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At least 163 records · Page 9

All sources NASA NTRS DOE OSTI

DOE OSTI2025

Characterization of Gramicidin A in Triblock and Diblock Polymersomes and Hybrid Vesicles via Continuous Wave Electron Paramagnetic Resonance Spectroscopy

Studying membrane proteins in a native environment is crucial to understanding their structural and/or functional studies. Often, widely accepted mimetic systems have limitations that prevent the study of some membrane proteins. Micelles, bicelles, and liposomes are common biomimetic systems but have problems with membrane compatibility, limited lipid composition, and heterogeneity. To overcome these limitations, polymersomes and hybrid vesicles have become popular alternatives. Polymersomes form from amphiphilic triblock or diblock copolymers and are considered more robust than liposomes. Hybrid vesicles are a combination of lipids and block copolymers that form vesicles composed of a mixture of the two. These hybrid vesicles are appealing because they have the native lipid environment of bilayers but also the stability and customizability of polymersomes. Gramicidin A was incorporated into these polymersomes and characterized using continuous wave electron paramagnetic resonance (CW-EPR) and transmission electron microscopy (TEM). EPR spectroscopy is a powerful biophysical technique used to study the structure and dynamic properties of membrane proteins in their native environment. Spectroscopic studies of gramicidin A have been limited to liposomes; in this study, the membrane peptide is studied in both polymersomes and hybrid vesicles using CW-EPR spectroscopy. Lineshape analysis of spin-labeled gramicidin A revealed linewidth broadening, suggesting that the thicker polymersome membranes restrict the motion of the spin label more when compared to liposome membranes. Statement of Significance: Understanding membrane proteins’ structures and functions is critical in the study of many diseases. In order to study them in a native environment, membrane mimetics must be developed that can be suitable for obtaining superior biophysical data quality to characterize structural dynamics while maintaining their native functions and structures. Many currently widely accepted methods have limitations, such as a loss of native structure and function, heterogeneous vesicle formation, restricted lipid types for the vesicle formation for many proteins, and experimental artifacts, which leaves rooms for the development of new biomembrane mimetics. The triblock and diblock polymersomes and hybrid versicles utilized in this study may overcome these limitations and provide the stability and customizability of polymersomes, keeping the biocompatibility and functionality of liposomes for EPR studies of membrane proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗

NASA NTRS2022

Periodic Solar Wind Structures Observed in Measurements of Elemental and Ionic Composition in situ at L1

Mesoscale periodic structures observed in solar wind plasma serve as an important diagnostic tool for constraining the processes that govern the formation of the solar wind. These structures have been observed in situ and in remote data as fluctuations in proton and electron density. However, only two events of this type have been reported regarding the elemental and ionic composition. Composition measurements are especially important in gaining an understanding of the origin of the solar wind as the composition is frozen into the plasma at the Sun and does not evolve as it advects through the heliosphere. Here, we present the analysis of four events containing mesoscale periodic solar wind structure during which the Iron and Magnesium number density data, measured by the Solar Wind Ion Composition Spectrometer (SWICS)on board the Advanced Composition Explorer spacecraft, are validated at statistically significant count levels. We use a spectral analysis method specifically designed to extract periodic signals from astrophysical time series and apply it to the SWICS 12-minute native resolution dataset. We find variations in the relative abundance of elements with low first ionization potential, mass dependencies, and charge state during time intervals in which mesoscale periodic structures are observed. These variations are linked to temporal or spatial variations in solar source regions and put constraints on the solar wind formation mechanisms that produce them. Techniques presented here are relevant for future, higher-resolution studies of data from new instruments such as Solar Orbiter’s Heavy Ion Sensor.

