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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

High-fidelity wave data from MarineLabs CoastScout™ buoys supporting WEC demonstration at Scripps Pier

Two MarineLabs CoastScout™ buoys were deployed off La Jolla, California in February 2020 to provide high-resolution wave elevation time series data in support of CalWave Power Technologies’ XWave WEC deployment. The buoys are positioned approximately 300m from a longterm wave monitoring station operated by the Coastal Data Information Program. Both CoastScout hull types showed excellent agreement with the reference Datawell Directional Waverider MkIII (Hs r 2 =0.94, m0 r 2 =0.88). The CoastScout buoys maintained 100% uptime throughout an initial 6- month intercomparison period. CalWave used 5-Hz wave train data from this period to drive physical hardware-in-the-loop tests of the XWave power take-off. Throughout the deployment, the CoastScout buoys will provide near-real-time bulk wave parameters to help CalWave operators safely and efficiently operate the WEC. In post-processing, high-fidelity wave resolution will be used to associate individual waves with onboard measurements from Fiber Bragg Grating strain gauges and external pressure sensors.

16 TIDAL AND WAVE POWER↗
DOE OSTI2021

Mesoscale Convective Systems Dominate the Energetics of the South Asian Summer Monsoon Onset

The onset of the South Asian summer monsoon (SASM) is featured as an abrupt increase of precipitation and atmospheric column-integrated moist static energy (MSE). Using convection permitting simulations, a novel cloud tracking technique, and an MSE budget, the relative roles of mesoscale convective systems (MCSs) and non-MCS isolated deep convection in the SASM onset are studied. The analysis shows MCSs play a crucial role in the sudden increases of rainfall, diabatic MSE sources, and the subsequent enhanced export of column-integrated MSE during the onset. A “diabatic sources-energy export” plane analysis delineates the different roles of MCSs and non-MCS deep convection in the SASM onset. Although deep convection always leads to a net energy export, mesoscale organization of deep convection dominates the convection associated positive feedbacks that accelerate the energy cycle of the SASM onset. Sensitivity experiment shows that the results are insensitive to the model resolutions.

Chen, Xingchao↗
DOE OSTI2020

Integrating high resolution drone imagery and forest inventory to distinguish canopy and understory trees and quantify their contributions to forest structure and dynamics

Tree growth and survival differ strongly between canopy trees (those directly exposed to overhead light), and understory trees. However, the structural complexity of many tropical forests makes it difficult to determine canopy positions. The integration of remote sensing and ground-based data enables this determination and measurements of how canopy and understory trees differ in structure and dynamics. Here we analyzed 2 cm resolution RGB imagery collected by a Remotely Piloted Aircraft System (RPAS), also known as drone, together with two decades of bi-annual tree censuses for 2 ha of old growth forest in the Central Amazon. We delineated all crowns visible in the imagery and linked each crown to a tagged stem through field work. Canopy trees constituted 40% of the 1244 inventoried trees with diameter at breast height (DBH) > 10 cm, and accounted for ~70% of aboveground carbon stocks and wood productivity. The probability of being in the canopy increased logistically with tree diameter, passing through 50% at 23.5 cm DBH. Diameter growth was on average twice as large in canopy trees as in understory trees. Growth rates were unrelated to diameter in canopy trees and positively related to diameter in understory trees, consistent with the idea that light availability increases with diameter in the understory but not the canopy. The whole stand size distribution was best fit by a Weibull distribution, whereas the separate size distributions of understory trees or canopy trees > 25 cm DBH were equally well fit by exponential and Weibull distributions, consistent with mechanistic forest models. The identification and field mapping of crowns seen in a high resolution orthomosaic revealed new patterns in the structure and dynamics of trees of canopy vs. understory at this site, demonstrating the value of traditional tree censuses with drone remote sensing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Global and local texture development during initial plastic deformation of cold-pilgered Zircaloy-4 tubing

