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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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At least 577 records · Page 32
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Middle to Late Holocene Sea Surface Temperature and Productivity Changes in the Northeast Pacific

Variations of the sea surface temperature (SST) and primary productivity in the northeast Pacific have far‐reaching implications. In addition to influencing the regional and global temperature and hydroclimate, these conditions also control marine ecosystems and their services, which subsequently impact regional economies. Yet, our understanding of the variability and controls of northeast Pacific SST and productivity on timescales exceeding observational records remains limited. Here, we use marine sediment records from seven locations, spanning 25.2°N–59.6°N, in the northeast Pacific to characterize the millennial‐scale variability of SST and productivity from 9,000 to 1,000 years BP. We explore the dynamics of their spatiotemporal evolution and compare these data with transient climate model outputs to identify potential drivers. Through a heat budget analysis and optimal fingerprinting analysis, we characterize the spatial pattern of forcings. We find that SST varied spatially in the northeast Pacific, with higher latitudes exhibiting greater magnitude changes than lower latitudes, which differs from previous work suggesting regional synchronicity and coherence during the Holocene. Our analysis did not find evidence for coherent variability of primary producer community nor carbon export, highlighting the difficulty of identifying the complex interactions between environmental conditions, producers, and carbon export. Model‐proxy disagreement demonstrates the need for higher resolution model frameworks, but shows nonetheless that observed variability in the proxy records can be explained by a combination of greenhouse gas and orbital forcing. Here we suggest that the complex SST variations and marine ecosystem responses to forced changes are important factors that can drive disagreements in model projections.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Enabling the broader adoption of fusion simulation on complex geometry

This project addressed a key barrier to advanced fusion and nuclear simulation: the difficulty of performing high-fidelity Monte Carlo neutronics directly on complex, real-world CAD geometry. Traditional workflows require engineers to rebuild CAD models as simplified constructive solid geometry, a time-consuming and error-prone process that limits design iteration and broader adoption of simulation tools. The goal of this Phase I SBIR was to make CAD-based neutronics practical, accessible, and robust for industrial and research users. During the project, Coreform significantly enhanced the Direct Accelerated Geometry Monte Carlo (DAGMC) workflow and fully integrated it into Coreform Cubit as a first-class capability. Major achievements include optimized material assignment and surface meshing workflows, substantial performance improvements to geometry imprinting and preparation, native export of DAGMC models, and new visualization tools to support OpenMC source definition and lost-particle debugging. Coreform also expanded Cubit’s capabilities as a full OpenMC preprocessor, including the ability to convert OpenMC constructive solid geometry models back into CAD for visualization, multiphysics coupling, and debugging. In collaboration with Argonne National Laboratory, the project delivered comprehensive new DAGMC documentation and training materials, transforming DAGMC from a research-oriented tool into a production-ready workflow. Results were disseminated through tutorials, conference training, and multiple well-attended webinars demonstrating integrated CAD-based neutronics and multiphysics workflows. Overall, this project demonstrated that high-fidelity Monte Carlo simulations can be performed directly on complex CAD geometry, reducing setup time, improving usability, and enabling faster, more informed design decisions for fusion and nuclear energy systems.

42 ENGINEERING↗
DOE OSTI2024

Engineering Active Sites of Metal/Metal Oxide Catalysts by Oxide Ligand Overlayers

Abstract Engineering sites of supported metal catalysts is essential to enhancing activity and selectivity. Such enhancement is typically achieved by particle size modification, surface alloying, or attaching molecular ligands. Yet, control strategies for complex, multifunctional molecules and catalysts, where selectivity is crucial, are lacking. Here, we demonstrate that submonolayer WO x with tunable coverage preferentially decorates well‐coordinated Pt terrace sites as a stable ligand. By combining experimental kinetics with probe molecules, in situ spectroscopies, and first‐principles modeling, we show that the WO x coverage on Pt modifies the metal‐to‐acid site balance while retaining the acid strength intact and results in optimal reactivity for metal‐acid catalyzed reactions at a specific metal, size, and support‐dependent WO x coverage. The oxide can also alter the reactant adsorption mode, reversing selectivity and pathways from terrace‐ to step‐dominated, as evidenced in furfural decarbonylation and hydrogenation. The insights open avenues for improving metal/metal oxide catalysts beyond the specific system.

