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Artificial intelligence tools for enzyme engineering and metabolic engineering

Enzyme engineering and metabolic engineering drive innovation in energy biotechnology. In recent years, artificial intelligence (AI) has supported successful applications in designing effective enzymes and productive microbial cell factories. This review summarizes recent advances in enzyme redesign using protein language models, de novo enzyme design with generative models, and AI tools for engineering metabolism and related cellular phenotypes. Across these areas, AI models are shifting from single modality inputs to integrated representations of protein function, metabolic pathways, and cell states. We emphasize that unifying the diverse data representations across scales will be necessary for advancements in energy biotechnology.

Volk, Michael [Univ. of Illinois at Urbana-Champai↗

NASA Tech Briefs, March 2006

Topics covered include: Medical Signal-Conditioning and Data-Interface System; Instruments for Reading Direct-Marked Data-Matrix Symbols; Processing EOS MLS Level-2 Data; Ground Processing of Data From the Mars Exploration Rovers; Estimating Total Electron Content Using 1,000+ GPS Receivers; NASA Solar Array Demonstrates Commercial Potential; Improved Control of Charging Voltage for Li-Ion Battery; Programmable Pulse-Position-Modulation Encoder; Wavelength-Agile External-Cavity Diode Laser for DWDM; Pattern-Recognition Processor Using Holographic Photopolymer; Submicrosecond Power-Switching Test Circuit; Three-Function Logic Gate Controlled by Analog Voltage; Integrated System for Autonomous Science; Montage Version 3.0; Utilizing AI in Temporal, Spatial, and Resource Scheduling; Satellite Image Mosaic Engine; Architecture for Control of the K9 Rover; HFGMC Enhancement of MAC/GMC; Automated Activation and Deactivation of a System Under Test; Cleaning Carbon Nanotubes by Use of Mild Oxygen Plasmas; Generating Aromatics From CO2 on Mars or Natural Gas on Earth; Attaching Thermocouples by Peening or Crimping; Heat Treatment of Friction-Stir-Welded 7050 Aluminum Plates; Generating Breathable Air Through Dissociation of N2O; High-Performance Scanning Acousto-Ultrasonic System; Correction for Thermal EMFs in Thermocouple Feedthroughs; Using Quasiparticle Poisoning To Detect Photons; Estimating Resolution Lengths of Hybrid Turbulence Models; Education and Training Module in Alertness Management; Cargo-Positioning System for Next-Generation Spacecraft; Micro-Imagers for Spaceborne Cell-Growth Experiments; Holographic Solar Photon Thrusters; Plasma-Based Detector of Outer-Space Dust Particles; and Generation of Data-Rate Profiles of Ka-Band Deep-Space Links.

Source record↗

Progressively Enabling Earth Independent Medical Operations (EIMO)

This panel presents the findings from a series of Technical Interchange Meetings (TIMs) hosted by the Exploration Medical Capability Element (ExMC) in NASA’s Human Research Program. The topics for the TIMs were derived from a 2-day conference of senior leaders and subject matters experts that collectively outlined a multi-faceted strategy designed to optimize crew health and performance through an increasingly autonomous medical approach. The first abstract in this panel outlines the scope of issues related to data collection, usage, transmission and computing capacity to facilitate EIMO. The second presentation provides an overview of the challenges in developing curricula and advanced training tools to baseline knowledge, skills and abilities (KSA), verify clinical competency and assure retention during prolonged durations inherent in exploration-class missions. An overview of the complicated medical supply and resource chain necessary to facilitate EIMO is provided in the third presentation of this panel. The final presentation in this EIMO panel surveys the breadth and depth of demands on cognitive load expected to be experienced by crew on an exploration mission and proposes strategies to mitigate the prospect of cognitive overload through methods to shift task load from the crew to multi-modal artificial intelligence based medical support systems. Taken together, these presentations summarize the challenges to be expected and potential solution spaces to be explored and developed to progressively enable increasing autonomous medical operations to support crewed missions beyond low earth orbit. Through EIMO focused pre-mission planning, integrated data architecture design, innovative training development and AI-assisted task load management, the gradual transition of medical care and decision making from terrestrial to space-based assets enabling support of astronaut health and performance and reducing overall mission risk is achievable.

