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At least 487 records · Page 27

Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide–MHC Binding Predictions

The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell–based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2D b are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., Kd < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell–based vaccines.

60 APPLIED LIFE SCIENCES↗

Machine Learning on Heterogeneous, Edge, and Quantum Hardware for Particle Physics (ML-HEQUPP)

The next generation of particle physics experiments will face a new era of challenges in data acquisition, due to unprecedented data rates and volumes along with extreme environments and operational constraints. Harnessing this data for scientific discovery demands real-time inference and decision-making, intelligent data reduction, and efficient processing architectures beyond current capabilities. Crucial to the success of this experimental paradigm are several emerging technologies, such as artificial intelligence and machine learning (AI/ML) and silicon microelectronics, and the advent of quantum algorithms and processing. Their intersection includes areas of research such as low-power and low-latency devices for edge computing, heterogeneous accelerator systems, reconfigurable hardware, novel codesign and synthesis strategies, readout for cryogenic or high-radiation environments, and analog computing. This white paper presents a community-driven vision to identify and prioritize research and development opportunities in hardware-based ML systems and corresponding physics applications, contributing towards a successful transition to the new data frontier of fundamental science.

Gonski, Julia [SLAC]↗

Artificial Intelligence/Machine Learning Technology in Power System Applications

The primary purpose of this report is to provide an overview of the advancement in artificial intelligence and machine learning (AI/ML) technologies and their applications in power systems. It offers a foundation for understanding the transformative role of AI/ML in power systems and aims to stimulate further research and development in this area. This report begins with a historical perspective of AI/ML technologies, then explores their advancement to today’s prominence. The document highlights key contributors to the success of AI/ML technologies, including increased computational power, greater data availability, innovative algorithms, and advanced tools. It further introduces various AI/ML techniques, including supervised, unsupervised and reinforcement learning, graph neural networks, and generative AI. It also emphasizes the critical importance of ensuring the safety, security, and trustworthiness of these AI/ML techniques within this sector. The report reviews the recent representative advancements in various power system applications enhanced by AI/ML techniques, underscoring key developments and their transformative impact as evidenced by numerous studies. It also explores both the opportunities and challenges associated with the application of AI/ML technologies to improve power system applications. While the report extensively covers AI/ML applications in power systems, focusing primarily on the technical and operational aspects, it may not thoroughly explore the sociopolitical, economic, and broader regulatory implications of AI/ML integration in power systems. AI/ML techniques hold significant potential for enhancing power system applications; however, they are not omnipotent. It is crucial to acknowledge their limitations and understand that they may not be able to address all challenges in the power system domain. Various factors must be considered that influence the implementation, adoption, and effectiveness of AI/ML solutions, including but not limited to safety, security, transparency, and trustworthiness. Additionally, the incorporation of advanced human–machine interfaces is essential, as it enables humans to validate the effectiveness of AI/ML solutions while remaining actively engaged, fostering trust in AI/ML deployment. Finally, the report summarizes AI/ML research activities supported by the Department of Energy (DOE) Office of Electricity (OE) through the Advanced Grid Modeling (AGM) program. The work aligns with the interests and mission of DOE-OE AGM, with the report serving as a resource for identifying existing progress and for pinpointing future applications within AI/ML that need further exploration and support.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Artificial Intelligence for Autonomous Molecular Design: A Perspective

Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

A characterization of recombinant Arabidopsis FRIABLE1 (FRB1) reveals robust rhamnogalacturonan-I rhamnosyltransferase activity and critical catalytic residues

