Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “domain-specific languages”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Towards a Verifiable Domain-Specific Language for Hardware-Accelerated Stencils

Defining a domain-specific language (DSL) that supports vector-calculus abstractions eases the porting of partial differential equation (PDE) solvers to specialized architectures. Sufficiently high-level abstractions empower users to express universal laws with sufficient generality that the laws must always hold true within their domain of validity. A broad class of PDE solvers employs stencil-based algorithms, the target domain of Berkeley Lab's stencil accelerator chip co-design project. First released as open-source in January 2026, the Formal software framework lays a foundation for defining an embedded DSL based on composable operators that implement mimetic numerical methods -- stencil algorithms that guarantee satisfaction of discrete versions of important vector calculus theorems. The Formal DSL will be the frontend to a new class of stencil-PDE accelerators developed jointly by LBNL, UHCL, and UC Berkeley through the DOE Competitive Portfolios for Computer Science Project. This offers the potential of an order of magnitude acceleration for this important category of computational methods to serve the DOE mission. Future work on the Formal DSL will facilitate software verification via type-safe templates that enable problem-specific correctness proofs relying upon generic function theory and carefully crafted unit tests.

Rouson, Damian↗
DOE OSTI2025

Chemist: A Domain-Specific Language by Chemists for Chemists

Managing the complexity of quantum chemistry (QC) software is key to ensuring it remains accessible, maintainable, and reusable. Noticeably missing from the QC ecosystem are modules targeting bottleneck routines. Here we argue that this is likely due to the difficulty in defining interfaces for such modules. To that end, we introduce the open-source, publicly available Chemist library https://github.com/NWChemEx/Chemist. Chemist is a domain-specific language targeting the QC domain. Chemist has been developed focusing on performance and user-friendliness. Using Chemist, QC tasks are defined using familiar domain concepts such as molecules, wave functions, and operators. The domain objects are hierarchical to ensure a systematic encapsulation of information. Key features of Chemist include: extensibility, the ability to alias existing data, and the ability to succinctly define many common QC tasks. The usefulness of Chemist is demonstrated by discussing the interface of NWChemEx’s Fock build module and by showcasing a proof-of-concept self-consistent field algorithm containing uncertainty propagation.

Algorithms↗
DOE OSTI2026

Fortran mimetic abstraction language (Formal) v0.1.

The Fortran mimetic abstraction language ("Formal") is a domain-specific language (DSL) embedded in Fortran 202Y [1]. Formal provides novel software abstractions for simulating phenomena governed by the partial differential equations (PDEs) of vector and tensor calculus. Such equations model an extremely broad set of physical phenomena, ranging from atmospheric winds to light propagation. Formal's data structures and algorithms mimic in form and behavior continuous functions and operators. Formal supports these mathematical constructs using mimetic discretizations that define a discrete calculus satisfying various tensor calculus theorems, thereby ensuring high-fidelity representations of the physics being modeled. [2] Formal 0.1.0 also lays a foundation for the future use of Fortran 202Y type-safe templates to facilitate the formal verification of tensor contractions in computational physics and artificial intelligence [3]. [1] "Fortran 202Y" is Fortran standard committee's informal designation for the next Fortran revision, which will likely be "Fortran 2028". [2] Corbino, J. and Castillo, J. (2020) Journal of Computational and Applied Mathematics, https://doi.org/10.1016/j.cam.2019.06.042. [3] Haveraaen, M., Järvi, J., & Rouson, D. (2019). Reflecting on Generics for Fortran. https://j3-fortran.org/doc/year/19/19-188.pdf.

Rouson, Damian [Lawrence Berkeley National Laborat↗
DOE OSTI2025

Chemist

Chemist is a domain-specific language targeting the QC domain. Chemist has been developed focusing on performance and user-friendliness. Using Chemist, QC tasks are defined using familiar domain concepts such as molecules, wave functions, and operators. The domain objects are hierarchical to ensure a systematic encapsulation of information. Key features of Chemist include: extensibility, the ability to alias existing data, and the ability to succinctly define many common QC tasks.

