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At least 127 records · Page 7

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DOE OSTI2026

Building MCP-native hierarchical AI scientist ecosystems: a perspective on scaling multi-agent scientific discovery

Large language models (LLMs) are evolving from chatbots with limited tool-using capabilities to agentic AI systems that can perform deep research, assist in proposing hypotheses, help design experiments, automate data analysis, and draft scientific reports. However, there are currently two bottlenecks limiting LLMs' real-world impact on the broader scientific research community beyond academic demonstrations: lack of interoperability (repetitive manual tool-integration is required across scenarios) and the need for scalable coordination (unstructured communication and memory become brittle as the number of agents grows). In this Perspective, we argue that the next phase of agentic scientific discovery requires the development of an ecosystem of protocol-native agents and tools organized through hierarchies inspired by human society, beyond the current paradigm of a single monolithic “AI scientist”. We use Model Context Protocol (MCP) as a concrete example of an emerging interoperability layer for scientific tool and context exchange, and we propose three complementary pathways to increase the scaling capabilities of an MCP-native scientific ecosystem by addressing the composability issues: (1) MCP servers for high-value scientific tools maintained by domain experts, (2) automated transformation of existing code repositories into MCP services, and (3) autonomous invention and evolution of new agents and workflows. Finally, we provide a practical roadmap for scaling AI-driven scientific discovery by expanding tool supply and coordination in MCP-native scientific ecosystems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

Applications of Multibody for Everybody (M4E) in Marine Energy

Multibody for Everybody (M4E) is an open-source symbolic dynamics modeling framework designed to automate the derivation of equations of motion and simulation of constrained multibody systems using the joint coordinate formulation.

16 TIDAL AND WAVE POWER↗

DOE OSTI2024

Oscilloscope Data Push Program

This paper details the development of a Python program designed to automate the data acquisition and conversion for an oscilloscope for the purposes of a one-off/temporary data acquisition system for users that readily need data, and do not have the option of obtaining a Data Acquisition (DAQ) solution. Creating DAQ systems for analyzing a system requires expensive electronics and a dedicated team of engineers for support. Traditionally, manual data collection and processing are time consuming and prone to error. By automating these processes, the cost, efficiency and accuracy of data handling are improved upon. This project involves the creation of a program that interacts with the oscilloscope. During this interaction, there are various functions being performed such as the acquisition of waveform data via floating points, generating plots with the acquired wave points, and storing of floating points in a CSV file format for future reference and plotting purposes. While the initial aim of the project included continuous logging to a cloud database, this was deferred due to time constraints. The results portrayed an almost-instant rate of data collection with a buffer time, showcasing the potential for further integration and real-time data processing.

Osei-Tutu, Jason↗

DOE OSTI2025

Designing Antifouling and Antimicrobial Interfaces: Structural Characterization using CryoEM, Automated Microscopy, and AI Image Segmentation

The design of functionalized surfaces for interactions with biological systems is critical across sectors such as healthcare, energy, and agriculture. Tailoring materials for specific applications, such as antifouling and antimicrobial surfaces, demands a comprehensive understanding of topology and chemistry across multiple length and time scales on both biological and materials systems. This work presents the development and characterization of nanostructured surfaces with controlled topographies and chemistries that enhance bacterial membrane disruption, reduce biofilm formation, and improve antimicrobial and antifouling capabilities. Two specific use cases will be presented - the use of cellulose nanocrystals (CNCs) for bacterial growth inhibition and the development of antifouling surfaces to prevent protein and bacterial adsorption [1-4]. By leveraging large language models (LLMs) for image segmentation and training [5], we enable automated analysis of terabyte-scale cryogenic electron microscopy (cryoEM) datasets. This analysis provides statistical insights into the biotic/abiotic interface and facilitates automated electron microscopy experiments to mitigate time and dose. The integration of cryogenic electron tomography (cryoET) and cryogenic focused ion beam (cryoFIB) milling enables high-resolution, near-native-state imaging and 3D reconstructions of bio/material interfaces [6]. Orthogonal characterization techniques and computational modeling further enhances our understanding, offering a robust platform for the design and optimization of next-generation functional surfaces [7].