In this work we present a thorough characterization of the texture development during the initial step of a cold pilgering process of a Zircaloy-4 TREX tube, on which the axial cross section is reduced by 80% over a 40cm length with an overall Q-ratio of 2.34, followed by a recrystallization thermal treatment. Texture across a tapered specimen representing this working zone was characterized by neutron diffraction and high energy synchrotron x-ray diffraction at 28 positions (4 locations along its length and 7 locations across its thickness with 0.3 mm spatial resolution), and on the deformed end after the thermal treatment. Results show that the starting material (TREX tube) presents a texture gradient through its wall thickness, with the c poles aligned to the hoop direction at the outer surface (with radial and hoop Kearns factors: f R =0.36, f H = 0.50), and gradually rotating around the axial direction to become a quasi-radial orientation (~35 o out of the radial direction) at the inner surface ( f R =0.43, f H =0.35). The overall texture becomes more radial due to the cold pilgering, but the texture gradient remains during the whole deformation process, being always more radial at the inner surface, ( f R =0.53, f H =0.37 at 80%) than at the outer surface ( f R =0.41, f H =0.50at 80%). The most remarkable changes in texture produced by the rolling process is a 30 o rotation of the grains around their c-axis, producing a marked increase of the <11 2 ¯ 0> // axial fiber texture at expenses of the original <10 1 ¯ 0> // axial fiber texture observed in the TREX tube. The observed changes in texture during deformation were correctly explained by visco-plastic self-consistent (VPSC) modelling. This was achieved after the inclusion of the basal <a> slip system, which plays a central role to explain the 30 o rotation around the c-axis during deformation. The texture evolution was correctly described after the inclusion of a drag effect to grain rotation due to the interaction with neighbouring grains. The through thickness texture differences are greatly reduced by the recrystallization thermal treatment, with similar Kearns factors at the inner surface ( f R =0.50, f H =0.28) and the outer surface ( f R =0.48, f H =0.39). The predominance of the <10 1 ¯ 0> // axial fiber texture is recovered after recrystallization.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Site specific porosity-thermal performance correlations in neutron irradiated U-10Zr fuel

In this work, we present a site-specific three-dimensional analysis of porosity evolution in neutron-irradiated U–10Zr metallic fuel using high-resolution synchrotron X-ray tomography. Focused ion beam cubic lift-outs from four radial positions—fuel center, middle, edge, and fuel-cladding interaction (FCCI) zones—were imaged, reconstructed, and segmented to quantify pore volume, density, morphology, and pore connectivity. Porosity increased modestly from 5.5% at the center to 10.5% at the edge, yet pore number density increased by over two orders of magnitude in the fuel portion near the FCCI interface (from 4.8 x 10 4 to 6.0 x 10 6 pores/mm 3 ). Morphological classification revealed a progression from small spherical pores at the center to equiaxed and tortuous networks at the periphery, with enhanced orientation along the radial direction. Connectivity and permeability analysis reveal that the FCCI region maintains dense, highly interconnected pores despite a moderate volume fraction, enabling rapid fission gas transport and lanthanide migration. Effective thermal conductivity models incorporating sodium logging confirm that these site-specific pore features critically influenced heat transport during reactor irradiation. These findings demonstrate that pore topology—not just porosity fraction—controls thermal performance and thermal pathways in U–10Zr fuels, impacting fuel thermal performance in a reactor.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Innovative laser-based methods for monitoring fuel retention in ITER

This paper addresses the challenge of tritium inventory management in ITER and future fusion reactors, highlighting the importance of accurate tritium measurement and its spatial distribution within the vacuum vessel. Given ITER’s operational constraints, especially the limit on tritium retention, precise measurement is essential for both safety and regulatory compliance. To tackle these questions, the paper presents the T-monitor diagnostic system developed by Forschungszentrum Jülich, which uses Laser-Induced Desorption (LID) in combination with Diagnostic Residual Gas Analysis (DRGA) to measure hydrogen isotope concentrations on the surface of divertor tiles. The system integrates a high-power laser, advanced optical components, and a Fast Scanning Mirror Unit (FSMU) for accurate laser spot positioning with rapid response. Designed to measure in situ tritium retention, the diagnostic provides high-resolution spatial mapping, vital for evaluating detritiation strategies. The laser heating process increases the divertor surface temperature to 1600 K within the laser spot, promoting hydrogen isotope desorption. Accurate measurements require the precise control of laser parameters, including pulse duration and spot size, with a target relative accuracy of 20%. The optical design includes both in-vessel and ex-vessel components, such as durable high-reflectivity mirrors made of gold and copper, selected not only for their infrared performance but also for their transmission of visible wavelengths for observation purposes. To protect optical components from contamination, a pneumatic shutter is used.