Irena Gershkovich↗

NASA NTRS1993

XPS analysis of the effect of fillers on PTFE transfer film development in sliding contacts

The development of transfer films atop steel counterfaces in contact with unfilled and bronze-filled PTFE has been studied using X-ray photoelectron spectroscopy. The sliding apparatus was contained within the vacuum of the analytical system, so the effects of the native oxide, hydrocarbon, and adsorbed gaseous surface layers of the steel upon the PTFE transfer behavior could be studied in situ. For both the filled and the unfilled PTFE, cleaner surfaces promoted greater amounts of transfer. Metal fluorides, which formed at the transfer film/counterface interface, were found solely in cases where the native oxide had been removed to expose the metallic surface prior to sliding. These fluorides also were found at clean metal/PTFE interfaces formed in the absence of frictional contact. A fraction of these fluorides resulted from irradiation damage inherent in XPS analysis. PTFE transfer films were found to build up with repeated sliding passes, by a process in which strands of transfer filled in the remaining counterface area. Under these reported test conditions, the transfer process is not expected to continue atop previously deposited transfer films. The bronze-filled composite generated greater amounts of transfer than the unfilled PTFE. The results are discussed relative to the observed increase in wear resistance imparted to PTFE by a broad range of inorganic fillers.

Blanchet, T. A.↗

NASA NTRS2011

Land Surface Verification Toolkit (LVT) - A Generalized Framework for Land Surface Model Evaluation

Model evaluation and verification are key in improving the usage and applicability of simulation models for real-world applications. In this article, the development and capabilities of a formal system for land surface model evaluation called the Land surface Verification Toolkit (LVT) is described. LVT is designed to provide an integrated environment for systematic land model evaluation and facilitates a range of verification approaches and analysis capabilities. LVT operates across multiple temporal and spatial scales and employs a large suite of in-situ, remotely sensed and other model and reanalysis datasets in their native formats. In addition to the traditional accuracy-based measures, LVT also includes uncertainty and ensemble diagnostics, information theory measures, spatial similarity metrics and scale decomposition techniques that provide novel ways for performing diagnostic model evaluations. Though LVT was originally designed to support the land surface modeling and data assimilation framework known as the Land Information System (LIS), it also supports hydrological data products from other, non-LIS environments. In addition, the analysis of diagnostics from various computational subsystems of LIS including data assimilation, optimization and uncertainty estimation are supported within LVT. Together, LIS and LVT provide a robust end-to-end environment for enabling the concepts of model data fusion for hydrological applications. The evolving capabilities of LVT framework are expected to facilitate rapid model evaluation efforts and aid the definition and refinement of formal evaluation procedures for the land surface modeling community.

Kumar, Sujay V.↗

DOE OSTI2025

Single particle impact explorations on the role of powder heat treatments in cold spray: Effects of strength and oxide structure

In cold spray, the optimization of the powder feedstock for improving the final properties of the coating and for improving the process itself are two different objectives. This paper explores the latter, studying the relationship between powder pre-heat treatment and the kinetic bonding between the individual particles and the substrate. Using a laser-induced particle impact test (LIPIT), we investigate the effect of different heat treatments on the critical adhesion velocity of Al 6061. Although heat treatments change the strength of the powders as well as the thickness of the native oxide layer each by as much as ∼50 %, the critical adhesion velocity remains constant to within only ∼10 %. A deeper analysis reveals that these two factors change in somewhat complementary ways for the heat treatments explored here, leading to counteracting effects. By quantitatively evaluating these two microstructural factors in tandem, we find that they are roughly equally important in determining the critical adhesion velocity. These observations thus provide insight for the development of new heat treatment regimens that might lower the adhesion velocity.

Al 6061↗

DOE OSTI2020

Lithium oxidation and electrolyte decomposition at Li-metal/liquid electrolyte interfaces