Zhou, Jiahua↗
DOE OSTI2020

The influence of wintertime SST variability in the Western North Pacific on ENSO diversity

Abstract Sea surface temperature anomalies (SSTa) in the Western North Pacific (WNP) have been linked to the development of El Niño Southern Oscillation (ENSO) events a full year in advance. However, the contribution of the WNP precursor to the temporal evolution and spatial complexity of ENSO remains unclear. Using the preindustrial experiment of the Community Earth System Model as the control climate, a partially coupled experiment is conducted in which WNP SSTa are restored to the model climatology. By comparing the perturbed experiment to the control, we are able to clearly characterize ENSO’s response to WNP SST variability. We find that the WNP is predominantly linked to eastern Pacific (EP) ENSO events. Without SST variability in the WNP, central Pacific (CP) ENSO events are more likely to develop. This variation in ENSO flavor is controlled by how the WNP projects onto wind stress anomalies in the western equatorial Pacific, which in turn impacts the discharge and recharge of ocean heat during the ENSO cycle. Specifically, the removal of SSTa in the WNP weakens the buildup of ocean heat in the western equatorial Pacific, which then hinders the development of EP-type events.

Meteorology & Atmospheric Sciences↗
DOE OSTI2021

Comparison of Observations and Predictions of Daytime Planetary-Boundary-Layer Heights and Surface Meteorological Variables in the Columbia River Gorge and Basin During the Second Wind Forecast Improvement Project

The second Wind Forecast Improvement Project (WFIP2) is an 18-month field campaign in the Pacific Northwest U.S.A., whose goal is to improve the accuracy of numerical-weather-prediction forecasts in complex terrain. The WFIP2 campaign involved the deployment of a large suite of in situ and remote sensing instrumentation, including eight 915-MHz wind-profiling radars, and surface meteorological stations. The evolution and annual variability of the daytime convective planetary-boundary-layer (PBL) height is investigated using the wind-profiling radars. Three models with different horizontal grid spacing are evaluated: the Rapid Refresh, the High-Resolution Rapid Refresh, and its nested version. The results are used to assess errors in the prediction of PBL height within the experimental and control versions of the models, with the experimental versions including changes and additions to the model parametrizations developed during the field campaign, and the control version using the parametrizations present in the National Oceanic and Atmospheric Administration/National Centers for Environmental Prediction operational version of the models at the start of the project. Results show that the high-resolution models outperform the low-resolution versions, the experimental versions perform better compared with the control versions, model PBL height estimations are more accurate on cloud-free days, and model estimates of the PBL height growth rate are more accurate than model estimates of the rate of decay. Finally, using surface sensors, we assess surface meteorological variables, finding improved surface irradiance and, to a lesser extent, improved 2-m temperature in the experimental version of the model.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Bayesian learning of orthogonal embeddings for multi-fidelity Gaussian Processes

Uncertainty propagation in complex engineering systems often poses significant computational challenges related to modeling and quantifying probability distributions of model outputs, as those emerge as the result of various sources of uncertainty that are inherent in the system under investigation. Gaussian Processes regression (GPs) is a robust meta-modeling technique that allows for fast model prediction and exploration of response surfaces. Multi-fidelity variations of GPs further leverage information from cheap and low fidelity model simulations in order to improve their predictive performance on the high fidelity model. In order to cope with the high volume of data required to train GPs in high dimensional design spaces, a common practice is to introduce latent design variables that are typically projections of the original input space to a lower dimensional subspace, and therefore substitute the problem of learning the initial high dimensional mapping, with that of training a GP on a low dimensional space. Here in this paper, we present a Bayesian approach to identify optimal transformations that map the input points to low dimensional latent variables. The \projection" mapping consists of an orthonormal matrix that is considered a priori unknown and needs to be inferred jointly with the GP parameters, conditioned on the available training data. The proposed Bayesian inference scheme relies on a two-step iterative algorithm that samples from the marginal posteriors of the GP parameters and the projection matrix respectively, both using Markov Chain Monte Carlo (MCMC) sampling. In order to take into account the orthogonality constraints imposed on the orthonormal projection matrix, a Geodesic Monte Carlo sampling algorithm is employed, that is suitable for exploiting probability measures on manifolds. We extend the proposed framework to multi-fidelity models using GPs including the scenarios of training multiple outputs together. We validate our framework on three synthetic problems with a known lower-dimensional subspace. The benefits of our proposed framework, are illustrated on the computationally challenging aerodynamic optimization of a last-stage blade for an industrial gas turbine, where we study the effect of an 85-dimensional shape parameterization of a three-dimensional airfoil on two output quantities of interest, specifically on the aerodynamic efficiency and the degree of reaction

