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DOE OSTI2026

Alchemy: A Model-Based Approach for 2D to 3D Autonomous Nuclear System Design

Engineering design of nuclear power plant (NPP) piping and equipment systems frequently bypasses crucial 2D system planning, instead moving straight to 3D modeling. This often leads to designs that exceed building envelope constraints, forcing expensive and time-consuming redesigns. When 2D modeling is employed, it typically involves labor-intensive manual workflows that convert 2D drawings into 3D models, resulting in inefficiencies and errors across design iterations. These workflows further suffer from poor software interoperability and dependence on proprietary software ecosystems, thereby contributing to schedule delays and cost overruns. This paper presents Alchemy, an autonomous framework that transforms 2D system definitions into Industry Foundation Classes (IFC)-compliant 3D building information models (BIMs) for expediting nuclear facility design at the conceptual preliminary phase. Using a model-based approach, the framework treats the 2D system diagram as the central reference model employed to automatically generate all subsequent outputs, ensuring consistency between the system definition and the resulting physical design. A web-based interface enables engineers to define hierarchical system topologies including associated equipment, geometric properties, and connectivity requirements. A two-phase equipment layout optimization algorithm automatically computes collision-free spatial configurations within predefined building envelopes. An artificial intelligence (AI)-assisted pipe routing module then generates orthogonal, collision-free routing paths, allowing the user to select either an A* search-based method or an Ant Colony Optimization (ACO)-based method. All outputs are authored natively in IFC format, relying on open-source technologies and standardized formats in order to ensure extensibility and eliminate proprietary software dependencies. The proposed framework is validated on two representative pressurized-water reactor (PWR)-based case studies, for which it autonomously generates IFC-compliant 3D models in minutes, drastically reducing workflows that typically require hours of manual effort. The generated model demonstrates topologically correct equipment placement, physically plausible spatial relationships, and collision-free pipe routing consistent with known PWR loop configurations. This work represents a foundational step toward digital engineering for nuclear facility preliminary design, with future ongoing development targeting design code compliance and expanded system complexity.

97 - MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Inorganic Alterations in Unconventional Shale Reservoirs: Importance of Additive and Base Fluid Chemistry

The effective development of unconventional petroleum systems requires the use of significant water resources. In an effort to reduce the consumption of freshwater resources for hydraulic fracturing, highly saline produced waters are increasingly recycled for use as a base fluid. However, there are significant knowledge gaps regarding potential water–rock interactions resulting from the introduction of produced waters and associated additives into shale reservoirs such as formation and deposition of mineral scale, which can negatively affect hydrocarbon production through wellbore restriction and damage to hydraulically generated fractures. To assess the impacts of field stimulation practices in the subsurface, a series of laboratory experiments were completed using (a) three distinct sedimentary rock formations of the Midland Basin (Texas, USA) and (b) additives with two different base fluids: municipal fresh water and clean brine. The experimental approach used relevant injection sequences and mixing ratios in specialized reactors for 3 weeks. Static pressurized experiments and nonpressurized time-resolved experiments were undertaken. The resulting solids and liquids were analyzed by using a variety of laboratory- and synchrotron-based techniques. The use of an acid spearhead (15% HCl) resulted in texturing of both clay-rich and calcareous shales, which can temporarily enhance porosity but subsequently result in mineral scale deposition. The primary matrix scale was Fe(III)-bearing phases, which occurred in all experiments regardless of base fluid chemistry. Additionally, strontium sulfate (SrSO 4 ) precipitated on shale surfaces when clean brines were used. It was concluded that clean brine was the main source of Sr 2+ species, while persulfate breaker degradation and oxidation of pyrite were the sources of SO 4 2– . Sulfate scaling was more pronounced in clay-rich shales, suggesting that Sr sorption is important for promoting celestite formation. This work demonstrates that mineral scale deposition is a complex phenomenon, whereby the type and proportions of various mineral phases are determined from reservoir alteration processes and coprecipitation of constituents from injection fluids. In conclusion, the experimental results shown here should be considered when evaluating different base fluids and additives in order to mitigate mineral precipitation in unconventional shale reservoirs, which could result in reservoir degradation.