In this work, we examine the evolution of events occurring when a Li metal surface is in contact with a 2 M solution of a Li salt in a solvent or mixture of solvents, via classical molecular dynamics simulations with a reactive force field allowing bond breaking and bond forming. The main events include Li oxidation and electrolyte reduction along with expansion of the Li surface layers forming a porous phase that is the basis for the formation of the solid-electrolyte interphase (SEI) components. Nucleation of the main SEI components (LiF, Li oxides, and some organics) is characterized. The analysis clearly reveals the details of these physical–chemical events as a function of time, during 20 nanoseconds. The effects of the chemistry of the electrolyte on Li oxidation and dissolution in the liquid electrolyte, and SEI nucleation and structure are identified by testing two salts: LiPF 6 and LiCF 3 SO 3 , and various solvents including ethers and carbonates and mixtures of them. The kinetics and thermodynamics of Li 6 F, the core nuclei in the LiF crystal, are studied by analysis of the MD trajectories, and via density functional theory calculations respectively. The SEI formed in this computational experiment is the “native” film that would form upon contact of the Li foil with the liquid electrolyte. As such, this work is the first in a series of computational experiments that will help elucidate the intricate interphase layer formed during battery cycling using metal anodes.

25 ENERGY STORAGE↗

NASA NTRS2013

Feasibility of a Networked Air Traffic Infrastructure Validation Environment for Advanced NextGen Concepts

Abstract-Next Generation Air Transportation System (NextGen) applications reliant upon aircraft data links such as Automatic Dependent Surveillance-Broadcast (ADS-B) offer a sweeping modernization of the National Airspace System (NAS), but the aviation stakeholder community has not yet established a positive business case for equipage and message content standards remain in flux. It is necessary to transition promising Air Traffic Management (ATM) Concepts of Operations (ConOps) from simulation environments to full-scale flight tests in order to validate user benefits and solidify message standards. However, flight tests are prohibitively expensive and message standards for Commercial-off-the-Shelf (COTS) systems cannot support many advanced ConOps. It is therefore proposed to simulate future aircraft surveillance and communications equipage and employ an existing commercial data link to exchange data during dedicated flight tests. This capability, referred to as the Networked Air Traffic Infrastructure Validation Environment (NATIVE), would emulate aircraft data links such as ADS-B using in-flight Internet and easily-installed test equipment. By utilizing low-cost equipment that is easy to install and certify for testing, advanced ATM ConOps can be validated, message content standards can be solidified, and new standards can be established through full-scale flight trials without necessary or expensive equipage or extensive flight test preparation. This paper presents results of a feasibility study of the NATIVE concept. To determine requirements, six NATIVE design configurations were developed for two NASA ConOps that rely on ADS-B. The performance characteristics of three existing in-flight Internet services were investigated to determine whether performance is adequate to support the concept. Next, a study of requisite hardware and software was conducted to examine whether and how the NATIVE concept might be realized. Finally, to determine a business case, economic factors were evaluated and a preliminary cost-benefit analysis was performed.

McCormack, Michael J.↗

NASA NTRSDate not supplied

Advancing xEMU Lunar Dust Mitigation Devices

Fine, electrically charged, glass like dust particles caused significant damage to the Apollo EMU9 during lunar EVAs, identified as one of the greatest challenges to future exploration. Passive Lunar Dust Mitigation Devices (LDMD) were developed, within a SBIR Phase II, to prohibit this dust from interrupting venting space suit component operation. A Computational Fluid-Dynamics and Discrete Element Method (CFD-DEM) Simulation Tool was developed at the University of Colorado, Boulder to predict venting gas flow ability to self-clean adhered dust particles from LDMD surfaces. Lunar dust properties (i.e., adhesion and cohesion strengths) required to complete Simulation Tool analysis are relatively unknown due to considerable differences between the Earth and the Moon (i.e., gravity, humidity) and due to an absence of dust particles in their native state. Analytically determining gas flow velocity, density and direction within the fluid Boundary Layer, microns from LDMD surfaces presented a second challenge. Dusty Plasma Chamber testing is being performed at Auburn University, Auburn to observe electrostatically charged dust behavior as it adheres to LDMD prototypes and specific geometry and is then blown away by metered gas flow. Test articles were developed to offer insight into the impact of different flow geometries, surface roughness and dust removal within the gas Boundary-Layer. Observed dust behavior is currently being developed to support the CFD-DEM analysis. Many Simulation Tool analytical cases have been processed to support the intention of completing sensitivity studies to assess how different dust adherence values and Boundary Layer fluid properties impact LDMD self-cleaning effectivity.