42 ENGINEERING↗
DOE OSTI2024

Machine Learning Accelerated First-Principles Study of the Hydrodeoxygenation of Propanoic Acid

The complex reaction network of catalytic biomass conversions often involves hundreds of surface intermediates and thousands of reaction steps, greatly hindering the rational design of metal catalysts for these conversions. Here, we present a framework of machine learning (ML)-accelerated first-principles studies for the hydrodeoxygenation (HDO) of propanoic acid over transition metal surfaces. The microkinetic model (MKM) is initially parametrized by ML-predicted energies and iteratively improved by identifying the rate-determining species and steps (RDS), computing their energies by density functional theory (DFT), and reparameterizing the MKM until all the RDS are computed by DFT. The Gaussian process (GP) model performs significantly better than the linear ridge regression model for predicting both the adsorption free energies and transition state free energies. Parameterized with energies from the GP model, only 5–20% of the full reaction network has to be computed by DFT for the MKM to possess DFT-level accuracy for the TOF and dominant reaction pathway. While the linear ridge regression model performs worse than the GP model, its performance is greatly improved when only transition states are predicted by the regression model and adsorption energies are computed by DFT. Overall, we find that a high accuracy in adsorption free energies is more important for a reliable MKM than a high accuracy in TS free energies. Lastly, based on the GP model with GOH and GCHCHCO as catalyst descriptors, we build two-dimensional volcano plots in activity and selectivity that can help design promising alloy catalysts for HDO reactions of organic acids.

adsorption↗
DOE OSTI2021

Synthesis and Structure–Activity Characterization of a Single-Site MoO 2 Catalytic Center Anchored on Reduced Graphene Oxide

Molecularly derived single-site heterogeneous catalysts can bridge the understanding and performance gaps between conventional homogeneous and heterogeneous catalysis, guiding the rational design of next-generation catalysts. While impressive advances have been made with well-defined oxide supports, the structural complexity of other supports and the nature of the grafted surface species present an intriguing challenge. In this study, single-site Mo(=O) 2 species grafted onto reduced graphene oxide (rGO/MoO 2 ) are characterized by XPS, DRIFTS, powder XRD, N 2 physisorption, NH 3 -TPD, aqueous contact angle, active site poisoning assay, Mo EXAFS, model compound single-crystal XRD, DFT, and catalytic performance. NH 3 -TPD reveals that the anchored MoO 2 moiety is not strongly acidic, while Mo 3d 5/2 XPS assigns the oxidation state as Mo(VI), and XRD shows little rGO periodicity change on MoO 2 grafting. Contact angle analysis shows that MoO 2 grafting consumes rGO surface polar groups, yielding a more hydrophobic surface. The rGO/MoO 2 DRIFTS assigns features at 959 and 927 cm –1 to the symmetric and antisymmetric Mo=O stretching modes, respectively, of an isolated cis-(O=Mo=O) moiety, in agreement with DFT computation. Moreover, the Mo EXAFS rGO/MoO 2 structural data are consistent with isolated (C–O) 2– Mo(=O) 2 species having two Mo=O bonds and two Mo–O bonds at distances of 1.69(3) and 1.90(3) Å, respectively. rGO/MoO 2 is also more active than the previously reported AC/MoO 2 catalyst, with reductive carbonyl coupling TOFs approaching 1.81 × 10 3 h –1 . rGO/MoO 2 is environmentally robust and multiply recyclable with 69 ± 2% of the Mo sites catalytically significant. Altogether, rGO/MoO 2 is a structurally well-defined and versatile single-site Mo(VI) dioxo heterogeneous catalytic system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Learning heterogeneous reaction kinetics from X-ray videos pixel by pixel