Hydrogen isotopes↗
DOE OSTI2024

Deep learning-based spatiotemporal multi-event reconstruction for delay line detectors

Abstract Accurate observation of two or more particles within a very narrow time window has always been a challenge in modern physics. It creates the possibility of correlation experiments, such as the ground-breaking Hanbury Brown–Twiss experiment, leading to new physical insights. For low-energy electrons, one possibility is to use a Microchannel plate with subsequent delay lines for the readout of the incident particle hits, a setup called a Delay Line Detector. The spatial and temporal coordinates of more than one particle can be fully reconstructed outside a region called the dead radius. For interesting events, where two electrons are close in space and time, the determination of the individual positions of the electrons requires elaborate peak finding algorithms. While classical methods work well with single particle hits, they fail to identify and reconstruct events caused by multiple nearby particles. To address this challenge, we present a new spatiotemporal machine learning model to identify and reconstruct the position and time of such multi-hit particle signals. This model achieves a much better resolution for nearby particle hits compared to the classical approach, removing some of the artifacts and reducing the dead radius a factor of eight. We show that machine learning models can be effective in improving the spatiotemporal performance of delay line detectors.

Computer Science↗
DOE OSTI2022

Sweep-tracing algorithm: in silico slip crystallography and tension-compression asymmetry in BCC metals

Abstract Direct Molecular Dynamics (MD) simulations are being increasingly employed to model dislocation-mediated crystal plasticity with atomic resolution. Thanks to the dislocation extraction algorithm (DXA), dislocation lines can be now accurately detected and positioned in space and their Burgers vector unambiguously identified in silico, while the simulation is being performed. However, DXA extracts static snapshots of dislocation configurations that by themselves present no information on dislocation motion. Referred to as a sweep-tracing algorithm (STA), here we introduce a practical computational method to observe dislocation motion and to accurately quantify its important characteristics such as preferential slip planes (slip crystallography). STA reconnects pairs of successive snapshots extracted by DXA and computes elementary slip facets thus precisely tracing the motion of dislocation segments from one snapshot to the next. As a testbed for our new method, we apply STA to the analysis of dislocation motion in large-scale MD simulations of single crystal plasticity in BCC metals. We observe that, when the crystal is subjected to uniaxial deformation along its [001] axis, dislocation slip predominantly occurs on the {112} maximum resolved shear stress plane under tension, while in compression slip is non-crystallographic (pencil) resulting in asymmetric mechanical response. The marked contrast in the observed slip crystallography is attributed to the twinning/anti-twinning asymmetry of shears in the {112} planes relatively favoring dislocation motion in the twinning sense while hindering dislocations from moving in the anti-twinning directions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Neutrino Oscillations at the NOvA Experiment

NOvA is a long-baseline neutrino oscillation experiment located at Fermi National Accelerator Laboratory (Fermilab) in Batavia, IL, USA. Its main goal is to extract neutrino oscillation parameters by examining the disappearance of $\nu_\mu \ (\bar{\nu}_\mu)$ and the appearance of $\nu_e \ (\bar{\nu}_e)$ at its far detector. The experiment uses the NuMI beamline at Fermilab, which delivers a high-purity neutrino and antineutrino beam. NOvA consists of two functionally similar, high-resolution liquid scintillator tracking calorimeters, both placed 14.6 milliradians off the beam axis. The near detector, positioned 100 m underground and 1 km from the beam's origin, captures unoscillated $\nu_\mu (\bar{\nu}_\mu)$ and instrinsic beam $\nu_e \ (\bar{\nu}_e)$ events. The far detector, located 810 km away from the beam source in Ash River, Minnesota, measures both unoscillated $\nu_\mu \ (\bar{\nu}_\mu)$ and those that have oscillated into $\nu_\mu \ (\bar{\nu}_\mu) \to \nu_e \ (\bar{\nu}_e)$. This poster will cover the latest results on three-flavor neutrino oscillation parameters, derived from an exposure of neutrino beam of $26.60 \times 10^{20}$ POT and anti-neutrino beam exposure of $12.50\times 10^{20}$ POT including an additional low energy $\nu_e$ sample.

Singh, Ishwar [Delhi U.]↗
DOE OSTI2022

Viscoelastic Particle Focusing and Separation in a Spiral Channel

As one type of non-Newtonian fluid, viscoelastic fluids exhibit unique properties that contribute to particle lateral migration in confined microfluidic channels, leading to opportunities for particle manipulation and separation. In this paper, particle focusing in viscoelastic flow is studied in a wide range of polyethylene glycol (PEO) concentrations in aqueous solutions. Polystyrene beads with diameters from 3 to 20 μm are tested, and the variation of particle focusing position is explained by the coeffects of inertial flow, viscoelastic flow, and Dean flow. We showed that particle focusing position can be predicted by analyzing the force balance in the microchannel, and that particle separation resolution can be improved in viscoelastic flows.