Jay Lemery↗

Progressively Enabling Earth Independent Medical Operations (EIMO)

This panel presents the findings from a series of Technical Interchange Meetings (TIMs) hosted by the Exploration Medical Capability Element (ExMC) in NASA’s Human Research Program. The topics for the TIMs were derived from a 2-day conference of senior leaders and subject matters experts that collectively outlined a multi-faceted strategy designed to optimize crew health and performance through an increasingly autonomous medical approach. The first abstract in this panel outlines the scope of issues related to data collection, usage, transmission and computing capacity to facilitate EIMO. The second presentation provides an overview of the challenges in developing curricula and advanced training tools to baseline knowledge, skills and abilities (KSA), verify clinical competency and assure retention during prolonged durations inherent in exploration-class missions. An overview of the complicated medical supply and resource chain necessary to facilitate EIMO is provided in the third presentation of this panel. The final presentation in this EIMO panel surveys the breadth and depth of demands on cognitive load expected to be experienced by crew on an exploration mission and proposes strategies to mitigate the prospect of cognitive overload through methods to shift task load from the crew to multi-modal artificial intelligence based medical support systems. Taken together, these presentations summarize the challenges to be expected and potential solution spaces to be explored and developed to progressively enable increasing autonomous medical operations to support crewed missions beyond low earth orbit. Through EIMO focused pre-mission planning, integrated data architecture design, innovative training development and AI-assisted task load management, the gradual transition of medical care and decision making from terrestrial to space-based assets enabling support of astronaut health and performance and reducing overall mission risk is achievable.

John Lemery↗

Active Learning Surrogates for Integrating Electron Microscopy and Computational Insights from Simulations in Autonomous Experiments

Artificial Intelligence (AI) combined with simulations and experiments has great potential to accelerate scientific discovery across technology and pharmaceuticals. However, the gap between simulations and experiments is challenging due to disparities in time and scale, making it difficult to estimate properties like energy and electronic states from experiments, and to provide feedback based on theoretical insights.Our research addresses the challenge by developing unique deep kernel based surrogate models that learns from microscopic images, mapping structural features to energy differences from defect formation. We start with full-training using simulated images to determine optimal settings, establishing a baseline for active learning. Using these settings from the baseline, active learning is trained, and predicts structures along simulation trajectories based on uncertainty and energetic stability, thus reducing data requirements, simulation time and computational costs. The results demonstrate that the model achieves a low average error margin of approximately 0.03 meV, indicating good performance. To enhance feature extraction and reconstruction capabilities, we developed an autoencoder-decoder as additional surrogate to create latent space to capture essential features, enabling precise comparisons between simulations and experiments. The results from this model achieved a reconstruction loss of around 0.2 and accurately reconstructed molecular structures.Overall, this work advances the steering of experiments through computational simulations by employing a surrogate models that actively predicts the trajectories of structural evolution, achieving time-to-solution comparable to experimental measurements.

Saranathan, Gayathri [Hewlett-Packard]↗

Revolutionizing Energy Storage: AI, Automation, and Advanced Modeling as Catalysts for Next-Generation Breakthroughs

