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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 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Learning curves for drug response prediction in cancer cell lines

Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensitivity studies continue generating drug response data, a common question is whether the generalization performance of existing prediction models can be further improved with more training data. We utilize empirical learning curves for evaluating and comparing the data scaling properties of two neural networks (NNs) and two gradient boosting decision tree (GBDT) models trained on four cell line drug screening datasets. The learning curves are accurately fitted to a power law model, providing a framework for assessing the data scaling behavior of these models. The curves demonstrate that no single model dominates in terms of prediction performance across all datasets and training sizes, thus suggesting that the actual shape of these curves depends on the unique pair of an ML model and a dataset. The multi-input NN (mNN), in which gene expressions of cancer cells and molecular drug descriptors are input into separate subnetworks, outperforms a single-input NN (sNN), where the cell and drug features are concatenated for the input layer. In contrast, a GBDT with hyperparameter tuning exhibits superior performance as compared with both NNs at the lower range of training set sizes for two of the tested datasets, whereas the mNN consistently performs better at the higher range of training sizes. Moreover, the trajectory of the curves suggests that increasing the sample size is expected to further improve prediction scores of both NNs. These observations demonstrate the benefit of using learning curves to evaluate prediction models, providing a broader perspective on the overall data scaling characteristics. A fitted power law learning curve provides a forward-looking metric for analyzing prediction performance and can serve as a co-design tool to guide experimental biologists and computational scientists in the design of future experiments in prospective research studies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking

A critical step in structure-based drug discovery is predicting whether and how a candidate molecule binds to a model of a therapeutic target. However, substantial protein side chain movements prevent current screening methods, such as docking, from accurately predicting the ligand conformations and require expensive refinements to produce viable candidates. Here, we present the development of a high-throughput and flexible ligand pose refinement workflow, called “tinyIFD”. The main features of the workflow include the use of specialized high-throughput, small-system MD simulation code mdgx.cuda and an actively learning model zoo approach. We show the application of this workflow on a large test set of diverse protein targets, achieving 66% and 76% success rates for finding a crystal-like pose within the top-2 and top-5 poses, respectively. We also applied this workflow to the SARS-CoV-2 main protease (M pro ) inhibitors, where we demonstrate the benefit of the active learning aspect in this workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors

Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goal. Herein, we use molecular modeling approaches to identify and target potential novel pockets specific to Class IIA HDAC-HDAC4 at the interface between HDAC4 and the transcriptional corepressor component protein NCoR. These pockets were screened using an ensemble docking approach combined with consensus scoring to identify compounds with a different binding mechanism than the currently known HDAC modulators. Binding was compared in experimental assays between HDAC4 and HDAC3, which belong to a different family of HDACs. HDAC4 was significantly inhibited by compound 88402 but not HDAC3. Two other compounds (67436 and 134199) had IC50 values in the low micromolar range for both HDACs, which is comparable to the known inhibitor of HDAC4, SAHA (Vorinostat). However, both of these compounds were significantly weaker inhibitors of HDAC3 than SAHA and thus more selective, albeit to a limited extent. Five compounds exhibited activity on human breast carcinoma and/or urothelial carcinoma cell lines. The present result suggests potential mechanistic and chemical approaches for developing selective HDAC4 modulators.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Rational design and testing of abiotic stress‐inducible synthetic promoters from poplar cis ‐regulatory elements

Summary Abiotic stress resistance traits may be especially crucial for sustainable production of bioenergy tree crops. Here, we show the performance of a set of rationally designed osmotic‐related and salt stress‐inducible synthetic promoters for use in hybrid poplar. De novo motif‐detecting algorithms yielded 30 water‐deficit (SD) and 34 salt stress (SS) candidate DNA motifs from relevant poplar transcriptomes. We selected three conserved water‐deficit stress motifs (SD18, SD13 and SD9) found in 16 co‐expressed gene promoters, and we discovered a well‐conserved motif for salt response (SS16). We characterized several native poplar stress‐inducible promoters to enable comparisons with our synthetic promoters. Fifteen synthetic promoters were designed using various SD and SS subdomains, in which heptameric repeats of five‐to‐eight subdomain bases were fused to a common core promoter downstream, which, in turn, drove a green fluorescent protein (GFP) gene for reporter assays. These 15 synthetic promoters were screened by transient expression assays in poplar leaf mesophyll protoplasts and agroinfiltrated Nicotiana benthamiana leaves under osmotic stress conditions. Twelve synthetic promoters were induced in transient expression assays with a GFP readout. Of these, five promoters (SD18‐1, SD9‐2, SS16‐1, SS16‐2 and SS16‐3) endowed higher inducibility under osmotic stress conditions than native promoters. These five synthetic promoters were stably transformed into Arabidopsis thaliana to study inducibility in whole plants. Herein, SD18‐1 and SD9‐2 were induced by water‐deficit stress, whereas SS16‐1, SS16‐2 and SS16‐3 were induced by salt stress. The synthetic biology design pipeline resulted in five synthetic promoters that outperformed endogenous promoters in transgenic plants.

