pnnl/chemreasoner
ChemReasoner - Catalyst Discovery via Large Language Model-driven Reasoning
Choudhury, Sutanay↗
SEARCH · Engineering Papers
Results for “model discovery”
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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Tactical Analysis for Calculating Contextual Risk at Boundaries: Summary of Laboratory Directed Research & Development Effort
The Tactical Analysis for Calculating Contextual Risk at Boundaries (TACCRAB) tool is an innovative digital twin (DT) platform and automated risk algorithm designed to transform operational decision-making in structured screening environments, with an initial focus on Southern Border Land Ports of Entry (POEs). The invention provides integration points for advanced artificial intelligence, predictive modeling, and real-time data analysis to produce a comprehensive risk management tool that enables proactive, data-informed security strategies. The core inventive features of TACCRAB center on its unique risk algorithm, which dynamically calculates contextual risk by synthesizing historical data, near real-time streaming data from the checkpoints themselves, and AI-generated predictions. Unlike traditional risk assessment methods, TACCRAB utilizes a DT to provide comprehensive operational insights, allowing stakeholders to visualize, simulate, and optimize checkpoint configurations with unprecedented speed and contextual awareness. TACCRAB's key innovation lies in its ability to combine multiple complex inputs - including technology detection probabilities, resource availability, screening pathway characteristics, and threat actor behavioral patterns - into a unified risk calculation and update these inputs based on changing operational and environmental conditions. By leveraging a DT that continuously updates and learns from linked data, TACCRAB can suggest adaptive mitigation strategies that minimize risk while maintaining operational efficiency. Particularly novel is the platform's approach to decision support, which goes beyond static risk assessment. The DT provides dynamic metrics such as wait times, resource allocation effectiveness, and potential emerging threat scenarios, enabling users to view sophisticated, relevant what-if simulations and optimize checkpoint operations in near real-time. The system's architecture allows for generalized application across different screening environments, such as secure facilities, ports of entry, and soft targets, making it a versatile tool for security and operational management. The invention distinguishes itself through its comprehensive integration of predictive modeling, AI-driven pattern discovery, and user-friendly interface design. By combining these elements, TACCRAB transforms complex risk data into actionable insights, supporting decision-makers at various organizational levels - from booth agents making split-second screening decisions to checkpoint managers optimizing the day's resource allocation to strategic planners managing long-term investments.
45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗
Quantum-Inspired Bayesian Sampling for Uncertainty Quantification and Machine Learning (Final Technical Report)
With increasing simulation and measurement data, machine learning and artificial intelligence have been widely used in computational decision-making of complex engineering systems. The resulting tools, such as uncertainty quantification solvers, reinforcement learning, and physics-informed machine learning, have achieved great success in critical DOE tasks such as material discovery and design, energy system modeling and control, and numerical weather and climate prediction. A core topic in scientific machine learning and artificial intelligence is Bayesian inference: given an observed data set, people want to estimate the posterior distribution of a (possibly large) number of hidden parameters. Due to the flexibility and weak assumptions, Bayesian sampling has been the mainstream Bayesian inference solvers despite the rapid progress of approximate Bayesian inference. Classical Bayesian sampling methods such as Markov-chain Monte Carlo suffer from a low-acceptance rate due to the random walk nature, therefore state-of-the-art techniques use Hamiltonian Monte Carlo and its variants to efficiently draw posterior samples in a high dimension. The key idea of Hamiltonian Monte Carlo and its variants is to simulate the Hamiltonian dynamics of a classical particle with a fixed mass, and their performance significantly degrades when the posterior distribution is highly spiky or has multiple modes. Leveraging the idea of quantum physics, this project has investigated new theory, algorithms and applications of Bayesian inference (especially Bayesian sampling). The main results include: (1) novel quantum-inspired Bayesian sampling methods that can lead to better accuracy for challenging multi-modal or spiky distributions, (2) more scalable machine learning framework leveraging tensor-compressed Bayesian inference, and (3) Bayesian and sampling approaches for verifying the robustness of continuous and binary neural networks.
