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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

PET-FBA: A lightweight enzyme allocation and thermodynamics-constrained flux analysis approach to explore Escherichia coli metabolic adaptation to intracellular acidification

Escherichia coli employs diverse strategies to adapt to acidic environments that disrupt enzyme activity and the thermodynamic feasibility of essential reactions. To understand the impact of pH stress on cell metabolism, we present the PET-FBA (pH-, Enzyme protein allocation-, and Thermodynamics-constrained Flux Balance Analysis) framework. PET-FBA extends genome-scale modeling by integrating enzyme protein costs and reaction Gibbs free energy changes. Additionally, by incorporating pH-dependent enzyme kinetics in response to intracellular acidification, this framework enables the simulation of E. coli's metabolic adjustments across varying external pH levels. The model's accuracy is validated by comparing in silico growth simulations with experimental measurements under both anaerobic and aerobic conditions, as well as in silico gene knockouts of essential genes. By explicitly incorporating pH effects, our model accurately replicates the metabolic shift towards lactate production as the primary fermentation product at low pH in anaerobic conditions. This shift is only predicted when enzyme kinetics are dynamically adjusted as a function of pH. Further analysis revealed that this shift can be attributed to the reduced protein efficiency of the acetyl-CoA branch compared to lactate dehydrogenase under acidic stress, which then becomes crucial for maintaining NAD regeneration and cell growth at low pH. Furthermore, we identified strategies for enhancing cell growth under acidic anaerobic conditions by improving the enzyme activity of lactate dehydrogenase and pyruvate formate lyase, which increases NAD production efficiency and reduces enzyme protein allocation costs. Designed as a lightweight yet versatile framework, PET-FBA enables efficient genome-scale metabolic analysis. Using E. coli as a model system, our framework provides a systematic approach to understanding metabolic responses to environmental stress, pinpointing key metabolic bottlenecks, and identifying potential targets for strain optimization.

42 ENGINEERING↗
DOE OSTI2024

Bioenergy and Climate Change in Ukraine: How climate can impact the sustainability of bioenergy production

The Russian invasion has exacerbated Ukraine’s energy security issues, prompting a shift toward diversifying energy supply sources. Additionally, strategic documents aim to align Ukraine’s energy system with EU climate requirements, focusing on reducing reliance on fossil fuels and advancing decarbonization efforts. This report focuses on the expansion of bioenergy as an alternative source of energy in Ukraine. Current assessments suggest that Ukraine has substantial bioenergy potential, primarily from agricultural residues and energy crops. However, the challenges posed by climate change and the ongoing war might impact the outcome of these projections. This report highlights the importance of integrating climate factors into energy modeling using tools like the integrated assessment models to provide a comprehensive understanding of Ukraine’s bioenergy potential under various climate scenarios. It also emphasizes the need for climate-smart agriculture and forestry practices to mitigate risks, enhance energy efficiency, and support resilient crop supplies. Recommendations for stakeholders include diversification of the energy supply sources, developing adaptation strategies, diversifying bioenergy feedstocks, and ensuring robust decision-making to navigate the impacts of climate change on Ukraine’s energy system.

09 BIOMASS FUELS↗
DOE OSTI2021

Accelerating Clean Energy @Scale: Place-Based Solutions

Customized, holistic energy modeling and analysis is conducted across a wide range of geospatial scales -- from global to local. We will describe the value and importance of local, place-based solutions, particularly, how scientific insights, decision support, and technical assistance based on integrated, customized modeling and analysis, and in-depth stakeholder engagement can assist communities in translating their ambitions into implementable action plans.

clean energy↗
DOE OSTI2026

Overview of the Nephele Perturbed Parameter Ensemble for Aerosol‐Cloud Interactions in E3SMv3