09 BIOMASS FUELS↗
DOE OSTI2025

Dataset for Leveraging CryoEM and AI-Driven Morphological Feature Analysis for Insights on Bacterial Structures

This repository hosts an AI-assisted image segmentation and analysis pipeline for Pantoea sp. YR343 cryo-electron microscopy (cryoEM) datasets. The workflow automates membrane thickness measurements, flagella detection, and field-of-view (FOV) screening from low-dose, high-resolution cryoEM micrographs eliminating the need for slow manual annotation. By integrating deep-learning based segmentation (YOLOv11) with quantitative post-processing, this toolkit provides a scalable and reproducible way to study bacterial morphology under hydrated, near-native conditions. The GitHub repository for AI-based tools for cryoEM bacteria ultrastructures can be found here: https://github.com/Sireesiru/Cryo-EM-Ultrastructures/tree/main

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Mining a human transcriptome database for chemical modulators of NRF2

Nuclear factor erythroid-2 related factor 2 (NRF2) encoded by the NFE2L2 gene is a transcription factor critical for protecting cells from chemically-induced oxidative stress. We developed computational procedures to identify chemical modulators of NRF2 in a large database of human microarray data. A gene expression biomarker was built from statistically-filtered gene lists derived from microarray experiments in primary human hepatocytes and cancer cell lines exposed to NRF2-activating chemicals (oltipraz, sulforaphane, CDDOIm) or in which the NRF2 suppressor Keap1 was knocked down by siRNA. Directionally consistent biomarker genes were further filtered for those dependent on NRF2 using a microarray dataset from cells after NFE2L2 siRNA knockdown. The resulting 143-gene biomarker was evaluated as a predictive tool using the correlation-based Running Fisher algorithm. Using 59 gene expression comparisons from chemically-treated cells with known NRF2 activating potential, the biomarker gave a balanced accuracy of 93%. The biomarker was comprised of many well-known NRF2 target genes (AKR1B10, AKR1C1, NQO1, TXNRD1, SRXN1, GCLC, GCLM), 69% of which were found to be bound directly by NRF2 using ChIP-Seq. NRF2 activity was assessed across ~9840 microarray comparisons from ~1460 studies examining the effects of ~2260 chemicals in human cell lines. A total of 260 and 43 chemicals were found to activate or suppress NRF2, respectively, most of which have not been previously reported to modulate NRF2 activity. Using a NRF2-responsive reporter gene in HepG2 cells, we confirmed the activity of a set of chemicals predicted using the biomarker. The biomarker will be useful for future gene expression screening studies of environmentally-relevant chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Business Case Analysis for Artificial Intelligence-Large Language Model Technology Integration

AI-assisted processes are expected to enhance operational efficiency and improve decision-making, supporting the long-term economic viability of nuclear power plants. However, detailed business analyses of AI-generated cost savings are rarely performed. Given the recent industry interest in Large Language Model (LLM), the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program has conducted a comprehensive business case analysis of LLM Artificial Intelligence (AI) implementation in nuclear plant engineering workflows. The research employed three complementary business case approaches to evaluate impact of an LLM, using three representative engineering processes as use-cases: Boric Acid Corrosion (BAC) Evaluations, Maintenance Rule Evaluations, and 10 CFR 50.59 Screenings. Through detailed workload analyses and structured interviews, the study quantified significant efficiency improvements ranging from 11% to 59% across these processes. The research further considers how these efficiency gains could translate into tangible reliability improvements through enhanced engineering capacity. Analysis of historical plant trip data indicates that enabling engineers to focus on proactive reliability activities could provide substantial financial benefits through avoided outages, potentially generating greater value than the direct efficiency improvements alone. By documenting successful applications, implementation challenges, and strategic opportunities, this research provides nuclear utilities with a practical framework for evaluating the value of AI technology to support long-term operations through advanced digital technologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Identifying amyloid-related diseases by mapping mutations in low-complexity protein domains to pathologies

