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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Characterization of the Emissions and Crystalline Silica Content of Airborne Dust Generated from Grinding Natural and Engineered Stones

Abstract In this study, we systematically characterized the airborne dust generated from grinding engineered and natural stone products using a laboratory testing system designed and operated to collect representative respirable dust samples. Four stone samples tested included two engineered stones consisting of crystalline silica in a polyester resin matrix (formulations differed with Stones A having up to 90wt% crystalline silica and Stone B up to 50wt% crystalline silica), an engineered stone consisting of recycled glass in a cement matrix (Stone C), and a granite. Aerosol samples were collected by respirable dust samplers, total dust samplers, and a Micro-Orifice Uniform Deposit Impactor. Aerosol samples were analyzed by gravimetric analysis and x-ray diffraction to determine dust generation rates, crystalline silica generation rates, and crystalline silica content. Additionally, bulk dust settled on the floor of the testing system was analyzed for crystalline silica content. Real-time particle size distributions were measured using an Aerodynamic Particle Sizer. All stone types generated similar trimodal lognormal number-weighted particle size distributions during grinding with the most prominent mode at an aerodynamic diameter of about 2.0-2.3 μm, suggesting dust formation from grinding different stones is similar. Bulk dust from Stone C contained no crystalline silica. Bulk dust from Stone A, Stone B, and granite contained 60, 23, and 30wt% crystalline silica, respectively. In Stones A and B, the cristobalite form of crystalline silica was more plentiful than the quartz form. Only the quartz form was detected in granite. The bulk dust, respirable dust, and total dust for each stone had comparable amounts of crystalline silica, suggesting that crystalline silica content in the bulk dust could be representative of that in respirable dust generated during grinding. Granite generated more dust per unit volume of material removed than the engineered stones, which all had similar normalized dust generation rates. Stone A had the highest normalized generation rates of crystalline silica, followed by granite, Stone B, and Stone C (no crystalline silica), which likely leads to the same trend of respirable crystalline silica (RCS) exposure when working with these different stones. Manufacturing and adoption of engineered stone products with formulations such as Stone B or Stone C could potentially lower or eliminate RCS exposure risks. Combining all the effects of dust generation rate, size-dependent silica content, and respirable fraction, the highest normalized generation rate of RCS consistently occurs at 3.2-5.6 µm for all the stones containing crystalline silica. Therefore, removing particles in this size range near the generation sources should be prioritized when developing engineering control measures.

Public, Environmental & Occupational Health↗
DOE OSTI2023

nautilus : boosting Bayesian importance nested sampling with deep learning

ABSTRACT We introduce a novel approach to boost the efficiency of the importance nested sampling (INS) technique for Bayesian posterior and evidence estimation using deep learning. Unlike rejection-based sampling methods such as vanilla nested sampling (NS) or Markov chain Monte Carlo (MCMC) algorithms, importance sampling techniques can use all likelihood evaluations for posterior and evidence estimation. However, for efficient importance sampling, one needs proposal distributions that closely mimic the posterior distributions. We show how to combine INS with deep learning via neural network regression to accomplish this task. We also introduce nautilus, a reference open-source python implementation of this technique for Bayesian posterior and evidence estimation. We compare nautilus against popular NS and MCMC packages, including emcee, dynesty, ultranest, and pocomc, on a variety of challenging synthetic problems and real-world applications in exoplanet detection, galaxy SED fitting and cosmology. In all applications, the sampling efficiency of nautilus is substantially higher than that of all other samplers, often by more than an order of magnitude. Simultaneously, nautilus delivers highly accurate results and needs fewer likelihood evaluations than all other samplers tested. We also show that nautilus has good scaling with the dimensionality of the likelihood and is easily parallelizable to many CPUs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

EvoProtGrad (Directed Evolution for Proteins with Gradients) [SWR-23-48]

A Python package for directed evolution on a protein sequence with gradient-based discrete Markov chain monte carlo (MCMC). Users are able to compose custom models that map sequence to function with pretrained models, including protein language models (PLMs), to guide and constrain search. Our package natively integrates with the HuggingFace platform and supports PLMs from transformers. Our MCMC sampler identifies promising amino acids to mutate via model gradients taken with respect to the input (i.e., sensitivity analysis). We allow users to compose their own custom target function for MCMC by leveraging the Product of Experts MCMC paradigm. Each model is an "expert" that contributes its own knowledge about the protein's fitness landscape to the overall target function. The sampler is designed to be more efficient and effective than brute force and random search while maintaining most of the generality and flexibility. Additional information can be found in the related publication: https://iopscience.iop.org/article/10.1088/2632-2153/accacd

