels. We construct a synthetic pTi capable of transient plant and stable fungal transformation and characterize bottlenecks and solutions for complex polygenic synthetic pTi designs. Our reductionist approach demonstrates how bottom-up engineering can be used to dissect and elucidate the genetic underpinnings of complex biological traits, laying the foundation for future engineering to establish full synthetic control over the critical process of AMT.

Agrobacterium-mediated transformation↗

DOE OSTI2024

Extraction of Drell-Yan Angular Parameters in $pp$ Collisions with a 120 GeV Beam Energy Using a Deep-Learning Unfolding Algorithm

Dilepton production in pp collisions through the Drell-Yan process provides a crucial tool for studying the internal quark-gluon structure of the nucleon. By precisely measuring the $\cos2\phi$ asymmetry, where $\phi$ represents the azimuthal angle of the $l^{+}l^{-}$ pair in the Collins-Soper frame, we can gain valuable insights into the proton’s structure and the transverse momentum ($q_{T}$) dependence of the $\cos2\phi$ asymmetry. SeaQuest, a fixed-target Drell-Yan experiment at Fermilab, involved an unpolarized proton beam colliding with unpolarized LH$_{2}$ and LD$_{2}$ targets. Measurements obtained from experiments typically require corrections for detector ineﬀiciencies, smearing, and acceptance. Traditionally, these corrections involve “unfolding” the detector-level measurements through matrix operations. However, in higher-dimensional phase space, these conventional methods fail to scale effectively. To overcome these limitations, we employ an unbinned unfolding method that utilizes deep neural networks for unfolding higher-dimensional phase space. In this presentation, we will explain the design of the neural network architecture, our training strategies, and outline our plans to achieve conclusive results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2024

Automated Calibration for Rapid Optical Spectroscopy Sensor Development for Online Monitoring

An automated platform has been developed to assist researchers in the rapid development of optical spectroscopy sensors to quantify species from spectral data. This platform performs calibration and validation measurements simultaneously. Real-time, in situ monitoring of complex systems through optical spectroscopy has been shown to be a useful tool; however, building calibration models requires development time, which can be a limiting factor in the case of radiological or otherwise hazardous systems. While calibration time can be reduced through optimized design of experiments, this study approached the challenge differently through automation. The ATLAS (Automated Transient Learning for Applied Sensors) platform used pneumatic control of stock solutions to cycle flow profiles through desired calibration concentrations for multivariate model construction. Additionally, the transients between desired concentrations based on flow calculations were used as validation measurements to understand model predictive capabilities. This automated approach yielded an incredible 76% reduction in model development time and a 60% reduction in sample volume versus estimated manual sample preparation and static measurements. The ATLAS system was demonstrated on two systems: a three-lanthanide system with Pr/Nd/Ho representing a use case with significant overlap or interference between analyte signatures and an alternate system containing Pr/Nd/Ni to demonstrate a use case in which broad-band corrosion species signatures interfered with more distinct lanthanide absorbance profiles. Both systems resulted in strong model prediction performance (RMSEP < 9%). Lastly, ATLAS was demonstrated as a tool to simulate process monitoring scenarios (e.g., column separation) in which models can be further optimized to account for day-to-day changes as necessary (e.g., baseline correction). Ultimately, ATLAS offers a vital tool to rapidly screen monitoring methods, investigate sensor fusion, and explore more complex systems (i.e., larger numbers of species).

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

A Design for Remanufacturing Framework Incorporating Identification, Evaluation, and Validation: A Case Study of Hydraulic Manifold

In recent years, academic researchers and engineers in the industry have widely recognized the necessity of integrating remanufacturing considerations into product design iterations to advance sustainability objectives. Acknowledging the importance of design for remanufacturing (DfRem), efforts were made to develop tools and guidelines that could be implemented in practice. However, such methods largely rely upon experiential insights and qualitative assessments, leaving a gap in the ability to quantitatively assess the economic and environmental impacts of design choices. To bridge this gap, we investigate existing efforts and present a framework for DfRem that integrates established design and remanufacturing practices into a cohesive workflow with quantitative assessments. To demonstrate its efficacy for making practical design changes for remanufacturing, we apply the framework to a hydraulic manifold in a transmission system for heavy-duty tractors. Through this industry-relevant case study, we focus on showcasing the practical utility of our framework. Based on the identified design modifications from remanufacturability analysis, we estimate the reductions in life cycle costs, energy consumption, and emissions. Afterward, the modifications are tested using physical experiments with plans for integration into future iterations of the hydraulic manifold design and production. Here, we anticipate this framework can illustrate the process of remanufacturing that ensures improvements in sustainability while maintaining performance and reliability standards.