97 MATHEMATICS AND COMPUTING↗
AI in Astrophysics: Tackling Domain Shift, Model Robustness and Uncertainty
Artificial Intelligence (AI) is revolutionizing physics research from probing the large-scale structure of the Universe to modeling subatomic interactions and fundamental forces. Yet, a major challenge persists: AI models trained on simulations or old experiment / astronomical survey often perform poorly when applied to new data exposing issues of dataset (domain) shift, model robustness, and uncertainty in predictions. This talk will introduce common challenges in applying AI across domains and present solutions based on domain adaptation a set of techniques designed to improve model generalization under domain shift. We will cover foundational ideas, practical strategies, and current research frontiers in this area. Through examples in astrophysics, we'll explore how domain adaptation can help bridge the gap between synthetic and real-world data, improve trust in model outputs, and advance scientific discovery.
Ciprijanvoic, Aleksandra [Fermilab] (ORCID:0000000↗
Beyond the Standard Model physics prospects at the Deep Underground Neutrino Experiment
The Deep Underground Neutrino Experiment (DUNE) is an international project for neutrino physics and proton-decay searches, currently in the design and planning stages. Once built, DUNE will consist of two detectors exposed to the world's most intense neutrino beam. The near detector at Fermilab will record neutrino interactions near the beginning of the beam line. The other, much larger, detector, comprising four 10-kton liquid argon time projection chambers (LArTPCs), will be installed at a depth of 1.5 km at the Sanford Underground Research Facility in South Dakota, about 1,300 km away from the neutrino source. The unique combination of the high-intensity neutrino beam, DUNE's high-resolution near detector system, and massive LArTPC far detector enables a variety of probes of Beyond-the-Standard-Model (BSM) physics, from the discovery of new particles (sterile neutrinos or dark matter), to precision tests of beyond the three-flavor mixing paradigm, non-standard neutrino interactions (NSIs), heavy neutral leptons, and the detailed study of rare processes (e.g., neutrino trident production). This article reviews these physics topics and discusses the prospects for their discovery at the DUNE experiment.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Interplay between Perovskite Magic-Sized Clusters and Amino Lead Halide Molecular Clusters
Recent progress has been made on the synthesis and characterization of metal halide perovskite magic-sized clusters (PMSCs) with ABX 3 composition ( A = C H 3 N H 3 + or Cs + , B = P b 2 + , and X = C l − , Br - , or I - ). However, their mechanism of growth and structure is still not well understood. In our effort to understand their structure and growth, we discovered that a new species can be formed without the CH 3 NH 3 + component, which we name as molecular clusters (MCs). Specifically, CH 3 NH 3 PbBr 3 PMSCs, with a characteristic absorption peak at 424 nm, are synthesized using PbBr 2 and CH 3 NH 3 Br as precursors and butylamine (BTYA) and valeric acid (VA) as ligands, while MCs, with an absorption peak at 402 nm, are synthesized using solely PbBr 2 and BTYA, without CH 3 NH 3 Br. Interestingly, PMSCs are converted spontaneously overtime into MCs. An isosbestic point in their electronic absorption spectra indicates a direct interplay between the PMSCs and MCs. Therefore, we suggest that the MCs are precursors to the PMSCs. From spectroscopic and extended X-ray absorption fine structure (EXAFS) results, we propose some tentative structural models for the MCs. The discovery of the MCs is critical to understanding the growth of PMSCs as well as larger perovskite quantum dots (PQDs) or nanocrystals (PNCs).