Richard, Ryan [Ames Laboratory (AMES), Ames, IA (U↗
DOE OSTI2026

arco (Assembled Resource-Constrained Optimization) [SWR-26-030]

Arco (Assembled Resource-Constrained Optimization) is a memory-smart optimization DSL and solver for LP and MIP problems on constrained hardware. The software is an optimization framework built around a KDL-based domain-specific language and a CLI compiler/solver. You write optimization models in .kdl files, and the arco CLI compiles, validates, inspects, and solves them. Language bindings (Python today, more planned) provide programmatic access to the same engine. Built for harder optimization problems on constrained resources, Arco is intentional about every allocation, careful with stack and heap behavior, and relentless about minimizing memory usage so more systems can run real workloads. Arco is built primarily for internal use within our organization. You are welcome to try it, but we make no guarantees about API stability or robustness at this stage

Sanchez Perez, Pedro Andres [National Laboratory o↗
DOE OSTI2026

ToPolyAgent: AI agents for coarse-grained bead-spring topological polymer simulations

We introduce ToPolyAgent, a multi-agent AI framework for performing coarse-grained molecular dynamics (MD) simulations of topological polymers through natural language instructions. By integrating large language models (LLMs) with domain-specific computational tools, ToPolyAgent supports both interactive and autonomous simulation workflows across diverse polymer architectures, including linear, ring, brush, and star polymers, as well as dendrimers. The system consists of four LLM-powered agents: a Config Agent for generating initial polymer–solvent configurations, a Simulation Agent for executing LAMMPS-based MD simulations and conformational analyses, a Report Agent for compiling markdown reports, and a Workflow Agent for streamlined autonomous operations. Interactive mode incorporates user feedback loops for iterative refinements, while autonomous mode enables end-to-end task execution from detailed prompts. We demonstrate ToPolyAgent's versatility through case studies involving diverse polymer architectures under varying solvent conditions, thermostats, and simulation lengths. Furthermore, we highlight its potential as a research assistant by directing it to investigate the effect of interaction parameters on the linear polymer conformation, and the influence of grafting density on the persistence length of the brush polymer. By coupling natural language interfaces with rigorous simulation tools, ToPolyAgent lowers barriers to complex computational workflows and advances AI-driven materials discovery in polymer science. It lays the foundation for autonomous and extensible multi-agent scientific research ecosystems.

Ding, Lijie [Oak Ridge National Laboratory (ORNL),↗
DOE OSTI2025

Autogenerating a Domain-Specific Question-Answering Data Set from a Thermoelectric Materials Database to Enable High-Performing BERT Models

We present a method for autogenerating a large domain-specific question-answering (QA) dataset from a thermoelectric materials database. We show that a small language model, BERT, once fine-tuned on this automatically generated dataset of 99,757 QA pairs about thermoelectric materials, affords better performance in the field of thermoelectric materials compared to a BERT model fine-tuned on the generic English-language QA data set, SQuAD-v2. We further show that mixing the two data sets (ours and SQuAD-v2), which have significantly different syntactic and semantic scopes, allows the BERT model to achieve even better performance. The best-performing BERT model fine-tuned on the mixed data set outperforms the models fine-tuned on the other two data sets by scoring an exact match of 67.93% and an F1 score of 72.29% when evaluated on our test data set. This has important implications as it demonstrates the ability to realize high-performing small language models, with modest computational resources, empowered by domain-specific materials data sets which can be generated according to our method.

biological databases↗
DOE OSTI2025

Causal discovery from data assisted by large language models

Knowledge-driven discovery of novel materials necessitates the development of causal models for property emergence. While in the classical physical paradigm, the causal relationships are deduced based on physical principles or via experiment, the rapid accumulation of observational data necessitates learning causal relationships between dissimilar aspects of material structure and functionalities based on observations. For this, it is essential to integrate experimental data with prior domain knowledge. Here, we demonstrate this approach by combining high-resolution scanning transmission electron microscopy data with insights derived from large language models (LLMs). By applying ChatGPT to domain-specific literature, such as arXiv papers on ferroelectrics, and combining the obtained information with data-driven causal discovery, we construct adjacency matrices for directed acyclic graphs that map the causal relationships between structural, chemical, and polarization degrees of freedom in Sm-doped BiFeO 3 . This approach enables us to hypothesize how synthesis conditions influence material properties and guides experimental validation. Furthermore, the ultimate objective of this work is to develop a unified framework that integrates LLM-driven literature analysis with data-driven discovery, facilitating the precise engineering of ferroelectric materials by establishing clear connections between synthesis conditions and their resulting material properties.