design for X↗

DOE OSTI2024

hypredrive: high-level interface for solving linear systems with hypre

This software introduces a high-level interface designed to simplify solving linear systems using hypre, a renowned library for such computational challenges. It is crafted to be accessible and user-friendly, making the powerful capabilities of hypre available to a broader audience without requiring in-depth technical knowledge. The interface is characterized by its use of YAML for input, a format celebrated for its structured yet straightforward readability. This choice ensures that users can easily configure the software to meet their specific needs. Additionally, the software boasts an intuitive API that encapsulates hypre's functionalities, making it easier for users to interact with the process of solving linear systems. It is particularly beneficial for prototyping, offering a quick and efficient means to test various solver and preconditioner configurations. Furthermore, the software allows for the creation of an offline testing framework in which predefined linear systems are read from files and benchmarked with user-defined solution strategies. This makes it an invaluable tool for developers and researchers exploring and validating their computational models. Overall, the software serves as a bridge, bringing the advanced computational capabilities of hypre closer to users who may need more specialized technical expertise, thereby facilitating innovation and exploration in the field of numerical linear algebra.

Paludetto Magri, Victor↗

DOE OSTI2023

Design and requirements of a hydrogen component reliability database (HyCReD)

Hydrogen technologies are expected to play a key role in the decarbonization of several sectors including energy storage and transportation. Rigorous investigation and quantification of the risk and reliability issues associated with hydrogen technologies will be critical to ensuring both their wider adoption and safe, economical operations. Quantitative risk assessment (QRA) is an important tool that has been used to enable the safe deployment of many engineering systems, including hydrogen fueling stations and hydrogen storage systems. However, QRA studies require reliability data which is currently lacking for expanding applications of hydrogen systems. Here, to address this gap, we present a new structure for a hydrogen component reliability database (HyCReD) that can be used to generate reliability data to be used in QRA, reliability, safety studies, maintenance planning, and more. Building on our previous work examining four major hydrogen safety data collection tools (West et al., 2022) [1], our approach in this work was to consult scientific literature on reliability data collection as well as a number of existing reliability engineering databases in the oil & gas, chemical processing, and nuclear power plant sectors. The evaluation of these databases led to identifying best practices to be implemented in a data collection framework for a hydrogen component reliability database. Based on these best practices, a set of 24 requirements for the proposed database are presented, covering its characteristics and the types of data to be collected. We define the structure of the HyCReD database and 25 data elements to be collected, spanning system description, failure, shutdown, or near-miss events, and maintenance events. The data elements are then defined according to international standards used in the safety and reliability practice and potential choice lists are provided for each field. Since this database is being piloted for hydrogen fueling stations, a generic station component hierarchy developed by West (2021) [2] is used to standardize system data. Finally, we demonstrate populating the database with information extracted from five narrative reports on hydrogen fueling station incidents.

08 HYDROGEN↗

DOE OSTI2023

Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering

Abstract CRISPR-Cas9 tools have transformed genetic manipulation capabilities in the laboratory. Empirical rules-of-thumb have been developed for only a narrow range of model organisms, and mechanistic underpinnings for sgRNA efficiency remain poorly understood. This work establishes a novel feature set and new public resource, produced with quantum chemical tensors, for interpreting and predicting sgRNA efficiency. Feature engineering for sgRNA efficiency is performed using an explainable-artificial intelligence model: iterative Random Forest (iRF). By encoding quantitative attributes of position-specific sequences for Escherichia coli sgRNAs, we identify important traits for sgRNA design in bacterial species. Additionally, we show that expanding positional encoding to quantum descriptors of base-pair, dimer, trimer, and tetramer sequences captures intricate interactions in local and neighboring nucleotides of the target DNA. These features highlight variation in CRISPR-Cas9 sgRNA dynamics between E. coli and H. sapiens genomes. These novel encodings of sgRNAs enhance our understanding of the elaborate quantum biological processes involved in CRISPR-Cas9 machinery.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