Reaction rates at spatially heterogeneous, unstable interfaces are notoriously difficult to quantify, yet are essential in engineering many chemical systems, such as batteries and electrocatalysts. Experimental characterizations of such materials by operando microscopy produce rich image datasets, but data-driven methods to learn physics from these images are still lacking because of the complex coupling of reaction kinetics, surface chemistry and phase separation. Here we show that heterogeneous reaction kinetics can be learned from in situ scanning transmission X-ray microscopy (STXM) images of carbon-coated lithium iron phosphate (LFP) nanoparticles. Combining a large dataset of STXM images with a thermodynamically consistent electrochemical phase-field model, partial differential equation (PDE)-constrained optimization and uncertainty quantification, we extract the free-energy landscape and reaction kinetics and verify their consistency with theoretical models. We also simultaneously learn the spatial heterogeneity of the reaction rate, which closely matches the carbon-coating thickness profiles obtained through Auger electron microscopy (AEM). Across 180,000 image pixels, the mean discrepancy with the learned model is remarkably small (<7%) and comparable with experimental noise. Our results open the possibility of learning nonequilibrium material properties beyond the reach of traditional experimental methods and offer a new non-destructive technique for characterizing and optimizing heterogeneous reactive surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

M3 milestone: Advanced contact 2021

This report describes advanced contact approaches and implementations in FY21 for use in emerging reactors with geometries that differ from LWR/EBR-II cylindrical fuel. Contact remains a challenging and crucially important component of our modeling toolkit. While significant improvements have been made through mortar and automatic differentiation, we explored advanced approaches (i.e., dual mortar) that yields better conditioned systems and will improve the robustness and performance of BISON contact problems. This effort is relevant to emerging reactor types, such as micro reactors and the corresponding complex and numerous contact surfaces. In this report, improvements of the mortar-based contact formulation are described. Benchmark problems and BISON assessment cases are included to demonstrate the improvements and advantages that are brought by the recent capability. Remaining issues are discussed and corresponding development plans are outlined.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

Evaluation of Turbulence and Dispersion in Multiscale Atmospheric Simulations over Complex Urban Terrain during the Joint Urban 2003 Field Campaign

Abstract This paper evaluates the representation of turbulence and its effect on transport and dispersion within multiscale and microscale-only simulations in an urban environment. These simulations, run using the Weather Research and Forecasting Model with the addition of an immersed boundary method, predict transport and mixing during a controlled tracer release from the Joint Urban 2003 field campaign in Oklahoma City, Oklahoma. This work extends the results of a recent study through analysis of turbulence kinetic energy and turbulence spectra and their role in accurately simulating wind speed, direction, and tracer concentration. The significance and role of surface heat fluxes and use of the cell perturbation method in the numerical simulation setup are also examined. Our previous study detailed the model development necessary for our multiscale simulations, examined model skill at predicting wind speeds and tracer concentrations, and demonstrated that dynamic downscaling from mesoscale to microscale through a sequence of nested simulations can improve predictions of transport and dispersion relative to a microscale-only simulation forced by idealized meteorology. Here, predictions are compared with observations to assess qualitative agreement and statistical model skill at predicting wind speed, wind direction, tracer concentration, and turbulent kinetic energy at locations throughout the city. We also investigate the scale distribution of turbulence and the associated impact on model skill, particularly for predictions of transport and dispersion. Our results show that downscaled large-scale turbulence, which is unique to the multiscale simulations, significantly improves predictions of tracer concentrations in this complex urban environment. Significance Statement Simulations of atmospheric transport and mixing in urban environments have many applications, including pollution modeling for urban planning or informing emergency response following a hazardous release. These applications include phenomena with spatial scales spanning from millimeters to kilometers. Most simulations resolve flow only within the urban area of interest, omitting larger scales of turbulence and regional influences. This study examines a method that resolves both the small and large-scale flow features. We evaluate simulation accuracy by comparing predictions with observations from an experiment involving the release of a tracer gas in Oklahoma City, Oklahoma, with emphasis on correctly modeling turbulent fluctuations. Our results demonstrate the importance of resolving large-scale flow features when predicting transport and dispersion in urban environments.