Emami, Patrick↗
DOE OSTI2023

Generalized Bayesian Framework for Evaluation of Integral Benchmark Experiments

A recently published generalized Bayesian optimization framework has provided a way to retract any or all of the three common assumptions underlying the conventional Generalized Linear Least Squares (GLLS) optimization method based on the concepts introduced in Ref. [2]. These assumptions are: 1. Perfection: The model used for data evaluation and the prior probability distribution function (PDF) of generalized data are perfect. 2. Normality: The prior and posterior PDF are normal. 3. Linearity: The model is linear. In this work we outline how the framework in [1] could be directly adopted for improved evaluation of nuclear criticality integral benchmark experiments (IBEs) by: 1. Removing the first assumption alone by utilizing the concept of imperfections introduced in [1] to enable evaluation in the presence of discrepancies between the data and model or of missing covariance information by a GLLS method that will be seen as a generalization of the conventional GLLS method employed by the TSURFER code, and by 2. Removing the remaining two assumptions by implementing a Markov Chain Monte Carlo method for computation of the posterior PDF in the SAMPLER code, where TSURFER and SAMPLER are the uncertainty quantification (UQ) codes for IBEs in the SCALE code system based on the GLLS and the stochastic method, respectively. The graphic in Figure 1 categorizes the methods discussed in terms of the assumptions that they employ to determine posterior PDFs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Automated Airborne Pathogen Monitoring for Agriculture (CRADA Final Report)

As part of the Cyclotron Road program, Root Applied Sciences investigated the use of DNA-based assays under field conditions to detect airborne plant pathogens in environmental samples. Robust DNA-based assays are critical for automated monitoring of plant pathogen concentrations in the air using Root’s air samplers. A fully automated air sampler coupled with DNA-based assays capable of operating under field conditions will accelerate the delivery of disease risk alerts based on airborne inoculum loads. Timely and accurate alerts of pathogen loads in the air can help growers manage airborne diseases more precisely, avoiding fungicide applications when there is no threat, and focusing cultural practices in the right areas. This project built upon other work done by Root to study the in-field performance of a liquid DNA-based assay for detection of grape powdery mildew. Growers working with Root’s airborne powdery mildew monitoring system have reported 20-80% reductions in pesticides.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Deployment of salt sample extraction system at an engineering-scale electrorefiner

The goal of the salt sampling program at Argonne is to develop and deploy automated molten salt sampling approaches for interfacing relevant unit operations with salt analysis to improve the timeliness of sampling-based accountancy measurements. Two technologies under development in support of this goal are a vacuum sampling loop module and a high-throughput pneumatic sample generator module. Compared to traditional point sampling approaches (i.e., dip probes), the vacuum sampling loop facilitates the collection of a larger cross-section of the bulk salt in order to collect more representative samples. The vacuum sampling approach also eliminates the risk of dross contamination of samples and avoids the use of moving parts in the salt. The pneumatic sample generator module is used to facilitate high-throughput sample analysis to improve the measurement precision of any given analytical technique by averaging out random sampling and measurement errors. In FY21, two methods for integrating these two modules were tested including direct fluidic coupling and coupling using a solid salt transfer mechanism. Solid salt transfer was ultimately selected over fluidic coupling, primarily to enable the transport of samples over longer distances to support automated at-line integration with high-precision techniques (such as microcalorimetry) that cannot withstand the conditions near an electrorefining process. To facilitate rapid solid salt coupling, new mechanisms were developed for rapidly charging and discharging salt sample tubes at the vacuum sampling loop and pneumatic sample generator modules, respectively. While the charging mechanism will be deployed in FY22, the discharge mechanism was tested in FY21 and is described here. The solid salt tube transfer method was deployed at one of Argonne’s engineering-scale electrorefiners to implement at-line high-throughput pneumatic micro-sample generation capabilities. The approach was used to generate precise uranium- and lanthanide-bearing electrorefiner micro-samples with the specific dimensions requested by researchers at Los Alamos National Laboratory for use in testing their novel microcalorimeter x-ray techniques. The solid salt transfer mechanism proved not only to be an effective means of integrating the precision sample generator with vacuum sampling, but also improved the performance of the sampler generator. To discharge salt from the sample tubes at the sampler generator, tube segments were inserted directly into the sample generator’s Helmholtz chamber and pressure pulse actuations were used to generate precision molten salt samples directly from the tube segments. The direct insertion of sample tubes into the sample generator enabled rapid loading of the salt and prevented salt from contacting most of the interior surfaces of the sample generator, which eliminated cross-contamination between runs. The vacuum sampling-loop tube charging mechanism will support high-throughput tube sampling operations by employing a dynamic vacuum filling process to fill short charge tubes that are configured to be rapidly connected and disconnected from the loop. The dynamic vacuum sampling operation will be automated, and sample tube handling can be executed with simple overhead actuation. Because the modular sampling approach described here eliminates the need for new high-radiation sample handling capabilities, salt-wetted seals, salt-wetted moving parts, and heated transfer lines outside the electrorefiner, it will address most of the remaining technical challenges for the at-line deployment of high-precision analytical techniques which will enable significant reductions in the time delay for sampling-based high-precision accountancy measurements.