Aerosol-cloud interactions (aci) are the leading source of uncertainty in inferring climate sensitivity from the historical record. Earth system models (ESMs) struggle to represent aci because the processes responsible for these phenomena occur at much finer time and space scales than can be resolved by any ESM. Observational constraints provide key benchmarks to test ESMs, but cannot be used alone to fully understand aci processes except in very specific cases where causality is controlled; some degree of modeling is required to infer aci and estimate radiative forcing. Here, we generate and characterize a perturbed parameter ensemble (PPE) in version 3 of the Energy Exascale ESM (E3SMv3). We perturb 25 parameters that govern aci processes over 250 members and integrate the model over present-day and preindustrial aerosol emissions. We find that the process representation in E3SMv3 is flexible and can generate global-mean effective radiative forcings due to aci (ERFaci) ranging from −3.0 to +0.9 W m −2 . The positive ERFaci values simulated by a portion of the PPE are implausible and result from parameter combinations that produce unrealistic top-of-atmosphere energy fluxes. While global-mean cloud droplet number concentration always increases in response to anthropogenic aerosol, cloud liquid water path can both increase and decrease, suggesting that precipitation suppression is not the only aerosol-cloud adjustment represented by E3SMv3. Analysis of which processes control liquid cloud adjustment in the PPE points toward stratiform precipitation processes and aerosol activation, which is consistent with many previous ESMs, as well as the new two-moment convective cloud microphysics in E3SMv3.

Nugent, Jacqueline M. [Univ. of Wyoming, Laramie, ↗
DOE OSTI2024

A Review of Modeling Approaches for Predicting Frost Growth and Defrosting on Tube-Fin Heat Exchangers: Preprint

Frost formation and growth on the evaporator surface is a common process that deteriorates the air-refrigerant heat transfer and restricts airflow. This degrades the performance of the vapor compression system by increasing temperature lift and air-side pressure drop. To accurately predict these effects during coil frosting, as well as the energy use and duration of the defrost process, there is a need to estimate the heat and mass transfer, momentum transport, and solid-liquid and liquid-vapor phase change. Therefore, in the past few decades, continuous effort has been made to model frosting and defrosting processes using approaches ranging from empirical correlations to computational fluid dynamic models. To provide a clearer overview for researchers, engineers, and manufacturers in this field, this paper provides a comprehensive literature review for frosting and defrosting models. The paper begins with theoretical background of frost formation and defrost processes, and then reviews the common modeling approaches in literature and their underlying assumptions when trying to account for various physical phenomenon. Based on the literature review, the most critical modeling effort for frost formation is the determination of frost densification rate and frost growth rate. Various methods to predict these two parameters are reviewed. Empirical correlations commonly used for frost density and thermal conductivity are presented and compared. For the defrost process, various multi-stage models have been proposed with different assumptions. Some assume the presence of air gap between the tube wall and the frost, while others consider the melted frost flow due to gravity. We also review physics-based and empirical approaches to integrate defrost models into heat pump models. We conclude by identifying research gaps and providing recommendations.

defrost↗
DOE OSTI2024

Risk Considerations of Transitioning CO2-EOR Field to CO2 storage Field: Case Study

In the United States (U.S.), carbon dioxide (CO2) injection wells at EOR sites are currently regulated as Class II wells under the U.S. Environmental Protection Agency’s (EPA) Underground Injection Control (UIC) program while dedicated geological CO2 storage (GCS) wells are considered Class VI wells. A CO2-EOR facility considering a transitioning from tertiary oil recovery to injecting CO2 for the primary purpose of long-term storage is required to obtain a Class VI permit where this transition poses an increased risk to underground sources of drinking water. This study considers how transitioning operations from CO2-EOR to storage can impact reservoir plume and pressure transient in the storage envelope, and how these changes could impact area of review and potential unwanted fluid migration. We developed a case study to assess subsurface response and leakage risks associated with a representative, hypothetical operation in a carbonate reservoir. This reservoir transitions from tertiary hydrocarbon recovery to dedicated GCS. Reservoir simulations were run for a set of credible CO2-EOR scenarios to estimate distributions of fluids phases and pressures throughout the model domain after CO2 flooding as well as forecasting the behavior of the reservoir after the transition to a dedicated storage phase. The evolutions from all simulated scenarios were used as the basis for leakage risk quantification using the National Risk Assessment Partnership’s Open-Source Integrated Assessment Model (NRAP-Open-IAM) with a novel reduced-order model to estimate time-dependent leakage of CO2, brine, and hydrocarbon fluids through potentially leaky wells. Results include a description of reservoir response, an estimate of the areal extent that could potentially be impacted by leakage to underground sources of drinking water, and estimates of the magnitude of potential leakage. Considerations for dedicated storage injection well selection, injectivity, and injection scheme performance and potential leakage risk are presented, with implications for risk assessment of well transition discussed. This study presents a risk-based workflow for the Class II to Class VI well transition. Integrating credible numerical simulation of viable CO2-EOR to dedicated CO2 storage with quantitative risk assessment tools, such as the NRAP-Open-IAM, will provide a valuable means to devise operational scenarios and inform decision-making related to storage benefit, leakage risk, and liability. Presented at the SPE/AAPG/SEG Carbon Capture Utilization and Storage Conference in Houston, TX, March 11-13, 2024.