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
TOI-1338: TESS’ First Transiting Circumbinary Planet
We report the detection of the first circumbinary planet (CBP) found by Transiting Exoplanet Survey Satellite (TESS). The target, a known eclipsing binary, was observed in sectors 1 through 12 at 30 minute cadence and in sectors 4 through 12 at 2 minute cadence. It consists of two stars with masses of 1.1 M {sub ⊙} and 0.3 M {sub ⊙} on a slightly eccentric (0.16), 14.6 day orbit, producing prominent primary eclipses and shallow secondary eclipses. The planet has a radius of ∼6.9 R {sub ⊕} and was observed to make three transits across the primary star of roughly equal depths (∼0.2%) but different durations—a common signature of transiting CBPs. Its orbit is nearly circular (e ≈ 0.09) with an orbital period of 95.2 days. The orbital planes of the binary and the planet are aligned to within ∼1°. To obtain a complete solution for the system, we combined the TESS photometry with existing ground-based radial-velocity observations in a numerical photometric-dynamical model. The system demonstrates the discovery potential of TESS for CBPs and provides further understanding of the formation and evolution of planets orbiting close binary stars.
79 ASTRONOMY AND ASTROPHYSICS↗
Conjugation-based genome engineering enables rapid prototyping and bioproduction in non-model bacteria
Abstract Non-model bacteria offer unique metabolic capabilities for sustainable bioproduction, yet their limited genetic accessibility hinders systematic strain development. Here we present conjugation-based serine recombinase-assisted genome engineering (cSAGE), a broad-host-range platform that enables predictable, iterative genomic integration in transformation-resistant bacteria. cSAGE combines conjugative DNA delivery, standardized low-copy vectors, orthogonal recombinases, and modular genetic parts to support rapid pathway assembly and cross-host benchmarking. Using purple nonsulfur bacteria as a testbed, we integrate promoter engineering, multi-payload genome modification, and genome-scale metabolic modeling to empirically evaluate host-dependent pathway performance. Applying this workflow, we identify strain-specific differences in photosynthetic conversion of lignin-derived p -coumarate to the thermoplastic precursor p -vinylphenol. By enabling genome engineering and functional comparison across diverse bacteria using a single plasmid system, cSAGE provides a general framework for non-model strain prototyping and biotransformation discovery.
Guzman, Michael S. [Department of Chemical Enginee↗
Charge order and superconductivity in a two-band model for infinite-layer nickelates
The recent discovery of superconductivity in infinite-layer nickelates has drawn considerable attention; however, a consensus on the fundamental building blocks and common ingredients necessary to understand and describe their ground states and emergent properties is lacking. A series of experimental and theoretical studies have suggested that an effective two-band Hubbard model with Ni 3d x 2 -y 2 and rare-earth (R) 5d character may describe the low-energy physics. In this report we study the ground state properties of this two-band model on four-leg cylinders using the density-matrix renormalization group (DMRG) technique to better grasp whether such a simple model can embody the essential physics. A key difference compared to single-band Hubbard materials is that the system is self-doped: even at overall half-filling, the R-band acts as an electron reservoir, hole-doping the Ni-layer and fundamentally altering the physics expected from an undoped antiferromagnet. On the four-leg cylinder, the ground state is consistent with a Luttinger liquid, with anti-phase modulations of the charge density in the Ni- and R-layers having corresponding wavevectors that lock together. Light hole doping away from 1/2 filling releases the locking between the Ni and the R charge modulations, as the electron density in the R-band decreases and eventually becomes exhausted at a hole doping concentration that depends sensitively on the effective splitting between the Ni and the R orbitals. The ground state of the doped system is consistent with a Luther-Emery liquid, possessing quasi-long-range superconducting correlations in the Ni layer, similar to the single-band Hubbard model. Our results are consistent with experimental observations and may help to reveal the microscopic mechanism for pairing and other emergent properties.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
EnergyPlus Model Context Protocol Server (EnergyPlus-MCP) v0.1
EnergyPlus-MCP is the first open-source Model Context Protocol server specifically designed for EnergyPlus building energy simulation. This innovative software enables AI assistants and other applications to interact programmatically with EnergyPlus through a standardized, secure interface, eliminating traditional technical barriers in building energy modeling. The software provides specialized tools across five functional domains: server management, model configuration and loading, comprehensive building component inspection, systematic model modification, and simulation execution with results visualization. Key features include automated HVAC system discovery and topology mapping, advanced schedule analysis, intelligent model validation, and interactive visualization capabilities. EnergyPlus-MCP's layered architecture ensures robust separation between protocol communication and domain expertise, enabling scalable deployment across organizations, educational institutions, and research teams. Unlike direct LLM approaches that suffer from inconsistent results and security gaps, EnergyPlus-MCP provides validated, reliable interactions while maintaining scientific rigor. This democratizes sophisticated building energy analysis, making EnergyPlus accessible to broader audiences through conversational interfaces and streamlined workflows.