Plant cell walls are glycan-rich extracellular matrices that fundamentally impact essential cellular processes, such as growth, adhesion, and cell shape acquisition. Understanding plant cell wall glycans requires the identification and characterization of the biosynthetic enzymes that produce these polymers. Most successful in vitro protein expression studies of plant cell wall glycosyltransferases have relied on insect, fungal/yeast, or human cell expression systems, whereas prokaryotic expression systems have been generally unsuccessful. Here, we show that Arabidopsis FRIABLE1 (FRB1)/rhamnogalacturonan-I rhamnosyltransferase 8 (RRT8) can be produced in Escherichia coli RosettaGami2 cells as N-terminal maltose-binding protein fusion proteins containing C-terminal 6X-His-tags. We also report the catalytic constants of FRB1/RRT8 with apparent K M and K cat values of 226 μM and 33 min -1 for UDP-Rhamnose and 117 μM and 28.7 min -1 for rhamnogalacturonan-I (RG-I), respectively. We examine the catalytic activities of mutated FRB1/RRT8 proteins based on an AlphaFold 3-generated FRB1/RRT8 protein structural model with a virtually docked UDP-Rha donor. Enzymatic characterization of the mutated and wildtype FRB1/RRT8 protein confirmed that mutation of predicted catalytic site amino acid residues resulted in a 20-fold reduction in RRT activity. FRB1 also robustly polymerizes RG-I in combination with RG-I galacturonosyltransferase 1. These results show how a robust E. coli expression system combined with artificial intelligence tools can be used to increase understanding of plant cell wall glycosyltransferase structure and function.

glycosyltransferase↗

AI-Powered Knowledge Graphs for Neuromorphic and Energy-Efficient Computing

The surge in scientific literature obscures breakthroughs and hinders the discovery of new research paths. We propose an artificial intelligence (AI) powered framework using large language models (LLMs) and knowledge graphs (KGs) to automate parts of scientific discovery, focusing on energy-efficient AI circuits. Our hybrid approach combines LLMs, structured data, and ontology-based reasoning to construct a comprehensive knowledge graph that integrates insights across computational neuroscience, spiking neuron models, learning rules, architectural motifs, and neuromorphic device technologies. This multi-domain representation enables the generation of hypotheses that connect biological function with implementable, energy-efficient hardware architectures. Using KG embeddings and graph neural networks, the framework generates hypotheses for novel circuits, validates them through optimization on exascale HPC systems, and with tools like SuperNeuro and Fugu, the most promising designs will be prototyped in hardware. This open-source system aims to accelerate discoveries and bridging neuroscience with hardware innovation, drive collaboration, and unlock new opportunities in low-power AI computing.

Gautam, Ashish [ORNL]↗

Electric Grid Security (EGS) FY24 Annual Report

Sandia’s Electric Grid Security program advances a national vision of a secure, resilient, and affordable electric system for all users. Our achievements reflect a strategic approach combining technology development; modeling, simulation, and data analytics; and partnered demonstrations and outreach to further the adoption of advanced grid and storage technologies. Our FY24 efforts leverage the strengths of our partnerships—spanning Sandia’s core science and technology competencies as well as external technology leaders—to develop the solutions today which enable the grid of tomorrow. Key accomplishments in this report that support our strategy span our technical program areas and include: • The advancement of energy storage technologies, including creation of a national Long Duration Energy Storage Consortium; • Applications of artificial intelligence and machine learning to enhanced grid operations and planning; • Development of solid-state power conversion technologies and a new medium-voltage research lab; • New technologies to assess wildfire vulnerabilities and mitigate potential impacts; • Advanced applications of new cybersecurity technologies with industry partners; • Contributions to understanding the impacts of electromagnetic pulses and geomagnetic disturbances on grid components; and • Digital twin development for hybrid microgrids with multiple generators, storage, and loads.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A ModEx Framework for Watershed Subsurface Investigation With Limited Geophysical Data Using Machine Learning and Hydrologic Modeling