Proteins including FUS, hnRNPA2, and TDP-43 reversibly aggregate into amyloid-like fibrils through interactions of their low-complexity domains (LCDs). Mutations in LCDs can promote irreversible amyloid aggregation and disease. We introduce a computational approach to identify mutations in LCDs of disease-associated proteins predicted to increase propensity for amyloid aggregation. We identify several disease-related mutations in the intermediate filament protein keratin-8 (KRT8). Atomic structures of wild-type and mutant KRT8 segments confirm the transition to a pleated strand capable of amyloid formation. Biochemical analysis reveals KRT8 forms amyloid aggregates, and the identified mutations promote aggregation. Aggregated KRT8 is found in Mallory–Denk bodies, observed in hepatocytes of livers with alcoholic steatohepatitis (ASH). We demonstrate that ethanol promotes KRT8 aggregation, and KRT8 amyloids co-crystallize with alcohol. Lastly, KRT8 aggregation can be seeded by liver extract from people with ASH, consistent with the amyloid nature of KRT8 aggregates and the classification of ASH as an amyloid-related condition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Efficient computational design of two-dimensional van der Waals heterostructures: Band alignment, lattice mismatch, and machine learning

Here, we develop a computational database, website applications (web-apps), and machine-learning (ML) models to accelerate the design and discovery of two-dimensional (2D) heterostructures. Using density functional theory (DFT) based lattice parameters and electronic band energies for 674 nonmetallic exfoliable 2D materials, we generate 226 779 possible bilayer heterostructures. We classify these heterostructures into type-I, -II, and -III systems according to Anderson’s rule, which is based on the relative band alignments of the noninteracting monolayers. We find that type II is the most common and type III the least common heterostructure type. We subsequently analyze the chemical trends for each heterostructure type in terms of the Periodic Table of constituent elements. The band alignment data can also be used for identifying photocatalysts and high-work-function 2D metals for contacts. We validate our results by comparing them to experimental data as well as hybrid-functional predictions. Additionally, we carry out DFT calculations of a few selected systems (MoS 2 /WSe 2 , MoS 2 /h-BN, and MoSe 2 /CrI 3 ), to compare the band-alignment description with the predictions from Anderson’s rule. We develop web-apps to enable users to virtually create combinations of 2D materials and predict their properties. Additionally, we use ML tools to predict band-alignment information for 2D materials. The web-apps, tools, and associated data will be distributed through the JARVIS-HETEROSTRUCTURE website. Our analysis, results, and the developed web-apps can be applied to the screening and design applications, such as finding alternative photocatalysts, photodetectors, and high-work-function (WF) 2D-metal contacts.

2-dimensional systems↗
DOE OSTI2026

Agentic framework for programmatic crystal structure generation using a fine-tuned worker–supervisor large language model

Platinum group metals (PGMs) underpin many catalytic technologies but face severe supply constraints, motivating the search for alternative materials and computational methods to accelerate discovery. While atomistic simulation tools such as Pymatgen and ASE have streamlined structure manipulation, they require detailed inputs, limiting accessibility for experimentalists and slowing early-stage exploration. Here, in this study, we present an AI-driven agentic framework that orchestrates worker–supervisor large language models (LLMs). The worker translates natural-language prompts of varying abstraction into valid crystallographic structures using a compact LLM fine-tuned with low-rank adaptation on a curated text–code–CIF dataset, emphasizing energy-efficient training. Benchmarking against the baseline CodeGen-350M-mono model shows that fine-tuning reduces hallucination rates from 100% to as low as 5% and improves structural match accuracy to up to 82% for fully specified inputs. Accuracy declines with decreasing prompt detail but remains nontrivial even when only stoichiometry and space group are provided, underscoring the LLM’s capacity for crystallographic inference. The supervisor Claude LLM evaluates the outputs and triggers iterative refinement through the worker’s built-in structure manipulation capabilities (e.g., supercell scaling, strain, vacancy, and substitution operations). We further demonstrate use cases for technologically relevant catalysts, including IrO 2 , pyrochlore Pb 2 Ir 2 O 7 , Ni 2 FeO 4 , and Ni 3 Mo, where the framework generates physically consistent structures that can be refined via geometry optimization. This work introduces a low-energy, language-driven pathway for integrating human and machine intelligence in materials design, paving the way for AI-assisted synthesis planning and high-throughput screening of complex oxides.