42 ENGINEERING↗
DOE OSTI2024

Addressing GPU memory limitations for Graph Neural Networks in High-Energy Physics applications

Introduction Reconstructing low-level particle tracks in neutrino physics can address some of the most fundamental questions about the universe. However, processing petabytes of raw data using deep learning techniques poses a challenging problem in the field of High Energy Physics (HEP). In the Exa.TrkX Project, an illustrative HEP application, preprocessed simulation data is fed into a state-of-art Graph Neural Network (GNN) model, accelerated by GPUs. However, limited GPU memory often leads to Out-of-Memory (OOM) exceptions during training, due to the large size of models and datasets. This problem is exacerbated when deploying models on High-Performance Computing (HPC) systems designed for large-scale applications. Methods We observe a high workload imbalance issue during GNN model training caused by the irregular sizes of input graph samples in HEP datasets, contributing to OOM exceptions. We aim to scale GNNs on HPC systems, by prioritizing workload balance in graph inputs while maintaining model accuracy. Our paper introduces diverse balancing strategies aimed at decreasing the maximum GPU memory footprint and avoiding the OOM exception, across various datasets. Results Our experiments showcase memory reduction of up to 32.14% compared to the baseline. We also demonstrate the proposed strategies can avoid OOM in application. Additionally, we create a distributed multi-GPU implementation using these samplers to demonstrate the scalability of these techniques on the HEP dataset. Discussion By assessing the performance of these strategies as data loading samplers across multiple datasets, we can gauge their effectiveness in both single-GPU and distributed environments. Our experiments, conducted on datasets of varying sizes and across multiple GPUs, broaden the applicability of our work to various GNN applications that handle input datasets with irregular graph sizes.

Lee, Claire Songhyun↗
DOE OSTI2022

A Comparative Multi-System Approach to Characterizing Bioactivity of Commonly Occurring Chemicals

A 2019 retrospective study analyzed wristband personal samplers from fourteen different communities across three different continents for over 1530 organic chemicals. Investigators identified fourteen chemicals (G14) detected in over 50% of personal samplers. The G14 represent a group of chemicals that individuals are commonly exposed to, and are mainly associated with consumer products including plasticizers, fragrances, flame retardants, and pesticides. The high frequency of exposure to these chemicals raises questions of their potential adverse human health effects. Additionally, the possibility of exposure to mixtures of these chemicals is likely due to their co-occurrence; thus, the potential for mixtures to induce differential bioactivity warrants further investigation. This study describes a novel approach to broadly evaluate the hazards of personal chemical exposures by coupling data from personal sampling devices with high-throughput bioactivity screenings using in vitro and non-mammalian in vivo models. To account for species and sensitivity differences, screening was conducted using primary normal human bronchial epithelial (NHBE) cells and early life-stage zebrafish. Mixtures of the G14 and most potent G14 chemicals were created to assess potential mixture effects. Chemical bioactivity was dependent on the model system, with five and eleven chemicals deemed bioactive in NHBE and zebrafish, respectively, supporting the use of a multi-system approach for bioactivity testing and highlighting sensitivity differences between the models. In both NHBE and zebrafish, mixture effects were observed when screening mixtures of the most potent chemicals. Observations of BMC-based mixtures in NHBE (NHBE BMC Mix) and zebrafish (ZF BMC Mix) suggested antagonistic effects. In this study, consumer product-related chemicals were prioritized for bioactivity screening using personal exposure data. High-throughput high-content screening was utilized to assess the chemical bioactivity and mixture effects of the most potent chemicals.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