Williams, Alexis [ORNL] (ORCID:0000000252835822)↗

DOE OSTI2023

A Multi-Dimensional Benefit Assessment of Automated Mobility Platforms (AMP) for Large Facilities: Mobility, Energy, Equity, and Facility Management & Design

The goal of the automated mobility platforms (AMPs) initiative is to raise the bar of service regarding equity and sustainability for public mobility systems that are crucial to large facilities, and doing so using electrified, energy efficient technology. Using airports as an example, the rapid growth in air travel demand has led to facility expansions and congested terminals, which directly impacts equity (e.g., increased challenges for Passengers with Reduced Mobility [PRMs]) and sustainability - both of which are important metrics often overlooked during the engineering design process. Therefore, to evaluate systems and inform critical near- and long-term decisions more effectively, a holistic evaluation framework is proposed focused on four key areas: (1) mobility, with emphasis on travel time and accessibility within an airport, (2) environment, focused on energy consumption and greenhouse gas (GHG) emissions associated with intra-airport mobility, (3) equity, specifically to the PRM community, but with an eye to the whole of society, and (4) built environment, or the fundamental changes in building design enabled by different mobility systems for larger and more flexible, functional, and energy-efficient structures. Below, AMPs are defined, and each metric is discussed further, all with a focus on airport mobility.

ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2023

Automated reactor physics analysis framework of High Flux Isotope Reactor low-enriched uranium silicide dispersion fuel designs

The High Flux Isotope Reactor (HFIR) is a versatile research reactor that provides one of the highest steady-state neutron fluxes of any reactor in the world. The HFIR reactor physics team investigated the conversion of the current 93 wt% highly enriched uranium U 3 O 8 -Al dispersion fuel to a 19.75% low-enriched uranium (LEU) U 3 Si 2 -Al dispersion fuel. The team continuously develops a Python module to streamline the analysis steps required for an LEU core design to ensure reproducible and agile design iteration. The Python module automates the data processing between analysis steps and automates the input perturbation for branch calculations and design changes. The automated framework has proven to significantly increase the efficiency and reproducibility of the reactor physics team to design High Flux Isotope Reactor (HFIR) LEU cores and thoroughly analyze performance metrics, safety metrics, and thermal safety margins. Consequently, the team can now respond rapidly to fuel fabrication engineer and thermal-hydraulic-structural analyst requests. Numerous combinations of LEU fuel designs are explored, of which two LEU fuel designs are presented here in this paper: a low density silicide design, and a high-density silicide design. Results show that both designs meet or exceed safety and performance metrics with exception for minor differences caused by the hardened spectrum from LEU.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2026

Optimal experimental design using eigenvalue-based criteria with Pyomo.DoE

New developments in automated optimal experimental design within the PSE+ software ecosystem. Advancements in user experience (to reduce the time taken to perform optimal experiment design) and computational capabilities (allowing more diverse experimental design) are shown with an example relevant to critical minerals and materials. Also, a small tutorial on science-based optimal experimental design and novel contributions therein are presented.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Evaluating pulse-shaping capabilities of next-generation pulsed power architectures