Jew, Adam D. [SLAC National Accelerator Laboratory↗

DOE OSTI2025

In Situ Analysis of Electron-Induced Chemical Transformations in Vapor-Phase-Synthesized Al-Based Inorganic–Organic Hybrid Thin Films for EUV Resist Platform

The rapid advancement and stringent requirements of extreme ultraviolet (EUV) lithography technology necessitate the development of advanced photoresist systems for next-generation microelectronics. Recent studies have demonstrated that inorganic-based hybrid photoresists offer notable improvements in EUV sensitivity, etch resistance, and greater insusceptibility to pattern collapse compared to their purely organic counterparts. However, variations in the synthesis/coating approaches and chemistry of inorganic–organic photoresists can result in distinct exposure mechanisms. In this work, an Al-based hybrid thin film resist system synthesized via molecular (atomic) layer deposition (MLD or MALD) is explored, focusing on its electron-beam and EUV patterning mechanisms. The Al-based hybrid thin films are deposited using trimethylaluminum (TMA) and the organic precursor hydroquinone, exhibiting a saturated growth rate within the temperature range of 150–200°C. In diluted tetramethylammonium hydroxide (TMAH)-based developer solutions, the electron-irradiated Al-based hybrid thin film system behaves as a negative tone resist, achieving a sensitivity of 10.4 mC/cm 2 at 0.1 kV electron beam lithography (EBL). Chemical changes induced by electron exposure are also analyzed in this study using X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and a unique infrared spectroscopy setup, revealing the potential cross-linking pathways. To further correlate the electron-induced chemical transformations with those mediated by EUV irradiations, a combination of X-ray photoemission electron microscopy/low-energy electron microscopy (XPEEM/LEEM) system is also employed. In conclusion, this study provides critical insights into the mechanisms underlying solubility switching and contributes to the design of advanced resist materials for EUV lithography.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Cell-Free-Based Thermophilic Biocatalyst for the Synthesis of Amino Acids from One-Carbon Feedstocks

Bioproduction from one-carbon compounds, such as formate, is an attractive prospect due to reduced energy requirements and the possibility for using CO 2 as a sustainable feedstock. Formate-fixing pathways engineered using Escherichia coli lysate-based cell-free expression (CFE) biocatalysts have the potential to route 100% of feedstock carbon toward chemical synthesis but are undermined by siphoning of in-pathway metabolites and cofactors by the CFE background metabolism. To address this limitation, we engineer a CFE-based thermophilic multienzyme biocatalyst for the synthesis of serine and glycine from formate, bicarbonate, and ammonia. After expression of the thermophilic formate-to-serine pathway in a one-pot reaction, the mesophilic E. coli CFE background machinery is removed by simple heat denaturation, eliminating the siphoning of cofactors, inpathway metabolites, and products. After bioprocess optimization, including pathway gene expression duration and chemical synthesis temperature, we achieve near stoichiometric conversion of formate and bicarbonate to serine and glycine, reaching 97% of stoichiometric yield. The use of a moderately thermophilic biocatalyst allowed chemical synthesis to take place at mesophilic temperatures, enabling the balance of optimal enzyme activity with minimal metabolite/cofactor thermal degradation. In a fed-batch experiment, the biocatalyst shows sustained chemical synthesis rates for 8 h, paving the way toward a continuous bioprocess. Finally, a sensitivity analysis of cofactor usage revealed that the most expensive cofactors, THF and NADPH, can be reduced by 5-fold without significantly lowering product yields. To the best of our knowledge, this is the first instance of expressing a thermophilic pathway in an E. coli lysate-based CFE system to generate a thermophilic biocatalyst for use at mesophilic temperatures. The CFEbased thermophilic formate-to-serine biocatalyst triples the combined serine and glycine yield previously obtained by a CFE-based mesophilic formate-to-serine biocatalyst (30%), and quadruple the yield obtained by a purified enzyme system (22%). Ultimately, this work opens the door to using E. coli lysate-based CFE for thermophilic biocatalyst generation to achieve high chemical synthesis yields.

bacteria↗

DOE OSTI2025

Development of an ERT‐Based Framework for Bentonite Buffers Monitoring From Laboratory Tests: 2. Quantitative Moisture Dynamics Estimation Model