TRACER-Tethersonde VOC data

One objective of TRACER-Tethersonde campaign was to deploy a volatile organic compound (VOC) sampler on the Tethered Balloon System (TBS) to create vertical profiles and characterize VOC composition. Volatile organic compounds (VOCs) are highly reactive precursor species that undergo atmospheric processing to form secondary products, including aerosol. VOC emissions are influenced by many factors that include but are not limited to temperature, time of day, local anthropogenic activities, and local vegetation, which result in large spatiotemporal variability. The vertical distribution of volatile species is crucial for understanding gas-phase processing for particle production but challenging to accomplish using currently available sampling devices. The standalone sampler built during the campaign enabled the execution of robust experimental designs, including sample collection using resin tubes at multiple altitudes on subsequent flights. Following field sampling, resin tubes were transported back to Baylor University for chemical analysis using a Markes International thermal desorption unit coupled with a gas chromatograph-tandem mass spectrometer (Thermo Scientific). The target analyte list includes biogenic and anthropogenic VOCs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

tbsinp (00)

The ice nucleation spectrometer (INS) is an offline analytical measurement system used to process filter samples for freezing temperature spectra of immersion-mode ice-nucleating particle (INP) number concentrations. It is almost identical to the Colorado State University (CSU) ice spectrometer design. The INS-AIR is specific to filter samples collected on aerial platforms, such as the DOE ARM tethered balloon system (TBS) operated by Sandia National Laboratories, using miniaturized aerosol filter samplers. Users are referred to the INS instrument handbook for INS-AIR sampler details. INS-AIR filter samples are collected during intensive operational periods at various ARM sites and then processed on the INS at CSU. This filter log contains the detailed metadata at all ARM sites where INP filter sample collection has occurred or is currently ongoing, including both ground-based routine INP sampling (INS) and TBS INP sampling (INS-AIR). Metadata include start and end times, vacuum line pressures and temperatures, and flow rates; total accumulated flow through each filter; and notes on collection issues or weather conditions. Users can also keep up to date with the status of filter and data processing, even before data are available on ARM’s Data Discovery. Users can contact INP mentors Jessie Creamean or Thomas Hill with any questions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Single-Use Destructive Assay for Uranium Hexafluoride Sampling

Sampling uranium hexafluoride (UF6) for the determination of enrichments by destructive analysis (DA) is a critical component in the International Atomic Energy Agency’s layered safeguards approach for uranium processing facilities. Typically, gram-quantity UF6 samples are collected during inspections and stored under tag-and-seal until transportation to an off-site analytical laboratory. The shipping times can be long, and evolving restrictions on radioactive/corrosive materials shipments may increasingly limit the IAEA’s ability to transport UF6 samples easily. Pacific Northwest National Laboratory has developed a low-cost UF6 sampling technology called Single-Use Destructive Assay (SUDA) that addresses these challenges, as well as provides DA sample geometries that can be tailored for different analytical methods, including potential on-site analyses. The SUDA samplers, along with a unique holder, are designed for direct attachment to existing taps at uranium processing facilities, allowing gaseous UF6 to come into direct contact with a zeolite film. The SUDA technology features the ability to capture uranium in a more easily shipped and handled form as the solid, more stable, and relatively less hazardous hydrated uranyl fluoride (UO2F2•nH2O), which is formed through the controlled hydrolysis of UF6. We have recently simulated uranium collection under enrichment plant sampling conditions to further improve our understanding of SUDA sampling. Presented here is our recent work on measuring the relationship between sampling conditions and uranium collection, which includes control of the uranium-mass-to-zeolite ratio and assessing variable UF6 gas and sampling parameters that can affect collection using the SUDA sampler.