AI agent↗
DOE OSTI2023

Exploring and Embracing Heterogeneity in Atomically Thin Energy Materials

Atomically thin semiconductors offer extraordinary opportunities for the manipulation of charge carriers, many-body optical excitations, quantum light emitters, and non-charge based quantum numbers. Confinement and reduced dielectric screening in these two-dimensional (2D) materials give rise to large characteristic energies so that many-body and quantum effects are important even at room temperature. Optical excitations in extended homogeneous areas have been investigated intensely, albeit mostly focusing on a limited set of materials, particularly transition metal dichalcogenides. Much less understood are light-matter interactions for other classes of 2D semiconductors, as well as effects that arise in heterogeneous materials, either near naturally occurring defects, impurities, edges and grain boundaries, or as a result of intentional interface formation in heterostructures. Addressing such systems experimentally involves significant challenges: Understanding the atomistic growth mechanisms of 2D semiconductors, so that novel systems with designed properties, specific ‘imperfections’, or controlled interfaces can be realized; and probing of local excitations at scales that match the relevant (micrometer to nanometer) length scales in heterogeneous materials. In this research project, we addressed these challenges by harnessing quantitative in-situ microscopy to study the growth of 2D and layered semiconductors and heterostructures, combined with local spectroscopic measurements of quasiparticles excited at the nanometer scale. An integral part of the research has been the development of novel experimental approaches, both for in-situ microscopy of synthesis and for nanometer-scale spectroscopy. In particular, advanced techniques were developed for cathodoluminescence in scanning transmission electron microscopy (STEM-CL) where a nanometer-focused electron beam is used to locally excite electron-hole pairs, excitons, as well as propagating hybrid light-matter modes such as exciton-polaritons. Experiments were guided and analyzed via computations of structure, chemistry, and excitation spectra. The particular materials focus has been on group IV chalcogenides, a family of less explored 2D/layered semiconductors whose diversity in crystal structure and properties promises access to novel materials architectures and the discovery of phenomena that can support emerging technology needs.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Material Plasma Exposure eXperiment (MPEX) High Heat Flux Bellows for Component Alignment in High Microwave Environment

The Material Plasma Exposure eXperiment (MPEX) device is a linear plasma device developed to perform plasma material interaction experiments under the conditions prototypic of a fusion reactor divertor. MPEX has multiple systems that must be precisely aligned to the plasma axis, including an electron cyclotron heating system that emits up to 400 kW of microwave power into the vacuum vessel. Five distinct systems require precise alignment on the MPEX device, thus requiring four bellows, all of which are adjacent to the plasma at a relatively high heat flux of approximately 47 kW/m2 and microwave power regions. The MPEX high heat flux bellows (HHFB) is designed to deliver 6 degrees of freedom positioning. The HHFB includes titanium–zirconium–molybdenum (TZM) inserts that are brazed into a Glidcop AL-15 body using a high-temperature braze alloy, thus blocking direct line of sight to an edge-welded bellows from the plasma and microwave screen to block microwaves from the bellows. Further, a custom ConFlat knife edge is machined into the Glidcop AL-15, so the vacuum flanges do not need a braze or weld joint on the vacuum interface. Fingerstock or copper mesh is used to restrict microwave power from entering the interstitial space between the water-cooled Glidcop AL-15 body and edge-welded bellows. Glidcop AL-15 was selected as the material of choice for the water-cooled body because it can maintain mechanical integrity at elevated temperatures, and it also allows for a high-temperature braze. TZM was selected for its machinability and compatibility with vacuum and plasma requirements. A test article is also being considered for a similarly shaped component, the MPEX limiter, that will demonstrate the integrity of the braze joint under high thermal load. Results from this testing will be extrapolated to deduce the lifetime and integrity of the HHFB design.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