Liu, Guoxiang↗
DOE OSTI2024

A fast and accurate domain decomposition nonlinear manifold reduced order model

Here, this paper integrates nonlinear-manifold reduced order models (NM-ROMs) with domain decomposition (DD). NM ROMs approximate the full order model (FOM) state in a nonlinear-manifold by training a shallow, sparse autoencoder using FOM snapshot data. These NM-ROMs can be advantageous over linear-subspace ROMs (LS-ROMs) for problems with slowly decaying Kolmogorov n-width. However, the number of NM-ROM parameters that need to be trained scales with the size of the FOM. Moreover, for “extreme-scale” problems, the storage of high-dimensional FOM snapshots alone can make ROM training expensive. To alleviate the training cost, this paper applies DD to the FOM, computes NM-ROMs on each subdomain, and couples them to obtain a global NM-ROM. This approach has several advantages: Subdomain NM-ROMs can be trained in parallel, involve fewer parameters to be trained than global NM-ROMs, require smaller subdomain FOM dimensional training data, and can be tailored to subdomain specific features of the FOM. The shallow, sparse architecture of the autoencoder used in each subdomain NM-ROM allows application of hyper-reduction (HR), reducing the complexity caused by nonlinearity and yielding computational speedup of the NM-ROM. This paper provides the first application of NM-ROM (with HR) to a DD problem. In particular, this paper details an algebraic DD reformulation of the FOM, training a NM-ROM with HR for each sub domain, and a sequential quadratic programming (SQP) solver to evaluate the coupled global NM-ROM. Theoretical convergence results for the SQP method and a priori and a posteriori error estimates for the DD NM-ROM with HR are provided. The proposed DD NM-ROM with HR approach is numerically compared to a DD LS-ROM with HR on the 2D steady-state Burgers’ equation, showing an order of magnitude improvement in accuracy of the proposed DD NM-ROM over the DD LS-ROM.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Quantifying Groundwater Response and Uncertainty in Beaver‐Influenced Mountainous Floodplains Using Machine Learning‐Based Model Calibration

Abstract Beavers ( Castor canadensis ) alter river corridor hydrology by creating ponds and inundating floodplains, and thereby improving surface water storage. However, the impact of inundation on groundwater, particularly in mountainous alluvial floodplains with permeable gravel/cobble layers overlain by a soil layer, remains uncertain. Numerical modeling across various floodplain structures considers topographic and sediment complexity and multidirectional flow, linking inundation to groundwater response. This study develops a model‐data integration workflow to address uncertainty in groundwater response to beaver‐induced inundations in a mountainous alluvial floodplain in the Upper Colorado River Basin. Uncertain factors include seasonal hydrologic dynamics, hydraulic conductivities, floodplain structures, and meteorological forcings. We employed an ensemble of groundwater models, based on geophysical and hydrologic data, with machine learning‐based calibration using a neural density estimator. This allowed us to quantify the vertical flux from the soil layer to the permeable gravel bed, the down‐valley underflow within the gravel bed, and their ratios. Results show a significant increase in the vertical flux relative to down‐valley underflow, from 2 during dry pond periods to 20 during wet periods, serving as an analogy for conditions without and with beaver ponds. The study highlights the influence of floodplain structure on groundwater storage, water balance, and water quality impacted by beaver ponds. A thick gravel bed layer, with a large down‐valley underflow, minimizes the effect of beaver‐induced inundation on water quality. We emphasize the need for field‐scale measurements of floodplain structure and improved characterization of evapotranspiration changes to reduce uncertainty in groundwater response. Plain Language Summary Beavers change the flow of water in river corridors by creating ponds, expanding wetlands, and flooding floodplains. This increases surface water area, promotes plant growth, and enhances biodiversity. However, the impact of this flooding on groundwater flow is not well understood, especially in mountainous areas with gravel layers where water moves easily beneath soil. In this study, we used numerical modeling to investigate how beaver ponds influence groundwater in a mountainous floodplain of the Upper Colorado River Basin. We adapted a machine learning method to validate our numerical models using multiple field data sets. Our findings show that beaver ponds significantly increase vertical water flow from the soil to the gravel during wet periods, compared to when the ponds are fully drained. The study also highlights the importance of floodplain structure in controlling both water flow in gravel layers along the river direction and vertical flow from the soil to the gravel with the presence of beavers. To reduce uncertainty in groundwater response, we emphasize the need for more field‐scale measurements of floodplain structure, hydraulic properties, and evapotranspiration changes. Key Points Floodplain structures and hydraulic conductivities are important for groundwater response with beaver ponds in mountainous floodplains Large down‐valley underflow in permeability‐stratified floodplains reduces beaver‐induced impacts on groundwater storage and water quality Machine learning‐based model calibration methods are effective for estimating posterior distributions of groundwater model parameters