42 ENGINEERING↗
DOE OSTI2023

Atomic layer deposition for surface area determination of solid oxide electrodes

Surface area measurements are important for characterizing porous solids, but commonly used methods such as Brunauer–Emmett–Teller (BET) gas adsorption and computed nanotomography are lacking for certain applications such as the development of solid oxide fuel cell electrodes, which often have absolute surface areas <1 m 2 and contain nanoscale features. Presented is a novel method for the surface area determination of samples with total measurable areas of 1–1000 cm 2 with a standard deviation ± 1 cm 2 , utilizing the atomic layer deposition (ALD) of Al 2 O 3 over microstructurally complex internal porosity. The volume of alumina is then quantified using plasma spectroscopy and converted to an area using the known ALD layer thickness. Under the modest ALD reactor soak times used (8.5 s), the precursor penetration depth is found to be ~50 μm, exceeding the requirement for uniformly coating SOFC functional layers. A model system, (La 0.8 Sr 0.2 ) 0.98 MnO 3–δ /Ce 0.9 Gd 0.1 O 1.95 (LSM/GDC) scaffolds of ~2.7 m 2 g –1 , was measured using the technique and compared against the BET method, and comparable results were obtained but with 1000 times less material needed. The technique is demonstrated for measurements in two example areas of active SOFC research: exsolved (Ni, Fe) nanoparticles on an Sr(Ti, Fe, Ni)O 3–δ electrode and PrO x catalyst nanoparticles infiltrated onto LSM/GDC scaffolds. Finally, the technique may be broadly useful wherever the accurate surface area determination of small absolute quantities of porous ceramic structures on the order of 0.1–50 m 2 g –1 is sought.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Properties of the neutron star crust: Quantifying and correlating uncertainties with improved nuclear physics

A compressible liquid-drop model (CLDM) is used to correlate uncertainties associated with the properties of the neutron star (NS) crust with theoretical estimates of the uncertainties associated with the equation of state (EOS) of homogeneous neutron and nuclear matter. For the latter, we employ recent calculations based on Hamiltonians constructed using chiral effective-field theory (χEFT). Fits to experimental nuclear masses are employed to constrain the CLDM further, and we find that they disfavor some of the χEFT Hamiltonians. The CLDM allows us to study the complex interplay between bulk, surface, curvature, and Coulomb contributions, and their impact on the NS crust. It also reveals how the curvature energy alters the correlation between the surface energy and the bulk symmetry energy. Here our analysis quantifies how the uncertainties associated with the EOS of homogeneous matter implies significant uncertainties for the composition of the crust, its proton fraction, and the volume fraction occupied by nuclei. We find that the finite-size effects impact the crust composition but have a negligible effect on the net isospin asymmetry of matter. The isospin asymmetry is largely determined by the bulk properties and the isospin dependence of the surface energy. The most significant uncertainties associated with matter properties in the densest regions of the crust, the precise location of the crust-core transition, are found to be strongly correlated with uncertainties associated with the Hamiltonians. By adopting a unified model to describe the crust and the core of NSs, we tighten the correlation between their global properties such as their mass-radius relationship, moment of inertia, crust thickness, and tidal deformability with uncertainties associated with the nuclear Hamiltonians.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Three-dimensional seismic characterization and imaging of the Soda Lake geothermal field

Accurate characterization of subsurface geophysical properties and detection of the fault system are essential for geothermal energy exploration and production. The Soda Lake geothermal field is in western Nevada with a complex fault system. Previous seismic characterization only produced a low-resolution, smooth velocity model along with a simple, conceptual fault model. Using optimized correlation-based full-waveform inversion, wavefield-separation-based reverse-time migration, and automatic fault detection techniques, we present 3D seismic characterization for the Soda Lake geothermal field using 3D surface seismic data acquired with Vibroseis sources. Here, we obtain 3D high-resolution velocity, density, and acoustic impedance models, 3D seismic images with different grid spacings, and a high-resolution fault system. Consistency check between the constructed faults and currently active injection and production geothermal wells verifies that our seismic inversion and imaging results and detected faults are reliable. These results can provide valuable information for optimizing well placement and geothermal energy production at the Soda Lake geothermal field.