Abstract The long‐term containment of high‐level radioactive waste in geological disposal repositories relies on Engineered Barrier Systems (EBS), with bentonite clay emerging as a candidate material due to its unique properties. Understanding moisture dynamics within bentonite buffers is crucial for EBS performance, as it directly influences the material's swelling capacity, thermal and hydraulic conductivity, mechanical properties, and long‐term evolution under complex thermal‐hydrological‐mechanical (THM) processes. This study develops an advanced Electrical Resistivity Tomography (ERT)‐based framework to quantitatively monitor moisture dynamics under THM conditions. Our framework extends the Waxman‐Smits model to incorporate the coupled effects of temperature, water content, fluid chemistry, and mechanical changes on bentonite's electrical properties. Utilizing HotBENT‐Lab data from our companion paper, which includes electrical conductivity, CT density, and thermocouple measurements, this study offers a novel methodological framework bridging different scales of the model. Our results show that the extended model can estimate water content from ERT data, capturing spatial and temporal variations in moisture distribution within bentonite columns. However, the model tends to overestimate water content compared to CT density‐derived measurements. We address this discrepancy by incorporating a simplified swelling effect model, which improves agreement between ERT and CT density‐based water content estimates. We also discuss model limitations, including simplified treatment of swelling and micropore effects, and propose a conceptual framework for transitioning from laboratory to field applications, addressing challenges such as parameter scalability, field validation methods, and integration of diverse data sources. This ERT‐based framework can potentially advance real‐world moisture monitoring of bentonite‐based EBS in nuclear waste repositories. Plain Language Summary Safely containing high‐level radioactive waste depends on barriers made from materials like bentonite clay, which is effective because it swells and seals in the waste. To ensure these barriers work well over time, it's important to understand how moisture moves through the clay. Our study developed a new method using ERT to monitor moisture levels in bentonite under conditions that mimic those in actual storage sites, including changes in temperature, water content, and mechanical stress. This study improved an existing model to better account for how these factors affect the clay, allowing us to create more accurate moisture maps. Initially, the proposed model overestimated the amount of water in the clay, but its accuracy was improved by factoring in how the clay swells when wet. This study also identified some limitations of the model and suggested ways to adapt it for use in real‐world waste storage sites. This new approach could lead to better monitoring and safety checks for nuclear waste storage systems, helping to ensure long‐term containment. Key Points This work develops an ERT‐based framework extending the Waxman‐Smits model to monitor bentonite moisture dynamics during coupled THM processes The extended model accurately estimates water content from Electrical Resistivity Tomography data, incorporating swelling effects to improve precision This work proposes a conceptual framework for transitioning from laboratory to field applications, advancing EBS monitoring in nuclear waste repositories

Chen, Hang↗

DOE OSTI2025

Exploring the Use of Non‐Invasive Drone‐Based Ground‐Penetrating Radar (GPR) to Characterize Biogenic Gas Dynamics in Subtropical Peat Soils

Peat soils are a critical component of the global carbon cycle as natural producers of biogenic greenhouse gases (e.g., methane and carbon dioxide) that accumulate within the soil and are released to the atmosphere. Previous studies have showed the ability of ground-based minimally-invasive geophysical methods such as ground-penetrating radar (GPR) to characterize carbon dynamics in peat soils. However, ground-based GPR is limited by scale of measurement and soil disturbance potentially altering gas releases during deployment. Here, we explore the potential of drone-based GPR for identification of hot spots and hot moments of gas accumulation and release in subtropical soils. Here, we collected drone-based GPR data sets across two grids (∼17,500 m 2 ) in the Everglades during January (dry season), September, and November (wet season) of 2023 to characterize peat thickness and seasonal variability of gas content. Results show that drone-based GPR is effective and efficient for: (a) capturing the temporal variation of in situ biogenic gas content in peat soils with changes between 1% and 25 % volumetric gas content over repeatable grids; (b) inferring a total peat thickness between 0.8 and 1.2 m; and (c) estimating flux releases of 63 and 135 mg CH 4 m −2 day −1 for specific locations and periods that are strikingly consistent with our coincident gas trap measurements. This work also indicates that (a) spatial distribution of gas content in the Everglades is strongly controlled by landscape morphology such as ridges and sloughs and (b) the temporal variation of gas content is seasonal with increased gas production during the wet season.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Hole transport layer selection for stable and efficient carbon electrode-based perovskite solar cells