This project evaluated the pulse shaping capabilities of next-generation pulsed power (NGPP) architectures. NGPP architectures share several common attributes including multiple independent pulse-generation lines, a radial water-insulated impedance transformer, and a central vacuum insulated load region. A multi-module circuit model was developed, incorporating independent pulse-generation lines and a 2-D transmission line mesh of the radial impedance transformer to assess the effects of azimuthal asymmetry in pulse-shaped experiments. Circuit model simulations demonstrated that NGPP architectures are able to produce the the desired current pulse shapes for exemplar NGPP experiments. Additionally, the project explored automated methods for experiment design, including derivative -ree optimization and machine learning. Pulse-shaped experiments require designers to determine machine parameters that reliably produce the desired current pulse at the load, a process that typically relies on expert knowledge and iterative adjustments using the Z circuit model. Given the increased complexity of NGPP systems, this manual approach may be impractical. While the evaluated methods do not eliminate the need for manual iteration, they can reduce the time required for experiment design. Derivative-free optimization automates much of the trial-and-error process, providing a close starting point for manual adjustments or making small modifications to near-final designs. Meanwhile, deep neural network methods can generate a good qualitative match to the desired current pulse in under one second without requiring circuit model simulations.

42 ENGINEERING↗

DOE OSTI2024

3D high-fidelity automated neutronics guided optimization of fusion blanket designs

The compact Fusion Pilot Plant (FPP) is defined in the recent National Academies of Sciences, Engineering, and Medicine report as the next step of fusion energy demonstration with a $50$ MWe peak net electricity production, $Q_e$ greater than $1$, and at least $3$ hours of continuous operation. This fusion pilot plant will be a test bed enabling materials, designs, and fuel management assessment, and it will represent an engineering challenge because of its high-fusion power and compact design targets. Previous reactor data is limited to experiments operating in different design space ranges. Therefore, design iterations and assessments should rely on high-fidelity first-principle theoretical and computational models. The high-fidelity integrated modeling of the plasma is a fundamental part of fusion energy research. However, the whole device modeling is often neglected, utilizing low-fidelity, system-level analysis. Recently, the need for high-fidelity multi-physics modeling was recognized, resulting in a selection of integrated tools. Further, autonomous design optimization requires a streamlined framework that perturbs the design point, reruns the analysis, and examines the outputs. However, high-fidelity analysis requires complex geometry specification that is difficult to perturb. This work presents the parametric CAD generation tool TRACER and a new neutronic workflow. TRACER allows the perturbation of the geometry representation, creating geometry files ready for further analysis. The streamlined neutronic workflow allows efficient and accurate calculations. The two new tools coupled together were used to perform a 3D high-fidelity multi-objective, multi-input optimization of an "ARC Class" compact tokamak design. The workflow was driven by an optimization driver for full automation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

Compact automated apparatus for rapid astatine recovery from nitric acid media: Design, application, and impurity characterization

We report automation of irradiated bismuth target dissolution and astatine recovery from nitric acid media has been achieved at Texas A&M University. This process can be controlled remotely; it does not require any chemical treatment or evaporation of dissolution solution prior to the separation of above-mentioned elements on an extraction chromatography column, making the final product ready within 20 min. The accompanying radio-impurities have been identified and successfully separated from astatine, leading to greater than 99% radiopurity of the desired fractions. The system consists of only one pump and a set of LabVIEW controlled valves, and allows the connection of up to 10 different columns, providing the opportunity to prepare a variety of air dry columns, which can be different column geometries, containing astatine ready for further chemistry or shipment to desired facilities.

42 ENGINEERING↗

DOE OSTI2023

A Novel Spatial-Temporal Variational Quantum Circuit to Enable Deep Learning on NISQ Devices