Roll-to-Roll Advanced Materials Manufacturing DOE Laboratory Collaboration (FY2020 Final Report)

R2R processing is used to manufacture a wide range of products for various applications which span many industrial business sectors. The overall R2R methodology has been in use for decades and this continuous technique traditionally involves deposition of material(s) onto moving webs, carriers or other continuous belt-fed or conveyor-based processes that enable successive steps to build a final version which serves to support the deposited materials. Established methods that typify R2R processing include tape casting, silk-screen printing, reel-to-reel vacuum deposition/coating, and R2R lithography. Products supported by R2R manufacturing include micro-electronics, electro-chromic window films, PVs, fuel cells for energy conversion, battery electrodes for energy storage, and barrier and membrane materials. Due to innovation in materials and process equipment, high-quality yet very low-cost multilayer technologies have the potential to be manufactured on a very cost-competitive basis. To move energy-related products from high-cost niche applications to the commercial sector, the means must be available to enable manufacture of these products in a cost-competitive manner that is affordable. Fortunately, products such as fuel cells, thin- and mid-film PVs, batteries, electrochromic and piezoelectric films, water separation membranes, and other energy saving technologies readily lend themselves to manufacture using R2R approaches. However, more early-stage research is needed to solve the challenge of linking the materials (particles, polymers, solvents, additives) used in ink and slurry formulations and the coating and drying processes to the ultimate performance of the final R2R product, especially for a process that uses multiple layers of deposition to achieve the end product. To solve the problems associated with these challenges, the R2R Collaboration is executing a research program with outcomes that will ultimately link modeling, processing, metrology and defect detection tools, thereby directly relating the properties of constituent particles and processing conditions to the performance of final devices. This collaborative approach was designed to foster identification and development of materials and processes related to R2R for clean-energy materials development. Using computational and experimental capabilities by acknowledged subject matter experts within the supported National Laboratory system, this project leverages the capabilities and expertise at each of five National Laboratories to further the development of multilayer technologies that will enable high-volume, cost-competitive platforms. A typical R2R process has three steps: (1) mixing of particles and various constituents in a slurry, (2) coating of the ink/slurry mixture on a substrate, and (3) drying/curing and processing of the coating. Final performance of devices made via R2R processes is dependent on the active materials (e.g., electrochemical particles in battery or fuel cell electrodes) and the device structure that stems from the governing component interactions within the various steps. However, a fundamental understanding of the underlying mechanisms and phenomena is still lacking, which is why industrial-scale R2R process development and manufacturing is still largely empirical in nature. The FY 2019 through FY 2021 program addresses aspects of the following two targets from the AMO Multi-Year Program Plan: (1) Target 8.1 Develop technologies to reduce the cost per manufactured throughput of continuous R2R manufacturing processes. (A) Increasing throughput of R2R processes by 5 times for batteries (to 50 square feet per minute (50 ft 2 /min)) and capacitors and 10 times for printed electronics and the manufacture of other substrates and MEs used in support of these products. (B) Developing resolution capabilities to enable registration and alignment that will detect, align, and co-deposit multiple layers of coatings and print < 1-micron (1 µm) features using continuous process scalable for commercial production. (C) Developing scalable and reliable R2R processes for solution deposition of ultra-thin (<10 nm) films for active and passive materials. (D) Develop in-line multilayer coating technology on thin films with yields greater than 95%. (2) Target 8.2 Develop in-line instrumentation tools that will evaluate the quality of single and multilayer materials in-process. (A) Developing in-line QC technologies and methodologies for real-time identification of defects and expected product properties “in-use/application” during continuous processing at all size-scales with a focus on the “micro” and “nano” scale traces, lines, and devices, i.e., <1 μm at 300 ft./min for R2R processing in air and <10 nm at 20 ft./min for vacuum (B) Developing technologies to increase the measurement frequency of surface rheology without significant cost increases with a goal of a 10-nanometer in-line profilometry at a production rate of 100,000 square millimeters per minute (100,000 mm 2 /min).