Perovskite solar cell (PSC) technology has achieved remarkable progress, with champion power conversion efficiencies (PCE) exceeding 26%. However, the long-term stability of PSCs remains a significant barrier to their widespread commercialization. Carbon-based PSCs (C-PSCs) have gained attention as a promising cost-effective and scalable production solution, replacing expensive metal electrodes and offering improved stability. Despite these advantages, C-PSCs face challenges in matching the performance of noble metal-based PSCs, particularly in terms of carrier extraction efficiency and reduced carrier recombination at the carbon/perovskite interface. The selection of hole transport materials (HTMs) is crucial for optimizing this interface, but comprehensive studies on HTM selection for C-PSCs are limited. This study systematically investigated three commonly used hole transport layers (HTLs): Spiro-OMeTAD, CuSCN, and PTAA. Our results show that Spiro-OMeTAD-based C-PSCs exhibit the best overall performance, achieving a PCE of 19.29%. CuSCN-based devices, while lower in efficiency (11.94% PCE), demonstrated superior stability, retaining approximately 60% of their initial performance after 500 hours under ambient conditions. PTAA-based devices achieved a PCE of 12.92% but exhibited significant degradation, maintaining only ∼35% of their original efficiency over the same duration. These findings highlight the importance of selecting HTLs that balance performance and stability and emphasize the need for further optimization to enhance the commercial viability of C-PSCs.

14 SOLAR ENERGY↗

DOE OSTI2026

Scalable, low-cost ink-based processing of high-performance silver selenide thermoelectrics

The growing global energy demand and its accelerating contribution to climate change emphasize the urgent need for sustainable energy conversion/harvesting technologies. Thermoelectric (TE) devices offer a compelling route to directly convert waste heat into electricity and enable solid-state cooling without moving parts or harmful refrigerants. Achieving their full potential requires not only higher TE performance (zT) but also scalable, low-cost manufacturing processes. Here, we introduce a transformative ink-based processing approach for scalable manufacturing of high-performance silver selenide-based TE materials and devices. Using a simple, high-throughput ink-mixing and blade coating strategy, our Ag 2 Se-based materials under the optimized composition and processing conditions yield an ultrahigh room-temperature power factor of 2.8 mW m −1 K −2 , over 100% higher than baseline samples and a reproducible figure of merit zT of 1 at room temperature. A thermoelectric generator (TEG) achieves a very competitive power density of 112 mW cm −2 at a 90 °C temperature difference between the hot and cold sides of the device, which is among the highest reported for silver selenide-based TE devices to date. This facile, scalable ink-based processing establishes a practical pathway toward industrial-scale manufacturing and widespread adoption of thermoelectric devices, advancing sustainable energy technologies.

Bappy, Md. Omarsany [University of Notre Dame, IN ↗

DOE OSTI2026

Model-based, in-situ, non-destructive qualification and certification of parts made by autonomous additive manufacturing

To address the significant productivity challenges associated with the qualification and certification (Q&C) tasks of additively manufactured (AM) parts, which have traditionally relied on rigorous post‐build inspection and testing, we propose an integrated framework that combines model‐based qualification and certification (MBQ&C) with autonomous additive manufacturing (AAM). MBQ&C employs high‐fidelity predictive models, developed within the Integrated Computational Materials Engineering (ICME) paradigm, to simulate process–structure–property–performance relationships for assessing a part’s fitness for use. Since predictive models are commonly machine learning (ML)-based or reduced-order surrogates of validated physics models, they run efficiently, enabling timely inference. In parallel, the self-driving AAM utilises ML-based adaptive, closed‐loop control strategies to avoid, mitigate, or repair defects and anomalies during fabrication, thereby increasing the likelihood of producing acceptable parts. A key feature of the combined AAM-MBQ&C framework is that predictive models explicitly incorporate defects or anomalies that persist after the build, using instance-specific data captured via in-situ sensing. This customisation enables a build‐specific assessment of fitness for use, rather than relying on nominal or generic parameters. Such individualised evaluation provides a robust basis for Q&C-related acceptance decisions relating to each build. Additionally, the rapid solution capabilities of ML or reduced-order models enable the determination of a part’s suitability for service shortly after build completion. As the framework matures, it has the potential to substantially reduce reliance on conventional point‐design approaches—such as time‐consuming post‐build computed tomography scanning and costly destructive testing. Thus, the AAM-MBQ&C framework represents a transformative, scalable strategy for quality assurance of AM components, as parts produced within a stable, validated, and certified envelope can be certified with reduced testing. Key benefits include: (1) significant gains in Q&C productivity through efficient, model-centric assessment; (2) performance-based classification of defects into critical and non-critical categories; (3) the ability to predict potential deviations in the performance of parts affected by real-time, adaptive process control interventions relative to those produced under a certified process, and (4) the enabling of virtual Q&C for service environments that are difficult, hazardous, or impractical to access or reproduce experimentally. Collectively, these capabilities strengthen the business case for AM, particularly for high‐consequence and mission‐critical applications. Finally, although this work focuses on powder-based AM, the proposed techniques could be extended to AM processes employing alternative feedstock forms.