Abstract Subsurface heterogeneity influences watershed hydrology strongly but remains difficult to characterize at catchment scales with sparse and costly field data. Geophysical surveys such as electromagnetic induction (EMI) provide local spatial subsurface images yet scaling them to watershed scales and converting EMI‐derived resistivity into hydraulic properties remains a challenge. We present a Model–Experiment (ModEx) framework that integrates limited EMI data with machine learning (ML) and hydrologic modeling to improve process representation and guide field investigations. Sparse EMI surveys were scaled to the catchment scale using a Random Forest model, and the resulting resistivity fields were combined with nearby borehole constraints to parameterize a hydrologic model. The EMI‐informed hydrological simulations improved predictions of streamflow sustained by subsurface flow and shallow saturation patterns. By combining EMI data and ML with hydrologic modeling, the ModEx framework guides future subsurface surveys, providing a transferable and efficient strategy for data–model integration across diverse watersheds. Plain Language Summary Mapping the underground network of soil and rock that controls water is essential for predicting floods and droughts, but seeing underground is difficult and expensive. We cannot drill everywhere, so scientists use geophysical tools to scan broad areas. There are two key challenges: these geophysical scans are often sparse across the whole watershed, and the geophysical data is hard to translate into water‐related properties. We used artificial intelligence to solve these problems. We taught a computer to find patterns linking the limited geophysical data to the land surface properties. This allowed it to fill in the gaps and create a complete, useful subsurface map for the entire watershed. This new map improves hydrologic simulations, leading to more accurate predictions of water movement in the watershed. It also helps scientists build better models with less data and generates a priority map showing where to measure next, making future investigations more efficient. Key Points Limited EMI scaled with ML improves catchment‐scale subsurface parameterization for hydrologic models The framework integrates hydrologic modeling with limited geophysical data to support subsurface investigation design ModEx framework offers a transferable data–model integration strategy that quantifies and reduces uncertainty guiding watershed studies

Chen, Hang↗

Energy and AI: Evaluating Future Grid and Water Stress Due to Data Centers

Projections of the need for new data centers to support Artificial Intelligence (AI) are large but highly uncertain. Recent projections indicate up to a 15% annual growth rate in data center electricity demand within the next 5-10 years. Given that most electric utilities are required to have a reserve margin of roughly the same magnitude as the projected growth in demand, these new data center loads could soon threaten resource adequacy and reliability unless data centers build their own generation, interruptible loads are negotiated, commensurate new capacity and/or transmission is built, or some combination of these options. Similarly, depending on the cooling technology and geographic location of new data centers, they could threaten water adequacy in water scarce regions. This presentation highlights the grid and water implications of new data centers to support AI.

Mongird, Kendall (ORCID:0000000328077088)↗

Toward Intelligent Multimodal Holography for Real-Time Chemical Imaging of Dynamic Ion Separation

Molecular-level visualization of ion transport and separation dynamics in complex environments is crucial for advancing energy systems, water purification, and critical materials recovery. Achieving this requires imaging platforms that combine structural sensitivity, chemical specificity, and real-time operation. Digital off-axis holography (DOAH) provides high-throughput, label-free quantitative phase imaging but inherently lacks chemical selectivity. Integrating DOAH with complementary spectroscopic channels such as fluorescence or hyperspectral imaging introduces the needed molecular specificity, while also creating challenges in multimodal data fusion, synchronization, and computational throughput. Artificial intelligence offers a powerful route to address these limitations by uniting physics-based reconstruction with data-driven interpretation. In this Perspective, we outline a framework for intelligent multimodal holography and demonstrate its potential using a preliminary AI-driven test case. Raw DOAH holograms of lanthanide solutions subjected to magnetic field gradients were analyzed using multi-agent AI workflows that autonomously selected reconstruction tools, extracted NMF components, and generated scientific claims consistent with true paramagnetic and diamagnetic behavior. This demonstration shows how AI-enabled reasoning can deliver real-time chemical–structural interpretation directly from raw holograms. Together, these advances define a path toward adaptive, intelligent holography platforms capable of supporting in situ chemical separations, dynamic ion transport analysis, and next-generation interfacial science.

Ricchiuti, Giovanna↗

Unsupervised machine learning discovery of structural units and transformation pathways from imaging data

We show that unsupervised machine learning can be used to learn chemical transformation pathways from observational Scanning Transmission Electron Microscopy (STEM) data. To enable this analysis, we assumed the existence of atoms, a discreteness of atomic classes, and the presence of an explicit relationship between the observed STEM contrast and the presence of atomic units. With only these postulates, we developed a machine learning method leveraging a rotationally invariant variational autoencoder (VAE) that can identify the existing molecular fragments observed within a material. The approach encodes the information contained in STEM image sequences using a small number of latent variables, allowing the exploration of chemical transformation pathways by tracing the evolution of atoms in the latent space of the system. The results suggest that atomically resolved STEM data can be used to derive fundamental physical and chemical mechanisms involved, by providing encodings of the observed structures that act as bottom-up equivalents of structural order parameters. The approach also demonstrates the potential of variational (i.e., Bayesian) methods in the physical sciences and will stimulate the development of more sophisticated ways to encode physical constraints in the encoder–decoder architectures and generative physical laws and causal relationships in the latent space of VAEs.