42 ENGINEERING↗
DOE OSTI2020

The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn’s Disease: A Randomized Diet Controlled Trial

Background: Crohn’s disease (CD) is a chronic inflammatory intestinal disorder associated with intestinal dysbiosis. Diet modulates the intestinal microbiome and therefore has a therapeutic potential. The aim of this study is to determine the potential efficacy of three versions of the specific carbohydrate diet (SCD) in active Crohn’s Disease. Methods: 18 patients with mild/moderate CD (PCDAI 15–45) aged 7 to 18 years were enrolled. Patients were randomized to either SCD, modified SCD(MSCD) or whole foods (WF) diet. Patients were evaluated at baseline, 2, 4, 8 and 12 weeks. PCDAI, inflammatory labs and multi-omics evaluations were assessed. Results: Mean age was 14.3 ± 2.9 years. At week 12, all participants (n = 10) who completed the study achieved clinical remission. The C-reactive protein decreased from 1.3 ± 0.7 at enrollment to 0.9 ± 0.5 at 12 weeks in the SCD group. In the MSCD group, the CRP decreased from 1.6 ± 1.1 at enrollment to 0.7 ± 0.1 at 12 weeks. In the WF group, the CRP decreased from 3.9 ± 4.3 at enrollment to 1.6 ± 1.3 at 12 weeks. In addition, the microbiome composition shifted in all patients across the study period. While the nature of the changes was largely patient specific, the predicted metabolic mode of the organisms increasing and decreasing in activity was consistent across patients. Conclusions: This study emphasizes the impact of diet in CD. Each diet had a positive effect on symptoms and inflammatory burden; the more exclusionary diets were associated with a better resolution of inflammation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Aerosol-induced closure of marine cloud cells: enhanced effects in the presence of precipitation

Abstract. The Weather Research Forecasting (WRF) version 4.3 model is configured within a Lagrangian framework to quantify the impact of aerosols on evolving cloud fields. Kilometer-scale simulations utilizing meteorological boundary conditions are based on 10 case study days offering diverse meteorology during the Aerosol and Cloud Experiments in the Eastern North Atlantic (ACE-ENA). Measurements from aircraft, the ground-based Atmosphere Radiation Measurement (ARM) site at Graciosa Island in the Azores, and A-Train and geostationary satellites are utilized for validation, demonstrating good agreement with the WRF-simulated cloud and aerosol properties. Higher aerosol concentration leads to suppressed drizzle and increased cloud water content in all case study days. These changes lead to larger radiative cooling rates at cloud top, enhanced vertical velocity variance, and increased vertical and horizontal wind speed near the base of the lower-tropospheric inversion. As a result, marine cloud cell area expands, narrowing the gap between shallow clouds and increasing cloud optical thickness, liquid water content, and the top-of-atmosphere outgoing shortwave flux. While similar aerosol effects are observed in lightly to non-raining clouds, they tend to be smaller by comparison. These simulations show a relationship between cloud cell area expansion and the radiative adjustments caused by liquid water path and cloud fraction changes. The adjustments are positive and scale as 74 % and 51 %, respectively, relative to the Twomey effect. While higher-resolution large-eddy simulations may provide improved representation of cloud-top mixing processes, these results emphasize the importance of addressing mesoscale cloud-state transitions in the quantification of aerosol radiative forcing that cannot be attained from traditional climate models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Giant nonlinear optical responses from photon-avalanching nanoparticles