42 ENGINEERING↗
DOE OSTI2023

Real-time mixed reality display of dual particle radiation detector data

Radiation source localization and characterization are challenging tasks that currently require complex analyses for interpretation. Mixed reality (MR) technologies are at the verge of wide scale adoption and can assist in the visualization of complex data. Herein, we demonstrate real-time visualization of gamma ray and neutron radiation detector data in MR using the Microsoft HoloLens 2 smart glasses, significantly reducing user interpretation burden. Radiation imaging systems typically use double-scatter events of gamma rays or fast neutrons to reconstruct the incidence directional information, thus enabling source localization. The calculated images and estimated ’hot spots’ are then often displayed in 2D angular space projections on screens. By combining a state-of-the-art dual particle imaging system with HoloLens 2, we propose to display the data directly to the user via the head-mounted MR smart glasses, presenting the directional information as an overlay to the user’s 3D visual experience. We describe an open source implementation using efficient data transfer, image calculation, and 3D engine. We thereby demonstrate for the first time a real-time user experience to display fast neutron or gamma ray images from various radioactive sources set around the detector. We also introduce an alternative source search mode for situations of low event rates using a neural network and simulation based training data to provide a fast estimation of the source’s angular direction. Using MR for radiation detection provides a more intuitive perception of radioactivity and can be applied in routine radiation monitoring, education & training, emergency scenarios, or inspections.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning

Accurate prediction of adsorption energies on heterogeneous catalyst surfaces is crucial to predicting reactivity and screening materials. Adsorption linear scaling relations have been developed extensively but often lack accuracy and apply to one adsorbate and a single binding site type at a time. These facts undermine their ability to predict structure sensitivity and optimal catalyst structure. Using machine learning on nearly 300 density functional theory calculations, we demonstrate that generalized coordination number scaling relations hold well for oxygen- and high-valency carbon-binding species but fail for others. Here we reveal that the valency and the electronic coupling of a species with the surface, along with the site type and its coordination environment, are critical for small species adsorption. The model simultaneously predicts the adsorption energy and preferred site and significantly outperforms linear scalings in accuracy. It can expose the structure sensitivity of chemical reactions and enable enhanced catalyst activity via engineering particle shape and facet defects. The generality of our methodology is validated by training the model with transition metal data and transferring it to predict adsorption energies on single-atom alloys.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Benchtop Autonomous Electrochemical Characterization System for Combinatorial Thin-Film Solid Oxide Electrodes

The design of materials for electrochemical energy conversion is complicated by a vast search space of candidate materials and multifaceted property requirements: multicarrier conductivity, stability, and catalytic activity are all necessary but rarely intersect. Although self-driving laboratories are rapidly rising to address such material optimization problems, the required infrastructure for integrated, large-scale robotic facilities can be cost-prohibitive. Here we develop and evaluate a closed-loop measurement system for efficient screening of proton-conducting oxide electrodes for ceramic fuel cells and electrolyzers, building on top of an existing benchtop instrument and integrating techniques for rapid impedance measurement and automated analysis. This system exemplifies a “minimum viable” self-driving implementation that can deliver substantial benefits with relatively simple infrastructure. Combinatorial thin-film microelectrode libraries are characterized with a recently developed joint time-domain and frequency-domain impedance measurement technique, which provides an order-of-magnitude acceleration relative to conventional impedance spectroscopy. The distribution of relaxation times is extracted from impedance data and analyzed without human intervention. These results feed an active learning and Bayesian optimization process that learns to predict electrochemical impedance as a function of material composition, measurement temperature, oxygen partial pressure, and electrical bias, which further reduces the screening time by tenfold with optimized experimental sequences. We apply this system to Ba⁡(Co,Fe,Zr,Y)⁢O 3−𝛿 combinatorial libraries and evaluate its effectiveness for learning material property trends and optimizing expensive-to-evaluate properties such as activation energy. This offers insights into key methodological aspects of practical autonomous experimentation, including surrogate model validation, cost-aware acquisition functions, and high-throughput data interpretation. Our results demonstrate the efficacy of the system for rapidly gathering information, but also highlight real-world experimental challenges of thin-film degradation and numerical instability in surrogate models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Revisiting Five Years of CASMI Contests with EPA Identification Tools

Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency’s (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding

Antigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptides into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental data set from the Immune Epitope Database, and theoretical data sets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of nine neutral residues from a six-residue subset with an average R 2 coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an receiver operating characteristic (ROC) AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2 value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting seven neutral residues from an eight-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