Thomas J Stapleton↗

NASA NTRS2009

A Survey of New Trends in Symbolic Execution for Software Testing and Analysis

Symbolic execution is a well-known program analysis technique which represents values of program inputs with symbolic values instead of concrete (initialized) data and executes the program by manipulating program expressions involving the symbolic values. Symbolic execution has been proposed over three decades ago but recently it has found renewed interest in the research community, due in part to the progress in decision procedures, availability of powerful computers and new algorithmic developments. We provide a survey of some of the new research trends in symbolic execution, with particular emphasis on applications to test generation and program analysis. We first describe an approach that handles complex programming constructs such as input data structures, arrays, as well as multi-threading. We follow with a discussion of abstraction techniques that can be used to limit the (possibly infinite) number of symbolic configurations that need to be analyzed for the symbolic execution of looping programs. Furthermore, we describe recent hybrid techniques that combine concrete and symbolic execution to overcome some of the inherent limitations of symbolic execution, such as handling native code or availability of decision procedures for the application domain. Finally, we give a short survey of interesting new applications, such as predictive testing, invariant inference, program repair, analysis of parallel numerical programs and differential symbolic execution.

Pasareanu, Corina S.↗

DOE OSTI2022

A catalytic dyad modulates conformational change in the CO 2 -fixing flavoenzyme 2-ketopropyl coenzyme M oxidoreductase/carboxylase

2-Ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is a member of the flavin and cysteine disulfide containing oxidoreductase family (DSOR) that catalyzes the unique reaction between atmospheric CO 2 and a ketone/enolate nucleophile to generate acetoacetate. However, the mechanism of this reaction is not well understood. Here, we present evidence that 2-KPCC, in contrast to the well-characterized DSOR enzyme glutathione reductase, undergoes conformational changes during catalysis. Using a suite of biophysical techniques including limited proteolysis, differential scanning fluorimetry, and native mass spectrometry in the presence of substrates and inhibitors, we observed conformational differences between different ligand-bound 2-KPCC species within the catalytic cycle. Analysis of site-specific amino acid variants indicated that 2-KPCC-defining residues, Phe501-His506, within the active site are important for transducing these ligand induced conformational changes. We propose that these conformational changes promote substrate discrimination between H + and CO 2 to favor the metabolically preferred carboxylation product, acetoacetate.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

EERC Final Topical Report – Findings on Subtask 3.2 – Produced Water Management Through Geologic Homogenization, Conditions, and Reuse