2020 LANL Contributions to the BATS Test in WIPP

The DOE Office of Nuclear Energy (DOE-NE) repository research and development program seeks to provide a sound technical basis for multiple viable disposal options, increase confidence in the robustness of generic disposal concepts, and develop science and engineering tools needed to support disposal concept implementation. Sandia, Los Alamos, and Lawrence Berkeley National labs are conducting research into salt, which includes the Brine Availability Test in Salt (BATS) field test at the Waste Isolation Pilot Plant (WIPP), a DOE Office of Environmental Management facility. BATS is leveraging the existing infrastructure associated with the WIPP to advance science informing generic disposal concepts. BATS is an ongoing heated borehole experiment being conducted in the WIPP underground. The goal of this experiment is to reduce the uncertainty associated with spent nuclear fuel disposition in geologic salt formations. The BATS experiments is designed to accomplish this by increasing our understanding of brine migration in salt, assessing damaged zones from mining and drilling, simulating a post-closure environment, confirming salt properties, and providing data for model validation. Phased testing for generic salt repository R&D was proposed in 2015. Subsequently, borehole thermal testing was developed as a first step in this process. This document summarizes the work conducted on the BATS experiment during fiscal year 2020 with an emphasis on the contributions by Los Alamos National Lab.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2024

Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering

Enzymes can be engineered at the level of their amino acid sequences to optimize key properties such as expression, stability, substrate range, and catalytic efficiency or even to unlock new catalytic activities not found in nature. Because the search space of possible proteins is vast, enzyme engineering usually involves discovering an enzyme starting point that has some level of the desired activity followed by directed evolution to improve its “fitness” for a desired application. Recently, machine learning (ML) has emerged as a powerful tool to complement this empirical process. ML models can contribute to (1) starting point discovery by functional annotation of known protein sequences or generating novel protein sequences with desired functions and (2) navigating protein fitness landscapes for fitness optimization by learning mappings between protein sequences and their associated fitness values. In this Outlook, we explain how ML complements enzyme engineering and discuss its future potential to unlock improved engineering outcomes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Induced Chirality in QDs Using Thermoresponsive Elastin-like Polypeptides

Circular dichroism (CD) spectroscopy has emerged as a potent tool for probing chiral small-molecule ligand exchange on natively achiral quantum dots (QDs). In this study, we report a novel approach to identifying QD–biomolecule interactions by inducing chirality in CdS QDs using thermoresponsive elastin-like polypeptides (ELPs) engineered with C-terminal cysteine residues. Our method is based on a versatile two-step ligand exchange process starting from monodisperse oleate-capped QDs in nonpolar media and proceeding through an easily accessed achiral glycine-capped QD intermediate. Successful conjugation of the ELPs onto the QDs is confirmed by the diagnostic CD response corresponding to the QD electronic transitions in the visible range. The resulting ELP:CdS conjugates demonstrate thermally reversible coacervation, as observed through dynamic light scattering, small-angle X-ray scattering, and electron microscopy. Furthermore, this research provides a foundation for using induced chirality in QD electronic transitions to probe QD conjugation to complex peptides and proteins, opening pathways for designing dynamic, stimuli-responsive hybrid nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Mitigating drought mortality by incorporating topography into variable forest thinning strategies

Abstract Drought-induced productivity reductions and tree mortality have been increasing in recent decades in forests around the globe. Developing adaptation strategies hinges on an adequate understanding of the mechanisms governing the drought vulnerability of forest stands. Prescribed reduction in stand density has been used as a management tool to reduce water stress and wildfire risk, but the processes that modulate fine-scale variations in plant water supply and water demand are largely missing in ecosystem models. We used an ecohydrological model that couples plant hydraulics with groundwater hydrology to examine how within-stand variations in tree spatial arrangements and topography might mitigate forest vulnerability to drought at individual-tree and stand scales. Our results demonstrated thinning generally ameliorated plant hydraulic stress and improved carbon and water fluxes of the remaining trees, although the effectiveness varied by climate and topography. Variable thinning that adjusted thinning intensity based on topography-mediated water availability achieved higher stand productivity and lower mortality risk, compared to evenly-spaced thinning at comparable intensities. The results from numerical experiments provided mechanistic evidence that topography mediates the effectiveness of thinning and highlighted the need for an explicit consideration of within-stand heterogeneity in trees and abiotic environments when designing forest thinning to mitigate drought impacts.