Gunasegaram, Dayalan↗

DOE OSTI2025

Enhancing electrocatalytic performance of RuO 2 -based catalysts: mechanistic insights, strategic approaches, and recent advances

Abstract Electrochemical water splitting presents the ultimate potential of hydrogen and oxygen production; however, regulating the rate and efficiency of water splitting is highly dependent on the accessibility of extremely efficient electrode materials for slow performance kinetics and large overpotential of both oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). Ruthenium oxide (RuO 2 ) based materials display high performance for OER and HER because of their capacity to bind oxygen, eminent catalytic activity, low cost compared to other precious metals, and stability in a wide pH range. However, there is still much space to promote the OER and HER activity and stability of RuO 2 to fulfill the necessity for practical applications in water splitting. Different researchers applied multiple approaches that boosted the catalytic performance of RuO 2 -based electrocatalysts toward overall water splitting. Herein, this review provides a comprehensive overview of recent advancements in RuO 2 -based materials in the field of water electrolysis for the generation of alternative energies. It gives a general description of water splitting in acidic and alkaline settings, including reaction mechanisms as well as common evaluation elements for the catalytic function of the materials. Most of the reviews reported based on RuO 2 materials are only focused on OER performance, but this review highlighted comprehensive ideas on different strategies like morphology design, electronic structure, electrolytes, and compositions for optimizing both electrocatalytic HER and OER functioning of RuO 2 -based electrocatalysts.

KC, Binod Raj (ORCID:0009000885806906)↗

DOE OSTI2025

Simulation driven adaptive sampling for neutron-diffraction based strain mapping of additively manufactured parts

Neutron diffraction based strain mapping is a useful technique for measuring residual strains in additively manufactured (AM) metal parts. The measurement is traditionally done by scanning the sample in a point-wise raster pattern to extract the strain at each position. Since the overall scan can span several hours, adaptive sampling approaches using Bayesian optimization based on Gaussian process (BO-GP) regression have been introduced—demonstrating that even with a fraction of the typically made measurements the dominant strain patterns in the sample can be reconstructed. However, the parameters of the BO-GP algorithm have to be carefully chosen for best performance, and the movement time between arbitrary points can offset the time savings from a reduced number of measurement locations. In this paper, we propose algorithms to refine the BO-GP based methods by using simulations of strain patterns in AM parts based on the materials and the process used to print them. We demonstrate that the simulated strain patterns can be used to help choose better parameters for the BO-GP based framework—leading to low reconstruction error for the final strain pattern. Furthermore, we show that the strain mapping experiment can be initialized with a sampling pattern learnt from the simulation data and ordered to reduce movement time, dramatically enabling reduction in the overall time required to run the baseline BO-GP method.

Gaussian process regression↗

DOE OSTI2025

Black-Starting Microgrids Using Inverter-Based Distributed Energy Resources

Recent trends in power systems show increasing deployment of inverter-based distributed energy resources (DERs) at the distribution level. Efforts have also been made to use inverter-based DERs for system restoration of critical sections of distribution feeders. In the past few years, there has been active consideration of using local grid-forming (GFM) DERs, which can form their own voltage and frequency, to black-start microgrids instead of waiting for the bulk system for supply restoration. However, using current-limited inverter-based DERs for black-start operations with high inrush currents can pose some technical challenges. This paper presents detailed electromagnetic transient studies on a digital real-time simulator to assess the operational feasibility of using local inverter-based GFM DERs for microgrid black-start operations as a bottom-up approach instead of a top-down approach where the substation is used to restore critical sections of the feeder. The paper presents key modeling details for distribution system components for studying GFM DER-based microgrid black-start operations. The paper presents simulation results comparing different black-start approaches using GFM DERs for two test systems: i) a simple test microgrid and ii) a real-world utility microgrid currently being designed and deployed by Holy Cross Energy in Colorado.