Causal inference↗
DOE OSTI2026

Wolf

The Workflow Orchestration Language Framework (WOLF) is an agentic framework grounded in natural language with an architecture inspired by reinforcement learning (RL)—designed to orchestrate, scale, and accelerate complex workflows. The concept of WOLF was born out of the very successful ASC Tri-lab Multi-Agent Design Assistant (MADA) project, but extends beyond its domain-specific design agents to provide a more general and extensible architecture. WOLF capitalizes on the lessons learned from MADA and is fully aligned with Sutton’s The Bitter Lesson—that the most enduring progress in AI comes from general-purpose methods that scale with computation, rather than narrow techniques built on domain-specific human knowledge. In this spirit, WOLF enables agents to autonomously learn workflows, capture strategies as reusable playbooks, and build a growing corpus of interpretable, auditable “wisdom artifacts.” These artifacts, expressed in natural language, bridge human and machine understanding while preserving adaptability and scalability as computational power continues to expand.

Boureima, Ismaeal↗
DOE OSTI2025

Automation of Vulnerability and Patch Management: Information Extraction, Association, and Optimization

Vulnerability and patch management is an integral part of a robust cybersecurity program, yet it grows increasingly complex due to the sheer amount of data that must be analyzed. Particularly in Operational Technology (OT) environments, analysis must be done manually because of the lack of automated solutions. Additionally, there are many steps in this process, from the initial discovery of the vulnerability to the implementation of its remediation, and each step in the process requires different data in order to be performed effectively. In this work, we provide approaches and strategies to assist operators in industrial or OT environments throughout the vulnerability management cycle. Security advisories provide key information about mitigation strategies, or actions that can be taken when a patch is unavailable or cannot be installed. Details of these strategies are not shared in public vulnerability databases and must be found manually. We approach this problem by designing a solution to automatically identify that information within vendor security advisories and retrieve it for operator use. We start with an approach that requires domain-specific knowledge of certain frequently-seen reference websites. Next, an approach that can work on an arbitrary website but relies on certain keywords. Finally, an approach that uses Natural Language Processing (NLP) methods and does not require specific knowledge or keywords. Each of these approaches is more general than its predecessor; we demonstrate high accuracy for all approaches Advisories also often contain details of affected products in non-standard or natural language formats. While this information can be easily understood when read by an operator, the non-standard format acts as a barrier to effective automation. We provide an approach for the first step in this process: identifying vendors in security advisories and mapping them to a standard framework for representing digital assets and software products. We evaluate five established string similarity algorithms, plus one of our own design that combines string similarity and information theory, on the task of mapping vendors to their corresponding entries in the Common Platform Enumeration (CPE) repository. Our results show that our proposed metric outperforms all others. Due to the constraints on time, finances, and personnel for organizations, Large Language Models (LLMs) may seem like attractive opportunities for security operators to speed up information gathering; however, it is still not clear whether LLMs can handle vulnerability management tasks well. To answer this question, we perform an empirical study of LLMs’ ability to provide consistent, accurate information about vulnerabilities in order to guide organizations in their adoption of LLMs. We observe poor performance for all models tested, suggesting that these models are not well-suited to the consistent retrieval of accurate vulnerability information. Finally, once vulnerabilities have been identified and any additional information has been obtained, operators must decide which remediation actions to implement based on their available resources. This already-complex problem becomes even more so when we consider that a vulnerability may have multiple avenues for remediation. We formulate this scenario as two knapsack problems and provide solutions, which we then compare against several existing strategies for vulnerability prioritization seen in real operational environments.