Li, Han [Lawrence Berkeley National Laboratory (LB↗
Turbulent field fluctuations in gyrokinetic and fluid plasmas
A key uncertainty in the design and development of magnetic confinement fusion energy reactors is predicting edge plasma turbulence. An essential step in overcoming this uncertainty is the validation in accuracy of reduced turbulent transport models. Drift-reduced Braginskii two-fluid theory is one such set of reduced equations that has for decades simulated boundary plasmas in experiment, but significant questions exist regarding its predictive ability. To this end, using a novel physics-informed deep learning framework, we demonstrate the first ever direct quantitative comparisons of turbulent field fluctuations between electrostatic two-fluid theory and electromagnetic gyrokinetic modelling with good overall agreement found in magnetized helical plasmas at low normalized pressure. This framework is readily adaptable to experimental and astrophysical environments, and presents a new technique for the numerical validation and discovery of reduced global plasma turbulence models.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Teaching AI when to care about gender
Natural Language Processing (NLP) is a branch of Artificial Intelligence (AI) concerned with solving language tasks by modeling large amounts of textual data. Some NLP techniques use word embeddings which are semantic models where machine learning (ML) is used to learn to cluster semantically related words by learning about word co-occurrences in the original training text. Unfortunately, these models tend to reflect or even exaggerate biases that are present in the training corpus. Here we describe the Word Embedding Navigator (WEN), which is a tool for exploring word embedding models. We examine a specific potential use case for this tool: interactive discovery and neutralization of gender bias in word embedding models, and compare this human-in-the-loop approach to reducing bias in word embeddings with a debiasing post-processing technique.
97 MATHEMATICS AND COMPUTING↗
Visual HPC Workflows for the Analysis of System Dynamics Models
Visual analytics supported by high performance computing (HPC) accelerates and enhances the discovery, exploration, and analysis of causal patterns in complex system dynamics (SD) models. We present a suite of visualization-assisted ensemble-based techniques for hypothesis generation and testing, and for sensitivity analysis. By employing HPC to provide parallel, on-demand simulation of SD models, one can “steer” an ensemble of simulated scenarios in real time as one first formulates and then informally tests those hypotheses: this provides rapid feedback for analysts to refine their understanding of the causal relationships emergent from a model. Such understandings can be followed and augmented by rigorous application of statistical methods, namely global variance-based sensitivity analysis, Monte-Carlo filtering, adaptive regional sensitivity analysis, and self-organized maps: here timely computation relies on HPC, while effective presentation emphasizes high-dimensional multivariate data visualization. Immersive visualization in virtual 3D environments provides an excellent adjunct to the traditional 2D graphics typically used for SD models, as it generates an embodied understanding of model behavior and facilitates an active, collaborative critique of model structure and output. Finally, we summarize prospects for HPC-enabled visual analytics applied to SD modeling.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
CHEMREASONER: Heuristic Search over a Large Language Model’s Knowledge Space using Quantum-Chemical Feedback
The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future. We introduce an AI-guided computational screening framework unifying linguistic reasoning with quantum-chemistry based feedback from 3D atomistic representations. Our approach formulates catalyst discovery as an uncertain environment where an agent actively searches for highly effective catalysts via the iterative combination of large language model (LLM)-derived hypotheses and atomistic graph neural network (GNN)-derived feedback. Identified catalysts in intermediate search steps undergo structural evaluation based on spatial orientation, reaction pathways, and stability. Scoring functions based on adsorption energies and barriers steer the exploration in the LLM's knowledge space toward energetically favorable, high-efficiency catalysts. We introduce planning methods that automatically guide the exploration without human input, providing competitive performance against expert-enumerated chemical descriptor-based implementations. By integrating language-guided reasoning with computational chemistry feedback, our work pioneers AI-accelerated, trustworthy catalyst discovery.
artificial intelligence↗
Flow matching meets biology and life science: a survey
Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions.