Pope, Timothy R.↗
DOE OSTI2020

Large Volume Airborne Contamination Monitoring To Support Nuclear Processes' Deactivation and Decommissioning

Current D and D operations at Hanford have demonstrated a flaw in the current state of the art capability of defining airborne contamination boundaries - Airborne particulate emissions of Pu-239 from CM2H operations on the Hanford Pu Finishing Plant were detected well beyond areas controlled for airborne Pu, putting numerous workers at risk for radiological assimilations - Current air samplers and CAM systems were surveying insufficient volumes of air to accurately predict where respiratory protection was required - Hanford is located in a high radon environment, making air monitoring for alpha emitting actinides challenging in high alpha radon induced backgrounds. - Inexpensive HEPA based home and industrial air purifiers filter significantly higher volumes of air than commercially available continuous-air monitoring (CAM) systems. - Inexpensive models capable of filtered air volumes exceeding 1000 times that of a CAM. - Detector system can be built to detect x-rays generated from actinide decay. - Branching ratios of x-rays are 4 orders of magnitude more intense from Plutonium decay than its gamma emissions. - Detector system can be a low resolution systems, as x-ray region of interest is not terribly congested. - Detection systems evaluated will be designed based on slabs of NaI or pixelated NaI or CsI panels. - Simple graphical user interface software will be developed to operate the detection system. - Concept is to deploy some of these air-purifying systems in nonradiological areas around SRNL to confirm radon can be rejected with confidence. - Generate some filters contaminated with plutonium via electroplated Pu or lab generated simulated particles. - then deploy units in known airborne radiological environments to establish systems ability to accurately measure actinide based hot particles Lab analyses will follow up the system analyses to ensure hot particles were correctly identified. Analysis by Scintillation: - Application of scintillation media to the surface of the filters is being explored. - Evaluating slabs of ZnS(Ag), application of powdered ZnS(Cu) and spray on Perkin Elmer Enhance. - Scintillation events would then be digitized with a digital camera and quantified. - Comparing against sensitivity of a PMT or SiPD readout. - Currently evaluating a Thorlabs 8 Megapixel Monochrome Scientific CCD Camera, hermetically sealed cooled package with a wide angle lens. - Wide angle lens allows complete view of HEPA filter from 7 inches away. - Images taken of glow in the dark paint, as well as plutonium-induced fluorescence. - Plutonium was flamed mounted on a 1 inch diameter stainless steel planchet, covered with a layer of mylar and a section of scintillating ZnS obtained from Eljon. - Currently working on reducing signal-to-noise levels to boost sensitivity. - Dark box to hold contaminated or electroplated source covered filters under fabrication. Analysis by x-ray Spectroscopy: - Branching ratios for x-ray emissions from Plutonium isotopes are orders of magnitude more intense than gamma-ray emissions. - The nuclear databases are incomplete on the branching ratios of some of the isotopes. - Evaluating some custom built SrI2 x-ray spectrometers vs a conventional windowed NaI detector. - SrI2 detectors are carbon-composite-windowed 51 mm x 51 mm. - MCNP calculations to establish self absorbance of filter media on 17 keV x-ray. Radon Rejection: - Activated charcoal pre-filter acts as a Radon trap. - Adding a time lapse feature to camera to aid in radon rejection. SRS Plutonium Fuel Form D and D Operations: Currently deploying air sampler to D and D operation of Pu-238 facility at SRS to generate some field samples to analyze.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

Efficient Subset Simulation using Hamiltonian Neural Network enhanced Markov Chain Monte Carlo Methods