Wang, Lijing↗
DOE OSTI2021

Convex Optimization of Integrated Power-Gas Energy Flow Model With Applications to Probabilistic Energy Flow

Energy flow calculation is a fundamental problem of the integrated power and gas system (IPGS) operation and planning. However, the nonlinear gas flow model introduces major challenges to the energy flow calculation. In this paper, we propose a tractably convex optimization model to solve the energy flow problem in IPGSs. It is demonstrated that the proposed optimization model has the same optimal solution as the original nonlinear steady energy flow model. Also, piecewise linearization is adopted to tightly linearize the nonlinear objective function of the model, which transforms the formulated convex optimization into a linear program one. Thus, the computation complexity of the proposed energy flow model is significantly reduced as compared with the existing methods. In addition, the proposed model can be extended to probabilistic energy flow estimation. Extensive case studies are conducted to validate the effectiveness of the proposed energy flow model using three IPGSs.

42 ENGINEERING↗
DOE OSTI2024

Integrated protonic ceramic electrochemical cell for sustainable energy economy using water-energy nexus framework

Reliance on fossil fuels will continue for the next decades even though there are global pushes away from it to mitigate the overarching climate challenge, most especially by its highest consumers and availability. While there is a hastening global shift away from fossil fuel, integrating its assets into this technology helps limit the risk and future losses of stranded assets and reduce the cost of investment in the new technologies. Moreover, the generation of electricity from intermittent renewable sources like solar and wind has witnessed a significant surge in recent years, leading to a pressing demand for practical energy storage systems. Electrical energy storage is anticipated to play a pivotal role in the future global energy system, facilitating load-leveling operations to support the greater integration of renewable and distributed generation. Reversible electrochemical cells (RECs) offer a promising option for addressing the fossil fuel assets integration and energy storage challenges through the interconversion between electrical and chemical energy and concurrent utilizing carbon emission. In their electrolysis mode, the RECs convert electricity into durable, storable, and portable valuable chemical fuels such as syngas and methane. Conversely, the produced chemical fuels can be used as reactants in the fuel cell mode to generate electricity on demand with minimal (hydrocarbons) or zero when H2 or NH3 is used emissions. However, a challenging goal for this type of technology remains to achieve optimal operation and high roundtrip efficiencies, which has hindered the deployment of previous electrochemical cells. This dissertation demonstrates how reversible protonic ceramic electrochemical cells (RePCECs) can be integrated with fossil fuel power plants and renewable energy sources as a potential energy storage system. In this work, integrated RePCEC systems are designed and examined using computational modeling at scales to determine appropriate system configurations and operating conditions that achieve high roundtrip efficiencies. Cell level design of the PCEC is the first approach, several cells are assembled for the stack level model that is integrated into combined cycle powerplant and solar photovoltaic for the system level model. After critical literature review, this answered the operational and integration research questions proposed to address these challenges. The designed systems perform two functions, utilizing captured CO2 and storing renewable energy through co-electrolysis of steam and CO2. The co-electrolysis reaction involves endothermic water electrolysis and exothermic methanation reaction. To enhance high roundtrip efficiency, there is a need for thermal balance and management in the electrolysis mode. This involves operating the RePCEC stack under conditions that favor methane production to balance out heat needed by water electrolysis, it crucial for the RePCEC system operation. Methanation is enhanced by low temperatures. Leveraging on fabricated BCZYYb-electrolyte RePCEC, the cell model designed revealed that the optimum temperature for methane production is 450℃ at atmospheric pressure. Thus, to achieve optimum system performance, operating in the temperature range 450-525℃ is recommended at the given configuration, combining between the optimum temperature for methane production and temperature for the optimum stack roundtrip efficiency. Configuration with carbon capture system and purge stream is the optimum configuration from the seven conceptualized and evaluated. The modeling outcomes include a thermodynamic examination of integrated RePCEC systems, calibration of cell and stack level models, and steady-state simulation and integration into a 600MW combined cycle power plant retrofitted with two two-stage membrane-based carbon capture system and a wastewater treatment and recovery unit. At 100% powerplant loading, the stack and system roundtrip efficiencies are 72% and 51.37% respectively. Adding a purge stream for produced hydrogen at the system downstream improves the efficiencies to 74 and 55.48% respectively. At atmospheric pressure and 525℃, the system model suggests that a stack roundtrip of 82% is achievable, and overall system efficiency increases by reducing the energy consumption by the balance of plant components for steam generation and storage. Economic analysis of the process gives levelized cost of methane as $2.24/MMBtu lower than the conventional production route that range between $3.46/MMBtu and $9.85/MMBtu. The lifecycle analysis shows that the global warming potential for the production of methane and hydrogen from the RePCEC system is 3.83 kg CO2 eq which is lower than 9.35 kg CO2 eq emission during steam methane reforming for hydrogen production. This answered both the environmental and economic concerns in the raised research question. The proposed RePCEC configuration and analysis carried out in this dissertation to address the surge in renewable energy and challenges with PCEC technology hold significant potential in achieving large-scale energy storage while simultaneously reducing carbon emissions. These advancements, coupled with suitable governmental policies and incentive programs, have the potential to economically disrupt the natural gas industries by using RePCEC systems for methane production, thereby making them more favorable for eventual implementation and commercialization.