97 MATHEMATICS AND COMPUTING↗

Topology optimization of an airfoil fin microchannel heat exchanger using artificial intelligence

High-performance microchannel heat exchangers are needed to supply heat for power conversion for nuclear microreactors. An airfoil fin microchannel design, constructed of Alloy 617 with helium as the working fluid, is analyzed and optimized using a design of experiments with artificial intelligence techniques. The use of airfoil fins offers the potential to reduce pressure drop across the heat exchanger, as compared to other types of channel configurations. A framework for topology optimization of airfoil fin printed circuit heat exchangers (PCHEs) has been developed that can be readily extended to different fin sizes and shapes, as well as different inlet and operating conditions, materials of construction, and working fluids. An optimization procedure is developed that employs computational fluid dynamics for a set of design points identified using Latin hypercube sampling. Computational fluid dynamics is used to analyze a simplified two-channel configuration where five design parameters are varied – inlet angle, fin scale, extent of staggering, transverse and longitudinal pitches. Two methods (a 5D polynomial and a regression neural network) are compared for generating surrogate models and the resulting response surface approximation is input to a genetic algorithm that is used to identify a set of optimal parameters. The optimal geometries are found across six channel Reynolds numbers ranging from 1000 to 5000, since inlet conditions affect flow through the heat exchanger. Additionally, a set of optimal designs that maximizes heat transfer and minimizes pressure drop is identified, and a thermal stress analysis is performed on the optimal design. Correlations for the Nusselt number and Darcy friction factor are developed that can be useful for thermal hydraulic analyses using system codes. Thermal stresses are analyzed and a brief discussion of the status of code cases of PCHEs for nuclear applications is given. Testing and thermomechanical modeling is needed to facilitate future code compliance of PCHEs for high pressure and high temperature applications.

42 ENGINEERING↗

2025 Workshop on Envisioning Frontiers in AI and Computing for Biological Research: Position Papers

This workshop aims to identify key research directions for transforming biology using artificial intelligence (AI), machine learning (ML) and computational methods to facilitate the discovery of new behaviors, mechanisms, and designs of biological processes relevant to DOE missions, underpinning a broader U.S. bioeconomy. By developing novel AI/ML technologies to analyze and interpret complex biological data, researchers can organize and simulate biological processes at various scales as well as advance predictive understanding and manipulation of biological systems. This integration of computation, experimentation, and next-generation experimental technologies can lead to discoveries in new biological behaviors and mechanisms relevant to DOE missions. The focus is on how advanced computational and mathematical methods can impact this mission by exploring digital twins, foundation models, automated laboratory experiments, modeling of complex living systems, and data-driven approaches for the biodesign of plants and microbial systems. While data management is important, it is not the primary focus of this workshop, which will assess the current state, trends, and AI/ML challenges at the interface between biology and computational science to identify opportunities for high-impact research at their intersection. The goal is to define research needs and opportunities that align with biological sciences, computational sciences, and applied mathematics research.

59 BASIC BIOLOGICAL SCIENCES↗

Geometric reasoning

Cognitive robot systems are ones in which sensing and representation occur, from which task plans and tactics are determined. Such a robot system accomplishes a task after being told what to do, but determines for itself how to do it. Cognition is required when the work environment is uncontrolled, when contingencies are prevalent, or when task complexity is large; it is useful in any robotic mission. A number of distinguishing features can be associated with cognitive robotics, and one emphasized here is the role of artificial intelligence in knowledge representation and in planning. While space telerobotics may elude some of the problems driving cognitive robotics, it shares many of the same demands, and it can be assumed that capabilities developed for cognitive robotics can be employed advantageously for telerobotics in general. The top level problem is task planning, and it is appropriate to introduce a hierarchical view of control. Presented with certain mission objectives, the system must generate plans (typically) at the strategic, tactical, and reflexive levels. The structure by which knowledge is used to construct and update these plans endows the system with its cognitive attributes, and with the ability to deal with contingencies, changes, unknowns, and so on. Issues of representation and reasoning which are absolutely fundamental to robot manipulation, decisions based upon geometry, are discussed here, not AI task planning per se.