59 BASIC BIOLOGICAL SCIENCES↗
A critical examination of compound stability predictions from machine-learned formation energies
Machine learning has emerged as a novel tool for the efficient prediction of material properties, and claims have been made that machine-learned models for the formation energy of compounds can approach the accuracy of Density Functional Theory (DFT). The models tested in this work include five recently published compositional models, a baseline model using stoichiometry alone, and a structural model. By testing seven machine learning models for formation energy on stability predictions using the Materials Project database of DFT calculations for 85,014 unique chemical compositions, we show that while formation energies can indeed be predicted well, all compositional models perform poorly on predicting the stability of compounds, making them considerably less useful than DFT for the discovery and design of new solids. Most critically, in sparse chemical spaces where few stoichiometries have stable compounds, only the structural model is capable of efficiently detecting which materials are stable. The nonincremental improvement of structural models compared with compositional models is noteworthy and encourages the use of structural models for materials discovery, with the constraint that for any new composition, the ground-state structure is not known a priori. This work demonstrates that accurate predictions of formation energy do not imply accurate predictions of stability, emphasizing the importance of assessing model performance on stability predictions, for which we provide a set of publicly available tests.
36 MATERIALS SCIENCE↗
Exploration of lattice Hamiltonians for functional and structural discovery via Gaussian process-based exploration–exploitation
Statistical physics models ranging from simple lattice to complex quantum Hamiltonians are one of the mainstays of modern physics that have allowed both decades of scientific discovery and provided a universal framework to understand a broad range of phenomena from alloying to frustrated and phase separated materials to quantum systems. Traditionally, exploration of the phase diagrams corresponding to multidimensional parameter spaces of Hamiltonians was performed using a combination of basic physical principles, analytical approximations, and extensive numerical modeling. However, exploration of complex multidimensional parameter spaces is subject to the classic dimensionality problem, and the behaviors of interest concentrated on low dimensional manifolds remain undiscovered. Here, we demonstrate that a combination of exploration and exploration–exploitation with Gaussian process modeling and Bayesian optimization allows effective exploration of the parameter space for lattice Hamiltonians and effectively maps the regions at which specific macroscopic functionalities or local structures are maximized. We argue that this approach is general and can be further extended well beyond the lattice Hamiltonians to effectively explore the parameter space of more complex off-lattice and dynamic models.
42 ENGINEERING↗
Rapid discovery of high hardness multi-principal-element alloys using a generative adversarial network model
Multi-principal element alloys (MPEAs) continue to gain research prominence due to their promising high-temperature microstructural and mechanical properties. Recently, machine learning (ML) and materials informatics have been used extensively for screening MPEAs, however, most of these efforts were focused on constructing classification and regression models for predicting phase stability and mechanical properties of known compositions. These approaches may accelerate the screening process but optimizing new compositions with desirable properties within a practical time frame from an infinitely large design space of MPEA systems remains a grand challenge. To tackle this composition optimization challenge, a generative adversarial network coupled with a neural-network ML model was utilized to design MPEAs by filtering compositions that have high hardness. Even in a high-dimensional space with 18 elements as descriptors, the ML model was able to generate optimized compositions from which one composition was found to have 10% higher hardness (941 HV) than the maximum in the training data (857 HV). Density-functional theory was used to provide thermodynamic and electronic insights to higher hardness of the new MPEA found. The present work can optimize compositions from a wide design space of 18 elements (including W, Ta and Nb) that presents an opportunity to synthesize new compositions for applications ranging from corrosion-resistant alloys to nuclear materials. Here the findings suggest that generative ML can greatly accelerate materials discovery by identifying novel compositions, which can serve as a data-informed tool to guide experiments.
36 MATERIALS SCIENCE↗