black start↗

DOE OSTI2025

SVM-Based Synchronized Fault Detection for 100% Renewable Microgrids

Traditional protection schemes face significant challenges when applied to microgrids with high penetrations of renewables with inverter-based resources (IBRs). The proliferation of advanced sensing and communication technologies has generated copious data, offering an opportunity to overcome these limitations using data-driven machine learning approaches. This work proposes a novel approach based on a support vector machine (SVM) for detecting faults within a 100% renewable microgrid. The approach encompasses a systematic offline training stage for the development of a linear SVM-based fault detection algorithm. This process covers offline data collection from the microgrid under study, the extraction of features such as positive- and negative-sequence components and the total harmonic distortion of the voltage and current measurements of the relays, and the design of the linear SVM-based classifier. During the online implementation, however, different classifiers can exhibit asynchronicity in detecting the fault inception at different subcycle-to-cycle period-level delays. To circumvent this asynchronicity issue, a separate algorithm is developed for each relay to estimate the fault inception time as close to the real fault time. The performance of the proposed SVM-based synchronized fault detection method is evaluated using online time-domain simulation studies on a microgrid test system. The results corroborate the reliability of the fault detection scheme when tested under various fault cases (fault types, locations, and impedances) and non-fault cases during both grid-tied and islanded operation modes.

100% microgrid↗

DOE OSTI2026

Survey of Deep Learning and Physics-Based Approaches in Computational Wave Imaging

Computational wave imaging (CWI) extracts hidden structure and physical properties of a volume of material by analyzing wave signals that traverse that volume. Applications include seismic exploration of the Earth’s subsurface, acoustic imaging and nondestructive testing (NDT) in material science, and ultrasound computed tomography (USCT) in medicine. Current approaches for solving CWI problems can be divided into two categories: those rooted in traditional physics and those based on deep learning. Physics-based methods stand out for their ability to provide high-resolution and quantitatively accurate estimates of acoustic properties within the medium. However, they can be computationally intensive and are susceptible to ill-posedness and nonconvexity typical of CWI problems. Machine learning (ML)-based computational methods have recently emerged, offering a different perspective to address these challenges. Diverse scientific communities have independently pursued the integration of deep learning in CWI. This review discusses how contemporary scientific ML techniques, and deep neural networks in particular, have been developed to enhance and integrate with traditional physics-based methods for solving CWI problems. We present a structured framework that consolidates existing research spanning multiple domains, including computational imaging, wave physics, and data science. This study concludes with important lessons learned from existing ML-based methods and identifies technical hurdles and emerging trends through a systematic analysis of the extensive literature on this topic.

42 ENGINEERING↗

DOE OSTI2024

Zone plate-based extreme ultraviolet mask microscope with through-pellicle imaging capability

Mirror-based and zone plate-based imaging systems are being used in actinic extreme ultraviolet (EUV) reticle review tools. With regard to zone plates, a short working distance is advantageous in terms of the required spectral bandwidth, manufacturability, and potential throughput and imaging performance. Zone plates therefore typically have a short working distance. The industry has adopted the use of an EUV pellicle to protect the photomask. Imaging photomask through-pellicle requires a working distance larger than 2.5 mm. A zone-plate-based EUV mask microscope with a 3-mm working distance has been commissioned at beamline 11.3.2 of the Advanced Light Source. Through-pellicle imaging at an exposure time of 2 s is demonstrated. The instrument achieves an image contrast of 95% on large features on a photomask with a tantalum-based absorber. Imaging down to 45-nm half pitch (mask scale) is demonstrated. A NILS of 2.55 is achieved on 60-nm half-pitch (mask scale) lines and spaces. These results demonstrate that zone-plate-based imaging systems can meet the requirements of an actinic EUV mask review tool in terms of imaging performance and throughput in an instrument compatible with EUV pellicles.