Woodbury, R. F.↗

Quantum Neural Networks: Issues, Training, and Applications

Our work in the field aims at explaining the limitations and expressive power of Quantum Machine Learning models, as well as finding feasible training algorithms that could be implemented in near-term Quantum Computers. The promise of Quantum Machine Learning is that by incorporating quantum effects, such as entanglement, into machine learning models researchers can improve model performance and understand more complex datasets. This pledge is particularly pronounced in the design of Quantum neural networks (QNNs), a promising framework for creating quantum algorithms, that promise to outperform classical models by combining the speedups of quantum computation with the widespread successes of deep learning. We show that applying this approach alone to quantum deep learning is problematic given that an excess of entanglement between the hidden and visible layers can destroy the predictive power of our QNN models. We address the barren plateau problem by suggesting the use of a generative, unbounded, nonlinear loss function with simple gradients. The loss function quantifies how much the quantum states generated by the QNNs differ from the data and the goal during training is to minimize it. Finally, we showcase how to use generative training to construct a "classical-quantum" neural network to accurately interpolate between the ground states of a Molecular Hamiltonian, a central question in Quantum Chemistry.

97 MATHEMATICS AND COMPUTING↗

A critical review of existing and emerging technologies and systems to optimize solid waste management for feedstocks and energy conversion

Solid waste generation and its accumulation is increasing at an alarming pace due to population growth and urbanization posing severe risks to health, safety, and natural ecosystems. Herein this review strategically addresses the challenges and solutions to increasing the sustainability footprint of solid waste management (SWM) systems by revealing multipronged approaches that reduce solid waste and handling costs while generating revenue and reducing greenhouse gas and related emissions. For example, the United States sends ~150 million tons of waste to landfills, which is composed of over 75% organic and recyclable materials having a potential to be diverted to alternative scenarios. The emergence of an automated upstream and downstream sorting process for solid waste to increase material diversion from landfills is a promising approach for creating sustainable SWM. The utilization of artificial-intelligence-enabled smart and automated systems at the home and industrial scales, comprehensive public re-education including awareness of the adverse effects of landfilled waste on the ecosystem, and more eco-friendly product development are required to significantly reduce landfills and their negative footprint.

09 BIOMASS FUELS↗

Accelerating Traction Motor Optimization Design with AI Surrogate Models

The advancement of artificial intelligence systems enables the use of data-driven physics-based surrogate models to explore design spaces rapidly and deeply for engineering projects. This work presents a surrogate model workflow that accelerates electric traction motor design optimization by replacing finite element analysis (FEA) with an artificial neural network (ANN) and using this model in a genetic algorithm for design optimization. A baseline interior permanent-magnet motor is parameterized and sampled to generate FEA-labeled training data, after which a feed-forward ANN predicts key outputs (e.g., loss components and weight). The validated surrogate enables genetic-algorithm optimization and deep search over the design space without new FEA runs, producing Pareto-optimal trade-offs between weight and losses and set of optimized designs for rapid downselection of manufacturable motor designs.

Ribeiro, Pedro [ORNL] (ORCID:0009000921026641)↗

Visualization Techniques in Space and Atmospheric Sciences

Unprecedented volumes of data will be generated by research programs that investigate the Earth as a system and the origin of the universe, which will in turn require analysis and interpretation that will lead to meaningful scientific insight. Providing a widely distributed research community with the ability to access, manipulate, analyze, and visualize these complex, multidimensional data sets depends on a wide range of computer science and technology topics. Data storage and compression, data base management, computational methods and algorithms, artificial intelligence, telecommunications, and high-resolution display are just a few of the topics addressed. A unifying theme throughout the papers with regards to advanced data handling and visualization is the need for interactivity, speed, user-friendliness, and extensibility.

Szuszczewicz, E. P.↗