McClanahan, Kylie↗
DOE OSTI2026

From Rules to Reasoning: A Survey of Large Language Model-Based Approaches to Scientific Hypothesis and Idea Generation

Scientific hypothesis generation represents a fundamental challenge in contemporary research due to exponentially expanding literature volumes and increasing disciplinary specialization. Large language models (LLMs) have emerged as transformative tools for automated scientific discovery, moving beyond traditional rule-based and literature-mining approaches. Four paradigmatic approaches define current LLM-driven hypothesis generation: direct prompting and fine-tuning methods, knowledge-enhanced frameworks integrating retrieval-augmented generation (RAG), multi-agent collaborative systems simulating research teams, and reasoning-focused approaches implementing cognitive architectures. Domain-specific applications demonstrate statistical equivalence to human expert performance in social psychology, experimental validation in biomedical research, and near-expert quality in astronomy. Evaluation methodologies encompass human expert assessment, LLM-as-judge frameworks, and comprehensive benchmarking systems. Technical challenges include hallucination management, knowledge integration limitations, and balancing novelty with feasibility. Future directions emphasize hybrid neural-symbolic architectures and sophisticated human-AI collaboration models for responsible scientific discovery acceleration.

AI-driven discovery↗
DOE OSTI2026

PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space

Background Protein language models (PLMs) have revolutionized protein fitness prediction, yet their application to rapidly evolving viral pathogens is often confounded by extreme sequence homology. This homology leads to “data leakage” in standard random validation splits, yielding inflated performance metrics that fail to translate into real-world biosurveillance utility. Results We present Protein Representation Inference for Mutation Evaluation (PRIME), a framework that integrates domain-specific fine-tuning with a rigorous position-stratified validation protocol to evaluate viral threats. Using a dataset of 347,432 SARS-CoV-2 receptor binding domain (RBD) sequences, we demonstrate that while random training data split yields deceptive R 2 values (> 0.90), they fail to generalize to novel mutational sites. By benchmarking models up to 650 M parameters, we show that domain-specific fine-tuning of the ESM-C 600 M model with correctly stratified data provides an initial demonstration of predictive signal for binding affinity and expression at unseen mutational sites of binding affinity and expression on unseen sites (R 2 ~0.23), a significant advancement over base foundation models which exhibit no predictive power (R 2 <0). PRIME’s embedding-based clustering identified 3.03% of bat coronavirus sequences as candidates for further experimental prioritization based on their functional similarity to human-infective strains in embedding space, offering a perspective complementary to traditional phylogenetic methods. Conclusion PRIME establishes a new benchmark for the application of PLMs in pathogen surveillance. Our findings demonstrate that state-of-the-art models and fine-tuning, when paired with stratified validation, provide biologically meaningful insights into pathogen evolution and zoonotic risk.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

HEPTAPOD: Orchestrating High Energy Physics Workflows Towards Autonomous Agency

Many workflows in high-energy-physics (HEP) stand to benefit from recent advances in transformer-based large language models (LLMs). While early applications of LLMs focused on text generation and code completion, modern LLMs now support orchestrated agency: the coordinated execution of complex, multi-step tasks through tool use, structured context, and iterative reasoning. We introduce the HEP Toolkit for Agentic Planning, Orchestration, and Deployment (HEPTAPOD), an orchestration framework designed to bring this emerging paradigm to HEP pipelines. The framework enables LLMs to interface with domain-specific tools, construct and manage simulation workflows, and assist in common utility and data analysis tasks through schema-validated operations and run-card-driven configuration. To demonstrate these capabilities, we consider a representative Beyond the Standard Model (BSM) Monte Carlo validation pipeline that spans model generation, event simulation, and downstream analysis within a unified, reproducible workflow. HEPTAPOD provides a structured and auditable layer between human researchers, LLMs, and computational infrastructure, establishing a foundation for transparent, human-in-the-loop systems.