The Presidential Symposium (PRES) at the 2025 Fall Meeting, hosted by the President’s Office and Energy and Fuels Division, American Chemical Society (ACS) in Washington, DC, brought together a diverse group of chemists, engineers, and materials scientists working in battery materials & systems, automation and artificial intelligence from academia, industry, and national laboratories. The accelerating demand for high-performance, scalable, and sustainable energy storage has catalyzed a paradigm shift in how materials are dis-covered, devices are engineered, and systems are optimized. This Presidential Symposium, entitled “Revolutionizing Energy Storage: AI, Automation, and Advanced Modeling Driving Next-Gen Breakthroughs”, brings together global leaders to unveil transformative strategies anchored in the AAA framework: Artificial Intelligence, Automation, and Advanced Modeling. Artificial Intelligence is redefining the frontiers of energy storage by enabling predictive design, real-time optimization, and intelligent control across diverse chemistries and architectures. Automation is streamlining the synthesis, characterization, and testing of battery materials, dramatically accelerating innovation cycles and unlocking scalable solutions for grid and mobility applications. Advanced Modeling, spanning atomic to system-level scales, provides unprecedented insight into electrochemical dynamics, degradation pathways, and thermal behavior, particularly when coupled with physics-informed machine learning and digital twin technologies. Digital twins, in turn, leverage the AAA framework by integrating real-time data, physics-based models, and AI predictions into dynamic virtual replicas, enabling proactive diagnostics, optimization, and system resilience. Together, these synergistic pillars are not only re-shaping the scientific landscape but also forging a new era of reproducible, data-driven, and resilient energy storage innovation. In conclusion, this symposium marks a pivotal moment in the convergence of computational intelligence and experimental rigor, charting the course for next-generation breakthroughs in lithium-ion, solid-state, and flow battery technologies.

Artificial Intelligence (AI)↗

Responsible Adoption of Artificial Intelligence (AI) in Electric Grid Operations

The future of the grid will be powered by AI—or undermined by it. Artificial intelligence is rapidly reshaping grid operations, improving fault detection, forecasting accuracy, and real-time optimization. As AI systems move closer to operational decision loops, however, they introduce new consequence pathways: expanded attack surfaces, model integrity risks, regulatory exposure, and human-automation challenges. This talk presents a consequence-driven framework for deploying AI responsibly in the electric grid. Attendees will gain practical strategies to strengthen resilience, boost reliability, and deploy AI securely — ensuring the grid of the future is not only smarter but safer.

25 - ENERGY STORAGE↗

An Earth System Digital Twin for Flood Prediction and Analysis

An Earth System Digital Twin (ESDT) is a dynamic, interactive, digital replica of the state and temporal evolution of Earth systems. It integrates multiple models along with observation data, and connecting them with analysis, AI, and visualization tools. Together, these enable users to explore the current state of the Earth system, predict future conditions, and run hypothetical scenarios to understand how the system would evolve under various assumptions. The NASA’s Advanced Information Systems Technology (AIST)’s Integrated Digital Earth Analysis System (IDEAS) project is to establish an extensible architectural solution to develop digital twins of our physical environment for Earth Science. IDEAS delivers a formal system architecture with mechanisms for the outputs of one model to feed into others; for driving models with observation data; and for harmonizing observation data and model outputs for analysis. To validate and demonstrate the IDEAS architecture, this project collaborates with the Space Climate Observatory (SCO)’s FloodDAM project and the Centre National d’Etudes Spatiales (CNES) to focus on floods detection, prediction and their impacts.

Kettig, Peter↗

Harnessing the Power of AI: Status and Expansion of Current Domestic Transport Security Through Flexible Embedded Hardware

As applications of Artificial Intelligence (AI) continue to expand, there are increasing opportunities to leverage applied AI methodologies with mobile transportation focused embedded systems. Current applications of AI in transportation focus on a variety of areas, including fuel efficiency, safety, security, and other broad fields of optimization or detection. To leverage these AI workflows and methodologies in the field, teams must utilize complex embedded systems capable of implementing these AI-enabled algorithms in real-time. In this paper, we will investigate how these algorithms can be integrated into existing technologies leveraging vehicle data - such as the Controller Area Network Transport Security Tracking and Reporting Unit (C-STAR). The C-STAR technology is an embedded platform with onboard computation capable of running next generation algorithms in vehicle systems AI, such as preventative maintenance, driver authentication, and transport security. As deployed in the field, the C-STAR has a limited AI functionality –this paper will directly discuss how a device like C-STAR can be utilized and the advantages of integrating these new technologies. We will open with relevant background information and transportation projects that leverage AI, focusing specifically on those around transport security such as vehicle identification, anomaly detection, and deterrence. We will then extend this into potential opportunities and scaling for AI methodologies using platforms like the C-STAR. Finally, we will speak directly to the challenges of deploying AI-powered workflows, such as computing power needs, bandwidth, hallucinations, and other regulatory considerations.