The Energy & Environmental Research Center (EERC) was awarded a contract by the North Dakota Industrial Commission (NDIC) Oil and Gas Research Program (NDIC No. G-051-101) to conduct a study on the recycling of water used in oil and gas operations, also known as produced water, from oil- and gas-producing regions of North Dakota as directed by Section 19 of North Dakota House Bill 1014. This final report provides a compilation of results of the study, which include regulatory, scientific, technological, and feasibility methods and considerations associated with North Dakota produced water management. The report provides a synopsis of this project’s previously submitted produced water assessment report entitled “Produced Water Management and Recycling Options in North Dakota” (Energy & Environmental Research Center, 2020), with updated values provided as appropriate. The report provides the results from the investigation of a novel produced water management strategy, referred to as geologic homogenization, conditioning, and reuse (GHCR), which aims to use a subsurface geologic formation as a natural medium for managing produced water recycling and reuse. Water management is a significant technical and economic challenge for sustainable oil and gas production, and water volumes are intrinsically linked to oil production volumes. North Dakota oil production rose to over 1.5 million barrels (MMbbl)/day in 2019, and despite a downturn in oil price in early 2020, North Dakota oil production has recovered to 1.1 MMbbl/day as of August 2021. Bakken petroleum system development between 2008 and 2020 has resulted in a nearly fourfold increase in produced water volumes to 642 MMbbl/yr in 2020 after peaking at 740 MMbbl/yr in 2019 and a fivefold increase in saltwater disposal (SWD) volumes to 565 MMbbl/yr in 2020 after a peak of 682 MMbbl/yr in 2019. Produced water and SWD volumes are forecasted to double by 2030. SWD is the primary method of produced water management used in North Dakota, with approximately 95% of the SWD volume occurring through subsurface injection into sandstones of the Dakota Group (Dakota). Localized pressurization of the Dakota resulting from SWD and projected increases in produced water volumes could impact the economics of North Dakota oil production. As a result, there is an emerging need to pursue alternative produced water management approaches, including recycling and reuse. While produced water recycling is not yet widespread, commercial operators are making strides in overcoming the technical challenges of using high salinity produced water in completion operations (Marathon Oil, 2020). As water management continues to be a key focal point in companies’ environmental, social, and governance (ESG) initiatives, focus on water management, including recycling, will likely continue to increase. Laboratory column testing, field sample collection, geologic modeling and numerical simulation, and techno-economic analysis all indicate that GHCR could feasibly be implemented as a potential water management option. Laboratory column testing and field sample collection indicate that the Inyan Kara sandstone and native formation fluid are capable of homogenizing with the Bakken produced water to a point where the fluid composition appears to stabilize. Extracting that stabilized fluid could be considered homogeneous and capable of providing individual batches of hydraulic fracturing fluid. Numerical simulation results indicate that extraction of fluids from the Inyan Kara in a GHCR implementation scenario is capable of reducing formation pressure, which would help ease localized pressurization of the Inyan Kara and extend the available capacity for nearby existing SWD wells. Economic analysis indicates that there are scenarios where GHCR implementation can be a competitive or even lower-cost option than a conventional water management approach. Site-specific conditions will dictate the economic potential of GHCR, but potentially attractive sites for GHCR implementation will be those that are located above a pressurized zone of the Inyan Kara, need six or more Bakken infill wells, and face high costs for conventional SWD and/or freshwater. Based on the regulatory review, drilling into the Inyan Kara for SWD and to harness as a source water for industrial use have precedent in North Dakota, and a workable regulatory solution for GHCR seems likely. However, restrictions in the state regarding surface storage and transport of produced fluids may limit some activities, which will affect how GHCR could ultimately be implemented. In summary, this study reveals pursuing GHCR can be a viable approach to water management in North Dakota. The GHCR concept addresses some of the challenges that hinder the more traditional approaches to recycling in the industry. Furthermore, an assessment of the current landscape of water management within the state reveals the ongoing trend of increasing volumes of produced water and SWD. Projections reveal that the volumes of produced water that need to be managed are expected to double over the next decade (Energy & Environmental Research Center, 2020). With the continued development of the Bakken and continuing driving factors related to ESG initiatives, implementing a practice such as GHCR is a feasible approach to adding recycling of produced water to industry within the state. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission Oil and Gas Research Program. References Energy & Environmental Research Center, 2020, Produced water management and recycling options in North Dakota: Final Report for North Dakota Legislative Management Energy Development and Transmission Committee and North Dakota Industrial Commission. Marathon Oil, 2020, Sustainability report: https://cdn.sanity.io/files/ghcnw9z2/website/ 91744eb6ef8fbe59505a911c6b8d2e8dd9a537fa.pdf?dl (accessed November 2021).

02 PETROLEUM↗

DOE OSTI2020

Biogenic Iron Sulfide Nanoparticles to Enable Extracellular Electron Uptake in Sulfate‐Reducing Bacteria

Abstract Microbes synthesize cell‐associated nanoparticles (NPs) and utilize their physicochemical properties to produce energy under unfavorable metabolic conditions. Iron sulfide (FeS) NPs are ubiquitous and are predominantly biosynthesized by sulfate‐reducing bacteria (SRB). However, the biological role of FeS NPs in SRB remains understudied. Now, conductive FeS NPs function is demonstrated as an electron conduit enabling Desulfovibrio vulgaris Hildenborough, an SRB strain, to utilize solid‐state electron donors via direct electron uptake. After forming FeS NPs on the cell surface, D. vulgaris initiated current generation coupled with sulfate reduction on electrodes poised at −0.4 V versus standard hydrogen electrode. Single‐cell activity analysis showed that the electron uptake and metabolic rate via FeS NPs in D. vulgaris were about sevenfold higher than those via native cell‐surface proteins in other SRB.