Quantum computing presents a promising approach for machine learning with its capability for extremely parallel computation in high-dimension through superposition and entanglement. Despite its potential, existing quantum learning algorithms, such as Variational Quantum Circuits (VQCs), face challenges in handling more complex datasets, particularly those that are not linearly separable. What’s more, it encounters the deployability issue, making the learning models suffer a drastic accuracy drop after deploying them to the actual quantum devices. To overcome these limitations, this paper proposes a novel spatial-temporal design, namely “ST-VQC”, to integrate nonlinearity in quantum learning and improve the robustness of the learning model to noise. Specifically, ST-VQC can extract spatial features via a novel block-based encoding quantum sub-circuit coupled with a layer-wise computation quantum sub-circuit to enable temporal-wise deep learning. Additionally, a SWAP-Free physical circuit design is devised to improve robustness. These designs bring a number of hyperparameters. After a systematic analysis of the design space for each design component, an automated optimization framework is proposed to generate the ST-VQC quantum circuit. The proposed ST-VQC has been evaluated on two IBM quantum processors, ibm-cairo with 27 qubits and ibmq-lima with 7 qubits to assess its effectiveness. The results of the evaluation on the standard dataset for binary classification show that ST-VQC can achieve over 30% accuracy improvement compared with existing VQCs on actual quantum computers. Moreover, on a non-linear synthetic dataset, the STVQC outperforms a linear classifier by 27.9%, while the linear classifier using classical computing outperforms the existing VQC by 15.58%.

Li, Jinyang↗

DOE OSTI2021

Machine Learning Tools Set for Natural Gas Fuel Cell System Design

This study is focusing on leveraging the system design tools set for the next-generation solid oxide fuel cell (SOFC) based natural gas fuel cell (NGFC) system. Conventionally, system design and optimization of NGFC systems rely heavily on traditional reduced order model (ROM) techniques and designers’ experience level. For overcoming the technical barriers of system design, multiple multi-physics models and machine learning (ML) tools have been utilized to automate the conceptual design process and enhance the reliability of solutions for the NGFC system. The proposed tools set includes a physics-informed ML tool for automated ROM construction that leverages advances in deep neural networks to significantly reduce ROM prediction error for the NGFC power island compared to traditional approaches. The constructed physics-informed ML ROM can be used in system design, and optimization tools set Institute for the Design of Advanced Energy Systems (IDAES) Process Systems Engineering (PSE) framework. The tools set also provides a user-friendly graphic user interface built within Jupyter Notebooks, and the complete tools set is open-source public available.

Wang, Dewei↗

DOE OSTI2023

Demonstration of the Human and Technology Integration Guidance for the Design of Plant-Specific Advanced Automation and Data Visualization Techniques

Nuclear power continues to be a safe, reliable, and carbon-free electricity generating source for the United States, though the cost of operating and maintaining the current United States nuclear power plant fleet has become uncompetitive with other sources. This gap is attributed to the advent of new digital instrumentation and control technologies that other electricity generating industries are currently leveraging to streamline work and greatly reduce operating, maintenance, and support costs. Digital instrumentation and control systems and control room modernization offers significant opportunities to reduce operating and maintenance costs to ensure the continued operation of the existing United States light-water reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2023

Development of Automated Material Handling System with Alternate Gripper Designs for the Purpose of Increased Performance & Worker Safety

Savannah River National Laboratory’s (SRNL) Surplus Plutonium Disposition (SPD) Program leads the development and transition of automated unit operations for the processing of Plutonium oxide. A mixing can is opened, filled with material, mixed, set inside of a die can, and finally punched into compressed material. Replication of the process is constructed in A-area, where the mixing can weighs 1.6 kg (3.5 lbs.) and the compressed material weighs 4 kg (8.8 lbs.). Due to the constant process of Plutonium disposition, the fatigue on workers and worker dose accumulates quickly over time. SPD aims to automate this process by using a robotic arm to replace the hands-on worker. Automation will: Reduce worker radiation dose; Increase process throughout; Reduce costs for the disposition of Plutonium oxide.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2026

Stations Tool for Automated Permitting (S-TAP) User Manual

The Stations Tool for Automated Permitting (S-TAP) is a spreadsheet-based plan review questionnaire designed to help automate and expedite the electric vehicle supply equipment (EVSE) permitting process. This manual goes into detail on the development of the tool and guidance for use cases of the tool.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

UEMtomaton: A Source-Available Platform to Aid in Start-up of Ultrafast Electron Microscopy Labs