The Monte Carlo method delivers an unbiased estimate of the probability of failure. However, the variance of the estimate depends on the number of evaluated samples. This number must be very large for estimations of a low probability of failure. If the evaluation of each sample is computationally expensive, the crude Monte Carlo simulation strategy is impracticable. Therefore, subset simulations are used to reduce the required number of evaluations. Subset simulations require a Markov Chain Monte Carlo sampler, such as the random walk Metropolis-Hastings algorithm. The algorithm, however, struggles with sampling in low-probability regions, especially if they are narrow. As a consequence, advanced Markov Chain Monte Carlo simulations have been developed. In particular, the Hamiltonian Monte Carlo method explores the target distribution rapidly. Driven by the idea of Hamiltonian dynamics, this sampler provides a non-random walk through the target distribution. The incorporation of subset simulation and Hamiltonian Monte Carlo methods has shown promising results for reliability analysis. One downside of the Hamiltonian Monte Carlo method is that gradient evaluations are computationally expensive, especially when dealing with high-dimensional problems and evaluating long trajectories. We show that integrating Hamiltonian neural networks in Hamiltonian Monte Carlo simulations significantly speeds up the sampling task. Furthermore, the enhancement of adaptive trajectory length within the Hamiltonian Monte Carlo results in the efficient proposal of the following states. Based on this recent enhancement, we provide a fast sampling strategy for subset simulations using Hamiltonian neural networks to replace the evaluation of the gradient and significantly speed up the Hamiltonian Monte Carlo simulation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Gradient-informed Hamiltonian Monte Carlo for multicomponent CALPHAD model optimization and uncertainty quantification

CALPHAD model parameter optimization is inherently challenging due to non-smooth objective functions, high-dimensional parameter spaces, and the need for uncertainty quantification (UQ). Traditional weighted nonlinear least squares approaches are computationally efficient but local, whereas black-box global optimizers and ensemble Markov Chain Monte Carlo (MCMC) methods provide broader exploration at substantial computational cost. The objective of this work is to combine the global exploration capability of gradient-informed Hamiltonian Monte Carlo – specifically the No-U-Turn Sampler (NUTS) – with local deterministic refinement using BFGS to efficiently optimize multicomponent CALPHAD models with minimal manual intervention. Analytic gradients are computed via the Jansson derivative framework. The methodology is demonstrated on the Cr—Fe binary system and extended to the Cr—Fe—Ni ternary system with 32 degrees of freedom. For Cr—Fe, NUTS achieves comparable or superior optimality relative to ensemble MCMC while requiring over an order-of-magnitude fewer likelihood evaluations. Parameter uncertainties are quantified through NUTS sampling and propagated to thermodynamic observables using local expansion, demonstrating a novel modular approach that combines binary and ternary parameter subsets without requiring global relaxation. These results establish gradient-informed exploration as a scalable strategy for multicomponent CALPHAD optimization and provide a practical route towards efficient higher-order database development with quantified uncertainty.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Physics-Informed Machine Learning of Dynamical Systems for Efficient Bayesian Inference

Although the no-u-turn sampler (NUTS) is a widely adopted method for performing Bayesian inference, it requires numerous posterior gradients which can be expensive to compute in practice. Recently, there has been a significant interest in physics-based machine learning of dynamical (or Hamiltonian) systems and Hamiltonian neural networks (HNNs) is a noteworthy architecture. But these types of architectures have not been applied to solve Bayesian inference problems efficiently. We propose the use of HNNs for performing Bayesian inference efficiently without requiring numerous posterior gradients. We introduce latent variable outputs to HNNs (L-HNNs) for improved expressivity and reduced integration errors. We integrate L-HNNs in NUTS and further propose an online error monitoring scheme to prevent sampling degeneracy in regions where L-HNNs may have little training data. We demonstrate L-HNNs in NUTS with online error monitoring consider several complex high-dimensional posterior densities and compare its performance to NUTS.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Reinforcement Learning-Guided Long-Timescale Simulation of Hydrogen Transport in Metals

Diffusion in alloys is an important class of atomic processes. However, atomistic simulations of diffusion in chemically complex solids are confronted with the timescale problem: the accessible simulation time is usually far shorter than that of experimental interest. In this work, long-timescale simulation methods are developed using reinforcement learning (RL) that extends simulation capability to match the duration of experimental interest. Two special limits, RL transition kinetics simulator (TKS) and RL low-energy states sampler (LSS), are implemented and explained in detail, while the meaning of general RL are also discussed. As a testbed, hydrogen diffusivity is computed using RL TKS in pure metals and a medium entropy alloy, CrCoNi, and compared with experiments. The algorithm can produce counter-intuitive hydrogen-vacancy cooperative motion. We also demonstrate that RL LSS can accelerate the sampling of low-energy configurations compared to the Metropolis–Hastings algorithm, using hydrogen migration to copper (111) surface as an example.

36 MATERIALS SCIENCE↗