Deng, Xiao↗

DOE OSTI2020

Biogenic Iron Sulfide Nanoparticles to Enable Extracellular Electron Uptake in Sulfate‐Reducing Bacteria

Deng, Xiao↗

DOE OSTI2020

A glycoprotein B-neutralizing antibody structure at 2.8 Å uncovers a critical domain for herpesvirus fusion initiation

Members of the Herpesviridae, including the medically important alphaherpesvirus varicella-zoster virus (VZV), induce fusion of the virion envelope with cell membranes during entry, and between cells to form polykaryocytes in infected tissues. The conserved glycoproteins, gB, gH and gL, are the core functional proteins of the herpesvirus fusion complex. gB serves as the primary fusogen via its fusion loops, but functions for the remaining gB domains remain unexplained. As a pathway for biological discovery of domain function, our approach used structure-based analysis of the viral fusogen together with a neutralizing antibody. We report here a 2.8 Å cryogenic-electron microscopy structure of native gB recovered from VZV-infected cells, in complex with a human monoclonal antibody, 93k. This high-resolution structure guided targeted mutagenesis at the gB-93k interface, providing compelling evidence that a domain spatially distant from the gB fusion loops is critical for herpesvirus fusion, revealing a potential new target for antiviral therapies. Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

TRACE Input Modernization

This work presents a Tom’s Obvious Minimal Language (TOML)-based representation of input for the US Nuclear Regulatory Commission’s TRAC/RELAP Advanced Computational Engine (TRACE) thermal hydraulics code. Implemented using the Workbench Analysis Sequence Processor (WASP), the approach maps traditional TRACE input structures to a hierarchical format composed of named parameters, typed values, and native data collections. The resulting representation preserves TRACE’s existing modeling capabilities while providing a modern, structured interface for model development and management. WASP further extends TOML through a file import directive that supports modular model composition and reusable input organization. In addition, WASP provides extended array data entry convenience with various data repeat and interpolation capabilities. Examples of the new TOML syntax are provided for major TRACE input categories, including hydraulic components, heat structures, control systems, and trip logic. The TOML representation establishes a foundation for improved validation, tooling, automation, and model maintainability while remaining compatible with existing TRACE workflows. To facilitate migration to the TOML-based input format, the TRACE executable now supports conversion of native TRACE input into an intermediate JSON representation. A Python utility subsequently transforms the JSON data into an equivalent TOML model. Lastly, the TRACE executable now supports execution using TOML-formatted input.

Lefebvre, Robert A. [Oak Ridge National Laboratory↗

NASA NTRSDate not supplied

Exergy-based Sensitivity Analysis of the Generic Hypersonic Vehicle using FUN3D

In this paper, the implementation of an exergy-based objective function and its adjoint gradient into NASA’s FUN3D solver is discussed and verified. In order to verify that the exergy-based functional is properly implemented, it is used to predict the drag of the Generic Hypersonic Vehicle (GHV), which is then compared to more traditional force-based drag predictions. In addition to the functional implementation, FUN3D’s adjoint capability was extended to obtain sensitivities. Results were verified using FUN3D’s native complex step method for di↵erentiation using a generic wing configuration. The complex and adjoint gradients yielded discrete agreement demonstrating correct implementation and that the functional can be used for gradient-based multidisciplinary analysis and optimization. Next, various trade studies are conducted on the GHV to understand the design space of the vehicle. Finally, an inverse design problem is solved to verify the utilized design optimization framework which is ready to be deployed for exergy-based optimizations in future work.

Neal L. Novotny↗

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↗