Cook, Adian [ORNL] (ORCID:0000000160825395)↗

Demonstration and Evaluation of Explainable and Trustworthy Predictive Technology for Condition-based Maintenance

The domestic nuclear power plant (NPP) fleet has historically relied on labor-intensive and time-consuming predictive maintenance (PdM) programs, thus driving up operation and maintenance (O&M) costs to achieve high-capacity factors. Artificial intelligence (AI) and machine-learning (ML) can help simplify complex problems such as diagnosing equipment degradation to enable more effective decision-making efforts. The benefits of AI will be felt through more efficient plant O&M, improved work processes, and better integration of people and technology. Together, these benefits hold the promise to make nuclear power more sustainable by reducing O&M costs while improving employee engagement. While AI and ML technologies hold significant promise for the nuclear industry, there are challenges or barriers to their adoption. Explainability and trustworthiness of AI are two salient challenges that need to be addressed for wider deployment of these technologies in NPPs. This research focuses specifically on addressing the explainability and trustworthiness of AI technologies to advance the human, technical, and organization (HTO) readiness levels in adopting a risk-informed PdM strategy at commercial NPPs. In addition, this approach can be adapted to enhance the acceptability of AI in other nuclear applications with a few application-specific modifications. The technical approach ensuring wider adoption of AI technologies was developed by Idaho National Laboratory (INL)—in collaboration with Public Service Enterprise Group (PSEG), Nuclear, LLC—by utilizing the circulating water system (CWS) at two PSEG-owned plant sites for demonstration. Focused user studies were performed in collaboration with subject matter experts (SMEs) from PSEG and other nuclear domains to enhance human and organization readiness by building trust in AI-informed technologies. VIsualization for PrEdictive maintenance Recommendation (VIPER)—a Battelle Energy Alliance, LLC, copyrighted software—was developed and expanded to provide a user-centric visualization by incorporating inputs from the collaborating utility, human factors engineering guidelines, and data analysts. The VIPER software enables users, who may be unfamiliar with ML in general, to be interactively engaged by asking technical questions about PdM, work orders, diagnosis results and their confidence levels, the kind of data being used, and the types of ML algorithms employed. This interactive engagement enhances explainability and builds trust. One of the enabling accomplishments was the integration of large language models (LLMs), both text-based and vision-based, in the VIPER software.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Task-level robot programming: Integral part of evolution from teleoperation to autonomy

An explanation is presented of task-level robot programming and of how it differs from the usual interpretation of task planning for robotics. Most importantly, it is argued that the physical and mathematical basis of task-level robot programming provides inherently greater reliability than efforts to apply better known concepts from artificial intelligence (AI) to autonomous robotics. Finally, an architecture is presented that allows the integration of task-level robot programming within an evolutionary, redundant, and multi-modal framework that spans teleoperation to autonomy.

Reynolds, James C.↗

NeuDiff Agent: a governed AI workflow for single-crystal neutron crystallography

Large-scale facilities increasingly face analysis and reporting latency as a limiting step in scientific throughput, particularly for structural studies that require iterative reduction, integration, refinement and validation. To improve the time to result and analysis efficiency, NeuDiff Agent is introduced as a governed, tool-using AI workflow for TOPAZ at the Spallation Neutron Source. NeuDiff Agent takes instrument data through reduction, integration, refinement and validation to a validated crystal structure and a publication-ready CIF. NeuDiff Agent coordinates established crystallographic tools under explicit governance by restricting actions to allowlisted tools, enforcing fail-closed verification gates at key workflow boundaries, and capturing complete provenance for inspection, auditing and controlled replay. The present benchmark is limited to structural crystallography for periodic structures; magnetic structure analysis and incommensurate or superspace refinement are outside the scope of the current workflow. Performance is assessed using a fixed prompt protocol and repeated end-to-end runs with two large language model backends, with user and machine time partitioned and intervention burden and recovery behaviors quantified under gating. In a reference-case benchmark, NeuDiff Agent reduces wall time from 435 min (manual) to 86.5 ± 4.7 to 94.4 ± 3.5 min (4.6–5.0× faster) while producing a validated CIF with no checkCIF level A or B alerts. These results establish a practical route to deploy agentic AI in facility crystallography while preserving traceability and publication-facing validation requirements.