Menzo, Tony [Alabama U.; Fermilab] (ORCID:00000002↗
DOE OSTI2025

LLMs for Mfg.—On the State of Large Language Models and Applications to Manufacturing

Additive Manufacturing (AM), referred to as 3D printing, has emerged as a key pillar of Industry 4.0 enabling layer-by-layer fabrication of intricate geometries from CAD models. In parallel, Large Language Models (LLMs), deep learning models for natural language generation trained on vast text corpora, have demonstrated unprecedented capabilities in understanding and generating human-like text. The convergence of these trends opens new opportunities at the intersection of AM and AI/ML, where LLMs can assist engineers and researchers in design, manufacture planning, and knowledge discovery. Recent academic work has begun to explore LLM applications in AM and adjacent fields, such as material science, mechanical engineering, and design for additive manufacturing. This exploration ranges from intelligent process planning to domain-specific knowledge retrieval. This survey provides a comprehensive review of current developments, focusing on peer-reviewed literature contributions that apply, adapt, and advance LLMs in general and domain-specific domains. We analyze state-of-the-art (SOTA) techniques, such as fine-tuning foundational models for specific domains, retrieval-augmented generation (RAG) pipelines, knowledge graph integration, and delve into the architectures and evaluation methods employed. The goal of this survey is to inform researchers and practitioners of the current capabilities and limitations of LLMs in general and in domain-specific applications, and to outline how these models are being tailored to meet the requirements of these applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

32 examples of LLM applications in materials science and chemistry: towards automation, assistants, agents, and accelerated scientific discovery

Abstract Large language models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 32 total projects developed during the second annual LLM hackathon for applications in materials science and chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Computer Science↗
DOE OSTI2025

Text Mining for Process–Structure–Properties Relationships in Metals

With the advent of large language models (LLMs), the vast unstructured text within millions of academic papers is increasingly accessible for materials discovery—although significant challenges remain. While LLMs offer promising few- and zero-shot learning capabilities, particularly valuable in the materials domain where expert annotations are scarce, general-purpose LLMs often fail to address key materials-specific queries without further adaptation. To bridge this gap, fine-tuning LLMs on human-labeled data is essential for effective structured knowledge extraction (Liu in The Importance of Human-Labeled Data in the Era of LLMs, 2023). Here, in this study, we introduce a novel annotation schema designed to extract generic process–structure–properties relationships from scientific literature. We demonstrate the utility of this approach using a dataset of 128 abstracts, with annotations drawn from two distinct domains: high-temperature materials (Domain I) and uncertainty quantification in simulating materials microstructure (Domain II). Initially, we developed a conditional random field (CRF) model based on MatBERT—a domain-specific BERT variant—and evaluated its performance on Domain I. Subsequently, we compared this model with a fine-tuned LLM (GPT-4o from OpenAI) under identical conditions. Our results indicate that fine-tuning LLMs can significantly improve entity extraction performance over the BERT-CRF baseline on Domain I. However, when additional examples from Domain II were incorporated, the performance of the BERT-CRF model became comparable to that of the GPT-4o model. These findings underscore the potential of our schema for structured knowledge extraction and highlight the complementary strengths of both modeling approaches.

Materials science↗
DOE OSTI2025

Intelligent Manufacturing Support: Specialized LLMs for Composite Material Processing and Equipment Operation

Engineering educational curriculum and standards cover many material and manufacturing options. However, engineers and designers are often unfamiliar with certain composite materials or manufacturing techniques. Large language models (LLMs) could potentially bridge the gap. Their capacity to store and retrieve data from large databases provides them with a breadth of knowledge across disciplines. However, their generalized knowledge base can lack targeted, industry-specific knowledge. To this end, we present two LLM-based applications based on the GPT-4 architecture: (1) The Composites Guide: a system that provides expert knowledge on composites material and connects users with research and industry professionals who can provide additional support and (2) The Equipment Assistant: a system that provides guidance for manufacturing tool operation and material characterization. By combining the knowledge of general AI models with industry-specific knowledge, both applications are intended to provide more meaningful information for engineers. In this paper, we discuss the development of the applications and evaluate it through a benchmark and two informal user studies. The benchmark analysis uses the Rouge and Bertscore metrics to evaluate our models’ performance against GPT-4o. The results show that GPT-4o and the proposed models perform similarly or better on the ROUGE and BERTScore metrics. The two user studies supplement this quantitative evaluation by asking experts to provide qualitative and open-ended feedback about our model’s performance on a set of domain-specific questions. The results of both studies highlight a potential for more detailed and specific responses with the Composites Guide and the Equipment Assistant.

Kapoor, Gunnika [Oak Ridge National Laboratory (OR↗