The steady rise in the number of ultrafast electron microscopy (UEM) labs, in addition to the opacity and lack of detailed descriptions of current approaches that would enable point-by-point construction, has created an opportunity for sharing common methods and instrumentation for (for example) automating data acquisition to assist in efficient lab start-up and to learn about common and robust protocols. In the spirit of open sharing of methods, we provide here a description of an entry-level method and user interface (UI) for automating UEM experiments, and we provide access to the source code and scripts (source-available) for ease of implementation or as a starting reference point for those entering or seeking to enter the field (https://github.com/CEMSFlannigan/UEMtomaton/releases/tag/v1.0). Core instrumentation and physical connections in the UEM lab at Minnesota are described. Interface communication schemes consisting of duo server-client pairs between critical components – the optical delay stage and the UEM digital camera – are presented, with emphasis placed on describing the logic and communications sequence designed to conduct automated series acquisitions. An application designed and programmed with C++/CLI as Windows Forms in Microsoft Visual Studio – dubbed UEMtomaton – is also presented. Key to the UI layout is centralization of the automation tasks and establishment of communication within the software rather than by interfacing with each individual workstation. It is our hope that this note provides useful insight for current and future UEM researchers, particularly with respect to generalizability and portability of the approach to emerging labs. Here, we note that while this basic, entry-level approach is certainly not the most sophisticated or comprehensive of those currently in use, we feel there is nevertheless value in clearly communicating a proven straightforward method to hopefully lower the barrier to entry into the field.

47 OTHER INSTRUMENTATION↗

DOE OSTI2025

Automated Construction of Artificial Lattice Structures with Designer Electronic States

Manipulating matter with a scanning tunneling microscope (STM) enables the creation of atomically defined artificial structures that host designer quantum states. However, the time-consuming nature of the manipulation process, coupled with the sensitivity of the STM tip, constrains the exploration of diverse configurations and limits the size of the designed features. In this study, we present a reinforcement learning (RL)-based framework for creating artificial structures by spatially manipulating carbon monoxide (CO) molecules on a copper substrate by using the STM tip. The automated workflow combines molecule detection and manipulation, employing deep-learning-based object detection to locate CO molecules and linear assignment algorithms to allocate these molecules to designated target sites. We initially perform molecule maneuvering based on randomized parameter sampling for sample bias, tunneling current set point, and manipulation speed. This data set is then structured into an action trajectory used to train an RL agent. The model is subsequently deployed on the STM for real-time fine-tuning of the manipulation parameters during structure construction. Our approach incorporates path-planning protocols coupled with active drift compensation to enable atomically precise fabrication of structures with significantly reduced human input while realizing larger-scale artificial lattices with the desired electronic properties. Furthermore, using our approach, we demonstrate the automated construction of an extended artificial graphene lattice and confirm the existence of a characteristic Dirac point in its electronic structure. Further challenges regarding the RL-based structural assembly scalability are discussed.

Algorithms↗

DOE OSTI2024

Self-driving laboratories to autonomously navigate the protein fitness landscape

Abstract Protein engineering has nearly limitless applications across chemistry, energy and medicine, but creating new proteins with improved or novel functions remains slow, labor-intensive and inefficient. Here we present the Self-driving Autonomous Machines for Protein Landscape Exploration (SAMPLE) platform for fully autonomous protein engineering. SAMPLE is driven by an intelligent agent that learns protein sequence–function relationships, designs new proteins and sends designs to a fully automated robotic system that experimentally tests the designed proteins and provides feedback to improve the agent’s understanding of the system. We deploy four SAMPLE agents with the goal of engineering glycoside hydrolase enzymes with enhanced thermal tolerance. Despite showing individual differences in their search behavior, all four agents quickly converge on thermostable enzymes. Self-driving laboratories automate and accelerate the scientific discovery process and hold great potential for the fields of protein engineering and synthetic biology.

Rapp, Jacob T. (ORCID:0000000226835204)↗