Xiao, Zhongcan [ORNL] (ORCID:0000000220761961)↗

AstraAI v1

AstraAI is an open-source, structure-aware AI coding agent designed for large scientific and DOE-HPC codebases such as AMReX-based applications. Unlike general-purpose coding assistants, AstraAI combines retrieval-augmented generation (RAG) with compiler-level Abstract Syntax Tree (AST) analysis to perform precise, scope-constrained code modifications. It identifies exact function spans, enforces locality of edits, and maintains cross-file invariants, enabling deterministic and build-safe transformations in complex C++/GPU environments. AstraAI is intended for developers working on large, evolving HPC frameworks where correctness, reproducibility, and structural integrity are critical. Typical use cases include modifying physics kernels, updating GPU device lambdas, and performing multi-file refactors without breaking compilation or runtime semantics. Compared to conventional LLM-based coding agents - even those with repository access - AstraAI provides structural guarantees rather than free-form text patches. It minimizes unintended diffs, prevents scope drift, preserves formatting and build stability, and reduces structural hallucinations. By integrating compiler tooling directly into the generation loop, AstraAI transforms AI-assisted coding from probabilistic text editing into deterministic, structure-preserving program transformation suitable for mission-critical scientific software.

Natarajan, Mahesh [Lawrence Berkeley National Labo↗

ORBIT-2 Dataset for Scaling Exascale Vision Foundation Models for Weather and Climate Downscaling

This dataset release corresponds to the work conducted in ORBIT-2: Scaling Exascale Vision Foundation Models for Weather and Climate Downscaling, where large-scale AI methods were applied to improve climate and weather resolution. The collection integrates four widely used, publicly available datasets: ERA5, PRISM, DAYMET, and IMERG. To prepare the data for ORBIT-2 model training and evaluation, we applied a preprocessing pipeline that generates paired low-resolution and high-resolution samples, enabling supervised downscaling experiments. The transformation from coarse to fine scales was performed using bilinear regridding, consistent with the procedures described in WeatherBench2, a community benchmark for weather and climate AI models. This dataset supports the development and evaluation of foundation models designed for weather and climate downscaling at exascale. Additional details on methodology and applications can be found in Wang et al., ORBIT-2 (arXiv:2505.04802, 2025).

54 ENVIRONMENTAL SCIENCES↗

Trust Not Verify? The Critical Need for Data Curation Standards in Materials Informatics

The importance of data curation has been recognized in multiple areas of research; however, the discussion of this important issue is only beginning to emerge in materials science. In this Perspective, we highlight the benefits of using the standardized data curation protocols in materials science and discuss current gaps in accurate and reproducible data reporting using case studies drawn from high-impact materials science papers and well-known databases such as the Crystallography Open Database (COD) and the Cambridge Structural Database (CSD). We argue that both experimental and computational materials scientists need to embrace a culture of rigorous data curation as part of modern research data management. We propose a sample data curation pipeline for materials chemistry and illustrate its use by creating two new materials chemistry databases. Here, we hope that this perspective will serve to catalyze further discussion and promote the continuous development of rigorous data curation practices within the materials science research community. We posit that adherence to best practices of data curation will promote and enhance the reliability, reproducibility, and integrity of materials research and enable the development of reliable AI and machine learning models that critically depend on the use of quality data.