15 GEOTHERMAL ENERGY↗
DOE OSTI2025

Structural Evolution of Mixed-Addenda Keggin Polyoxometalate Anions with Atom-by-Atom Substitution

Polyoxometalates (POMs) are molecular metal oxides with distinctive electronic properties that make them promising materials for applications in energy, sensors, and memory devices. One of the most promising methods of tuning the stability, photochromic, redox, and electron-spin properties of POMs is through the substitution of the metal “addenda” atoms that, along with oxygen, constitute their cage-like structures. Because traditional synthesis methods typically produce a distribution of POMs, the isolation and characterization of multimetallic POMs with predetermined stoichiometry remains challenging. The presence of multiple energetically accessible isomers further complicates the experimental characterization and theoretical modeling of multimetallic POMs. Herein, we leverage the distinguishing mass-selection capabilities of ion soft landing to prepare stoichiometrically selected Keggin PMo x W 12-x O 40 3- (x = 0 – 6, 8, 10, and 12) POMs on self-assembled monolayer surfaces free of the solvent molecules and counterions that often confound characterization of complex species at interfaces. The structures of the supported POMs are characterized with atom-by-atom precision using in situ infrared (IR) reflection absorption spectroscopy complemented by detailed density functional theory calculations. Our joint experimental and theoretical results reveal an almost linear shift in the positions of the IR bands towards lower wavenumbers with an increase in the number of lighter molybdenum atoms compared to heavier W atoms in PMoxW 12-x O 40 3- . The theoretical calculations also indicate that numerous isomeric structures may be populated at the experimental conditions and, consequently, contribute to the overall IR spectra. In conclusion, our findings indicate that in addition to the number of substituted addenda atoms and the presence of multiple isomeric structures, interactions with the surface play an important role in determining the IR spectra and structure of supported bimetallic POMs.

Prabhakaran, Venkateshkumar [Pacific Northwest Nat↗
DOE OSTI2024

Bridging molecular-scale interfacial science with continuum-scale models

Solid–water interfaces are crucial for clean water, conventional and renewable energy, and effective nuclear waste management. However, reflecting the complexity of reactive interfaces in continuum-scale models is a challenge, leading to oversimplified representations that often fail to predict real-world behavior. This is because these models use fixed parameters derived by averaging across a wide physicochemical range observed at the molecular scale. Recent studies have revealed the stochastic nature of molecular-level surface sites that define a variety of reaction mechanisms, rates, and products even across a single surface. To bridge the molecular knowledge and predictive continuum-scale models, we propose to represent surface properties with probability distributions rather than with discrete constant values derived by averaging across a heterogeneous surface. This conceptual shift in continuum-scale modeling requires exponentially rising computational power. By incorporating our molecular-scale understanding of solid–water interfaces into continuum-scale models we can pave the way for next generation critical technologies and novel environmental solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

A minimal complex of KHNYN and zinc-finger antiviral protein binds and degrades single-stranded RNA

Detecting viral infection is a key role of the innate immune system. The genomes of some RNA viruses have a high CpG dinucleotide content relative to most vertebrate cell RNAs, making CpGs a molecular marker of infection. The human zinc-finger antiviral protein (ZAP) recognizes CpG, mediates clearance of the foreign CpG-rich RNA, and causes attenuation of CpG-rich RNA viruses. While ZAP binds RNA, it lacks enzymatic activity that might be responsible for RNA degradation and thus requires interacting cofactors for its function. One of these cofactors, KHNYN, has a predicted nuclease domain. Using biochemical approaches, we found that the KHNYN NYN domain is a single-stranded RNA ribonuclease that does not have sequence specificity and digests RNA with or without CpG dinucleotides equivalently in vitro. We show that unlike most KH domains, the KHNYN KH domain does not bind RNA. Indeed, a crystal structure of the KH region revealed a double-KH domain with a negatively charged surface that accounts for the lack of RNA binding. Rather, the KHNYN C-terminal domain (CTD) interacts with the ZAP RNA-binding domain (RBD) to provide target RNA specificity. We define a minimal complex composed of the ZAP RBD and the KHNYN NYN-CTD and use a fluorescence polarization assay to propose a model for how this complex interacts with a CpG dinucleotide-containing RNA. In the context of the cell, this module would represent the minimum ZAP and KHNYN domains required for CpG-recognition and ribonuclease activity essential for attenuation of viruses with clusters of CpG dinucleotides.

Yeoh, Zoe C. (ORCID:0000000226949068)↗