Extreme ultraviolet↗

DOE OSTI2025

Meta Biome: a multiscale model integrating agent-based and metabolic networks to reveal spatial regulation in gut mucosal microbial communities

ABSTRACT Mucosal microbial communities (MMCs) are complex ecosystems near the mucosal layers of the gut essential for maintaining health and modulating disease states. Despite advances in high-throughput omics technologies, current methodologies struggle to capture the dynamic metabolic interactions and spatiotemporal variations within MMCs. In this work, we presentMetaBiome, a multiscale model integrating agent-based modeling (ABM), finite volume methods, and constraint-based models to explore the metabolic interactions within these communities. Integrating ABM allows for the detailed representation of individual microbial agents each governed by rules that dictate cell growth, division, and interactions with their surroundings. Through a layered approach—encompassing microenvironmental conditions, agent information, and metabolic pathways—we simulated different communities to showcase the potential of the model. Using ourin-silicoplatform, we explored the dynamics and spatiotemporal patterns of MMCs in the proximal small intestine and the cecum, simulating the physiological conditions of the two gut regions. Our findings revealed how specific microbes adapt their metabolic processes based on substrate availability and local environmental conditions, shedding light on spatial metabolite regulation and informing targeted therapies for localized gut diseases.MetaBiome provides a detailed representation of microbial agents and their interactions, surpassing the limitations of traditional grid-based systems. This work marks a significant advancement in microbial ecology, as it offers new insights into predicting and analyzing microbial communities. IMPORTANCE Our study presents a novel multiscale model that combines agent-based modeling, finite volume methods, and genome-scale metabolic models to simulate the complex dynamics of mucosal microbial communities in the gut. This integrated approach allows us to capture spatial and temporal variations in microbial interactions and metabolism that are difficult to study experimentally. Key findings from our model include the following: (i) prediction of metabolic cross-feeding and spatial organization in multi-species communities, (ii) insights into how oxygen gradients and nutrient availability shape community composition in different gut regions, and (iii) identification of spatiallyregulated metabolic pathways and enzymes inE. coli. We believe this work represents a significant advance in computational modeling of microbial communities and provides new insights into the spatial regulation of gut microbiome metabolism. The multiscale modeling approach we have developed could be broadly applicable for studying other complex microbial ecosystems.

Microbiology↗

DOE OSTI2025

Data Assimilation for Robust UQ Within Agent-Based Simulation on HPC Systems

Agent-based simulation provides a powerful tool for in silico system modeling. However, these simulations do not provide built-in methods for uncertainty quantification (UQ). Within these types of models a typical approach to UQ is to run multiple realizations of the model then compute aggregate statistics. This approach is limited due to the compute time required for a solution. When faced with an emerging biothreat, public health decisions need to be made quickly and solutions for integrating near real-time data with analytic tools are needed. We propose an integrated Bayesian UQ framework for agent-based models based on sequential Monte Carlo sampling. Given streaming or static data about the evolution of an emerging pathogen this Bayesian framework provides a distribution over the parameters governing the spread of a disease through a population. These estimates of the spread of a disease may be provided to public health agencies seeking to abate the spread. By coupling agent-based simulations with Bayesian modeling in a data assimilation, our proposed framework provides a powerful tool for modeling dynamical systems in silico. We propose a method which reduces model error and provides a range of realistic possible outcomes. Moreover, our method addresses two primary limitations of ABMs: the lack of UQ and an inability to assimilate data. Our proposed framework combines the flexibility of an agent-based model with UQ provided by the Bayesian paradigm in a workflow which scales well to HPC systems. We provide algorithmic details and results on a simulated outbreak with both static and streaming data.

Spannaus, Adam [ORNL] (ORCID:0000000225213657)↗

DOE OSTI2024

An Inverse Heat Conduction Algorithm Used to Calculate the Temperatures on the Inner and Outer Cylindrical Surfaces of an HMX-based PBX Explosive Annulus

In this work, a new Inverse Heat Conduction (IHC) algorithm is applied to estimate the surface temperatures at twelve locations on the inner and outer cylindrical boundaries of an HMX-based Plastic Bonded Explosive (PBX) annulus. This IHC algorithm was developed in references using a set of Direct Heat Conduction (DHC) solutions and a temperature correction method. The DHC solutions were calculated using a Galerkin based finite element (FE) method. This HMX based PBX annulus was used in the Large Scale Annular Cookoff (LSAC) experiment, Shot 5. The reason Shot 5 was chosen as a prototype mathematical model for this study is that the temperature was measured at eighteen locations in the midplane of the HMX-based PBX annulus. In addition, this annulus underwent an experimental thermal ignition and a deflagration that caused a thermal explosion and the disassembly of the experiment. The objective of this study is to describe how the application of the temperature correction algorithm produced the convergence of the DHC solutions to the measured temperatures at twelve internal locations in the midplane of the HMX-based PBX annulus.

36 MATERIALS SCIENCE↗