25 ENERGY STORAGE↗
DOE OSTI2025

Advancing Urban Water Resilience: Coproducing Knowledge through Civic–Academic Global Partnerships on Water and Climate

As extreme weather events become more pronounced, the vulnerabilities associated with the urban water supply and wastewater systems in megacities are intensified in multiple interconnected dimensions. These multifaceted water challenges can benefit from enhanced cross-sectoral collaboration and sharing of critical knowledge, which are essential for sustainable and adaptive water governance frameworks. In this context, the Megacity Alliance for Water and Climate (MAWAC)–Europe and North America Region (ENAR) Working Group convened a workshop in March 2023, followed by a subsequent workshop in London, United Kingdom, from 11 to 13 September 2024. These workshops aimed to investigate and devise solutions for the cascading hazards with water systems. The solutions examined various aspects focused on climate adaptation and mitigation, stormwater management, and the governance of water and wastewater systems. Additionally, discussions highlighted the importance of community engagement, economic considerations, equity, and effective communication in addressing these pressing challenges. Over the course of 3 days, experts from academia, government agencies, and industry engaged in meaningful discussions on digital modeling for integrated water management, climate-informed urban planning, and public–private–academic partnerships (Fig. 1). Case studies from cities such as New York, Los Angeles, London, Paris, and Chicago highlighted innovative governance strategies for managing water and wastewater systems, promoting water reuse, planning infrastructure, and fostering stakeholder-driven and stakeholder-informed adaptation. The workshop participants emphasized the need for data-driven decision-making, scalable governance models, and knowledge-sharing networks to enhance urban water governance for sustainability and resilience. This workshop report presents the key takeaways from the 3-day convening, providing a roadmap for integrating scientific research, policy frameworks, and emerging technologies to address water challenges faced by megacities.