Chemical structure↗

Engineering Privacy at the Edge: A Practical Guide to Differential Privacy in System Architectures

The rapid expansion of distributed and edge computing platforms—spanning autonomous vehicles, IoT sensors, and healthcare monitors—has heightened concerns about data privacy. Differential Privacy (DP) offers a rigorous mathematical framework to protect sensitive information while retaining analytical utility. This tutorial introduces the foundations of DP for both numerical and categorical datasets and extends the discussion to correlation-aware techniques tailored for structured and high-dimensional data. Hands-on demonstrations will begin with the PETINA (Privacy prEservaTIoN Algorithms) package for numerical data and continue with MIC-DP (Maximum Information Correlated Differential Privacy) for tabular data. Designed for researchers and practitioners in secure systems, embedded architectures, and AI accelerators, the tutorial emphasizes practical and scalable methods for integrating DP into real-world system designs.

Kotevska, Olivera [ORNL] (ORCID:0000000316772243)↗

AutoFocus: AI/ML-driven real-time wavefront diagnostics to autonomously align and optimize X-ray optics

We present an integrated system that combines advanced wavefront diagnostics with artificial intelligence (AI) to automate and optimize X-ray optics at synchrotron beamlines. This system couples real-time wavefront sensing with AI-driven control algorithms to achieve precise beam alignment, stabilization, and performance optimization. A key feature is the use of multi-fidelity transfer learning, which enables knowledge gained from both real-world beamline optimizations and ultra-realistic digital twin simulations to be effectively applied to in situ optimization. By leveraging multi-objective bayesian optimization, the system continuously refines its performance, reducing optimization time and minimizing the need for manual adjustments. Designed for seamless deployment, it operates with existing beamline hardware and provides an intuitive graphical interface. Initial deployments at the advanced photon source beamlines have demonstrated its ability to enhance beam stability, improve reproducibility, and significantly streamline alignment procedures. This AI-enhanced control framework represents a significant step toward fully autonomous beamline operation in next-generation synchrotron facilities.

Rebuffi, Luca [Argonne National Laboratory (ANL), ↗

An Ethics-Based Review of Generative Artificial Intelligence: Assuring Responsible Use (Version 1.0)

The rapid expansion of generative artificial intelligence (GenAI) has generated excitement regarding its potential benefits and concern over its ethical implications. Governments, corporations, and standards organizations have described ethical principles to direct GenAI's development and use; however, practical guidance for implementing these principles is limited. Addressing this gap is critical, especially considering the array of risks associated with GenAI, such as legal liabilities, privacy concerns, security threats, and potential misuse. Robust policies and procedures are critical to support responsible deployment of GenAI. This report examines Pacific Northwest National Laboratory (PNNL)’s approach to promoting responsible GenAI use. Proposed initiatives include developing policies based on ethical principles, creating a governance process to review projects relative to those principles, and implementing onboarding processes for training staff. The governance framework described in this report adapts the structure and principles of Institutional Review Boards (IRBs), traditionally used in human subjects research, for GenAI ethical review, providing oversight. Ethical principles guiding responsible GenAI usage include transparency and accountability, privacy, fairness, safety, security, and validity and reliability. To operationalize these principles, we propose forming a GenAI Assurance Council (GAC) that mirrors the IRB's structure. The GAC will evaluate GenAI projects across privacy, accountability, transparency, safety, security, fairness, and validity dimensions. Complementing policy and governance is AI literacy training to support staff understanding of GenAI's ethical implications. An initial training effort for AI Incubator Chat—a GenAI tool deployed at PNNL—showed promising results, underscoring the importance of clear guidelines and user accountability. Collaborative efforts and the dissemination of best practices are also discussed. The proposed GAC model and AI literacy training provide a blueprint for establishing ethical GenAI use and governance, offering practical tools to bridge the gap between ethical principles and real-world applications. The responsible integration of GenAI at PNNL entails a multifaceted approach involving policy development, ethical governance, and AI literacy training. The positive initial feedback and collaborative opportunities position PNNL to lead by example in GenAI's responsible use, reflecting a proactive stance in addressing the ethical, legal, and societal challenges associated with this emerging technology. PNNL's systematic and ethical approach to GenAI offers a model for other institutions to emulate, promoting safe and responsible technological advancements in the AI domain.

97 MATHEMATICS AND COMPUTING↗