Environmental Sciences & Ecology↗

DOE OSTI2021

BETO 2021 Peer Review - FCIC Task 6: High Temperature Conversion

The impacts of feedstock variability on pyrolysis processes are significant but poorly defined. Current engineering designs are based on empirical guidelines, useful only over a narrow range of feedstock properties. The objectives of this project are to (1) Develop science-based knowledge of how feedstock attributes and operational parameters impact pyrolysis process reliability and product quality; and (2) Build an experimental and computational toolset that predicts these outcomes, enabling processes to optimize reliability and product quality. Biomass is a complex feedstock. Controlling for and testing the effects of individual attributes is very challenging. This project couples multiscale experimentation and modeling to accurately capture the fundamental physics and chemistry of biomass flow and conversion behavior in feeding and pyrolysis reactor operations. Our focus is on pine residue attributes – anatomical fraction (bark, needles, wood), particle morphology (size/shape distribution, density, porosity), and chemical composition (extractives, biopolymers, alkali metals) – that impact product quality for downstream catalytic upgrading. Because detailed pyrolysis product characterization is limited, cutting-edge analytical techniques are being developed to reveal impactful product attributes. The tools and knowledge developed here will enable integrated pyrolysis-based processes that are more robust, flexible, and market-responsive with respect to feedstock variability.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2024

Challenges in the Use of AI-Driven Non-Destructive Spectroscopic Tools for Rapid Food Analysis

Routine, remote, and process analysis for foodstuffs is gaining attention and can provide more confidence for the food supply chain. A new generation of rapid methods is emerging both in the literature and in industry based on spectroscopy coupled with AI-driven modelling methods. Current published studies using these advanced methods are plagued by weaknesses, including sample size, abuse of advanced modelling techniques, and the process of validation for both the acquisition method and modelling. This paper aims to give a comprehensive overview of the analytical challenges faced in research and industrial settings where screening analysis is performed while providing practical solutions in the form of guidelines for a range of scenarios. After extended literature analysis, we conclude that there is no easy way to enhance the accuracy of the methods by using state-of-the-art modelling methods and the key remains that capturing good quality raw data from authentic samples in sufficient volume is very important along with robust validation. A comprehensive methodology involving suitable analytical techniques and interpretive modelling methods needs to be considered under a tailored experimental design whenever conducting rapid food analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Bottom-up design of actinide materials from molecular clusters: Demonstration of a general-purpose simulation capability leveraging machine-learned atomic potentials

Actinide thin-film coatings such as uranium dioxide (UO 2 ) play an important role in nuclear reactors and other mission-relevant applications, but realization of their potential requires a deep fundamental understanding of the chemical vapor deposition (CVD) processes used for their growth. The slow experimental progress can be attributed, in part, to the standard safety guidelines associated with handling uranium byproducts, which are often corrosive, toxic, and radioactive. Accurate simulation techniques, when used in concert with experiment, can improve laboratory safety, material durability, and deliverable timeframes. However, state-of-the-art computational methods are either insufficiently accurate or intractably expensive. To remedy this situation, in this project we suggested a machine-learning (ML) accelerated workflow for simulating molecular clustering toward deposition. As a benchmark test case, we considered molecular clustering in steam and assessed independent components of our workflow by comparing with measured thermodynamic properties of water. After analyzing each component individually and finding no fundamental barrier to realization of the workflow, we attempted to integrate the ML component, a Sandia-developed tool called FitSNAP. As this was the first application of FitSNAP to atoms and molecules in the gas phase at Sandia, the method required more fitting data than was originally anticipated. Systematic improvements were made by including in the fit data diatomic potentials, molecular single-bond-breaking curves, and symmetry-constrained intermolecular potentials. We concluded that our strategy provides a feasible pathway toward modeling CVD and related processes, but that extensive training data must be generated before it can be of practical use.

36 MATERIALS SCIENCE↗