Hydrologic models↗
DOE OSTI2020

Integrated Transportation-Energy Systems Modeling

Transportation is currently the least-diversified energy demand sector, with over 90% of global transportation energy use coming from petroleum product. After over a century of petroleum dominance, however, many leading experts anticipate major electrification trends that could disrupt the transportation energy demand landscape. These changes in electricity demand complement profound changes happening within electric power supply systems, including integration of variable renewables, distributed generation and storage, and greater participation in power system planning and operations from traditionally passive consumers. This broader context underscores the importance of understanding how transportation electrification will impact electricity demand, including changes in the load shapes that characterize the system and the opportunity to leverage flexible EV charging to more cost-effectively balance demand and supply. This talk provides an overview of recent findings on infrastructure requirements to support EV adoption, integration challenges and the impact of EV on power systems, and opportunities to leverage flexible (or smart) EV charging to support power system planning and operations.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗
DOE OSTI2024

Projecting Large Fires in the Western US With an Interpretable and Accurate Hybrid Machine Learning Method

More frequent and widespread large fires are occurring in the western United States (US), yet reliable methods for predicting these fires, particularly with extended lead times and a high spatial resolution, remain challenging. In this study, we proposed an interpretable and accurate hybrid machine learning (ML) model, that explicitly represented the controls of fuel flammability, fuel availability, and human suppression effects on fires. The model demonstrated notable accuracy with a F 1 -score of 0.846 ± 0.012, surpassing process-driven fire danger indices and four commonly used ML models by up to 40% and 9%, respectively. More importantly, the ML model showed remarkably higher interpretability relative to other ML models. Specifically, by demystifying the “black box” of each ML model using the explainable AI techniques, we identified substantial structural differences across ML fire models, even among those with similar accuracy. The relationships between fires and their drivers, identified by our model, were aligned closer with established fire physical principles. The ML structural discrepancy led to diverse fire predictions and our model predictions exhibited greater consistency with actual fire occurrence. With the highly interpretable and accurate model, we revealed the strong compound effects from multiple climate variables related to evaporative demand, energy release component, temperature, and wind speed, on the dynamics of large fires and megafires in the western US. Our findings highlight the importance of assessing the structural integrity of models in addition to their accuracy. They also underscore the critical need to address the rise in compound climate extremes linked to large wildfires.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Integration of Risk Survival Measures Estimated From Pre- and Posttreatment Computed Tomography Scans Improves Stratification of Patients With Early-Stage Non-small Cell Lung Cancer Treated With Stereotactic Body Radiation Therapy

To predict overall survival of patients receiving stereotactic body radiation therapy (SBRT) for early-stage non-small cell lung cancer (ES-NSCLC), we developed a radiomic model that integrates risk of death estimates and changes based on pre- and posttreatment computed tomography (CT) scans. We hypothesize this innovation will improve our ability to stratify patients into various oncologic outcomes with greater accuracy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Model Data for the Mesh Convergence Study Demonstrating Benefits of Mixed-polyhedral Mesh in Integrated Hydrology Simulations

This archived model data is related to a study introducing a unique method that employs a stream-aligned mixed-polyhedral mesh to effectively and accurately represent river valleys, stream corridors, and narrow engineered channels in integrated hydrology simulations. The study finds that utilizing stream-aligned mixed-polyhedral meshes in integrated hydrology simulations achieves accuracy on par with a finely refined TIN-based mesh while markedly diminishing computational costs. This archive contains scripts and data files needed to generate the ATS model input, including mesh and ATS input files, for all mesh scenarios using the Watershed Workflow package. Additionally, this archive also provides key outputs from the model simulations that are used in the analysis and post-processing scripts to reproduce figures in the manuscript. The Watershed Workflow package is implemented in Python3. The Jupyter notebooks can be executed through multiple open-source tools, for example, Anaconda Jupyter Lab, VS Studio Code, etc. Other data files include CSV and HDF5 files, which can be read through Python scripts. The input files for the ATS model, open-source integrated hydrology, and transport model are in XML format and can be edited in any commonly used text editors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Shadow masks predictions in SPARC tokamak plasma-facing components using HEAT code and machine learning methods

Here, this work uses machine learning (ML) to complement HEAT (Heat flux Engineering Analysis Toolkit) by developing 3-D footprint surrogate models for fast and accurate heat load calculations in the divertor of the SPARC tokamak. The focus is on shadowed regions, or magnetic shadows, caused by the 3-D geometry of plasma-facing components (PFCs). ML classifiers are employed to create a surrogate model for HEAT generated shadow masks, predicting these shadow masks and divertor heat flux profiles based on a diverse range of equilibria and only the plasma current, safety factor(q95) at the edge, and magnetic flux angles as input parameters. The ultimate goal is to integrate the model for real-time control and future operational decisions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