Avalanche phenomena use steeply nonlinear dynamics to generate disproportionately large responses from small perturbations, and are found in a multitude of events and materials. Photon avalanching enables technologies such as optical phase-conjugate imaging, infrared quantum counting and efficient upconverted lasing. However, the photon-avalanching mechanism underlying these optical applications has been observed only in bulk materials and aggregates, limiting its utility and impact. In this study we report the realization of photon avalanching at room temperature in single nanostructures-small, Tm 3+ -doped upconverting nanocrystals-and demonstrate their use in super-resolution imaging in near-infrared spectral windows of maximal biological transparency. Avalanching nanoparticles (ANPs) can be pumped by continuous-wave lasers, and exhibit all of the defining features of photon avalanching, including clear excitation-power thresholds, exceptionally long rise time at threshold, and a dominant excited-state absorption that is more than 10,000 times larger than ground-state absorption. Beyond the avalanching threshold, ANP emission scales nonlinearly with the 26th power of the pump intensity, owing to induced positive optical feedback in each nanocrystal. This enables the experimental realization of photon-avalanche single-beam super-resolution imaging with sub-70-nanometre spatial resolution, achieved by using only simple scanning confocal microscopy and without any computational analysis. Pairing their steep nonlinearity with existing super-resolution techniques and computational methods, ANPs enable imaging with higher resolution and at excitation intensities about 100 times lower than other probes. The low photon-avalanching threshold and excellent photostability of ANPs also suggest their utility in a diverse array of applications, including sub-wavelength imaging and optical and environmental sensing.

36 MATERIALS SCIENCE↗
DOE OSTI2021

High-Performance/-Precision/-Z(HPPZ) Scintillator Grids via Advanced Electrochemistry. Phase I – Project # 20210572MFR- Mid year review [Slides]

Scintillation grids with improved imaging resolution in time and space, are required for future mission needs at various facilities (pRad user station, LANSCE, DARHT, Scorpius etc). Current technologies use inorganic crystal scintillators, which are positioned within a high-Z scintillator septa. Dense and high-Z materials are optimal for gamma-ray detection making them promising candidates for development of high -performance/-precision/-Z (HPPZ) scintillator grids. The current resolution of standard chemical etching and fabrication processes of high-Z materials is very low, leading to undesired undercutting and ultimately reducing crystal performance efficiency. Goals are to: Perform initial feasibility studies with the aim of producing complex parts for applications with difficult-to-process high-Z material; Use of pulse and pulse-reverse electrochemical methods on additive approaches to produce high-precision Au and Re scintillator grids at a small scale; and, Follow up in Phase II with the delivery of a large-scale scintillator grid of the best material candidate with unprecedented properties for LANL needs determined in Phase I.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Supporting information for Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

In this work, we use few-shot learning to segment the body and vein architecture of P. trichocarpa leaves from high-resolution scans obtained in the UC Davis common garden. Leaf and vein segmentation are formulated as separate tasks, in which convolutional neural networks (CNNs) are used to iteratively expand partial segmentations until reaching stopping criteria. Our leaf and vein segmentation approaches use just 50 and 8 manually traced images for training, respectively, and are applied to a set of 2,634 top and bottom leaf scans. We show that both methods achieve high segmentation accuracy, in some cases exceeding even human-level segmentation. The leaf and vein segmentations are subsequently used to extract 68 morphological traits using traditional open-source image processing tools, which are validated using real-world physical measurements. For a biological perspective, we perform a genome-wide association study using the vein density trait to discover novel genetic architectures associated with multiple physiological processes relating to leaf development and function. In addition to sharing all of the few-shot learning code (see https://github.com/jlager/few-shot-leaf-segmentation), we are releasing all images, manual segmentations, model predictions, 68 extracted leaf phenotypes, and a new set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes. The data folder includes all images, ground truth segmentations, predicted segmentations, and extracted leaf traits. All images encode the sample ID in the file name by indicating the treatment, block, row, position, and leaf side, respectively. For example, the file, C_1_1_2_bot.jpeg, indicates the control treatment, block 1, row 1, position 2, and the bottom side of the leaf. Tabulated results include position IDs as well as the corresponding genotype IDs. The images folder includes the 2,906 high-resolution leaf scans taken in the field. The leaf_masks folder includes 50 ground truth segmentations used for training the leaf tracing algorithm. The leaf_preds folder includes the 2,906 predicted segmentations from the leaf tracing algorithm. The vein_masks folder includes 8 ground truth segmentations used for training the vein growing algorithm. The vein_preds folder includes the 1,453 predicted segmentations from the vein growing algorithm. The vein_probs folder includes the 1,453 predicted probability maps from the vein growing algorithm before thresholding. The genomes folder includes the set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes with a README file detailing the steps taken. The results folder includes: (i) raw values of the 68 predicted leaf traits in digital_traits.tsv, (ii) manually measured values of petiole length and width in manual_traits.tsv, (iii) thin plate spline (TPS) adjusted values of the vein density trait in vein_density_tps_adj.tsv, (iv) best linear unbiased prediction (BLUP) adjusted values of the vein density trait in vein_density_blups.tsv, and (v) GWAS results for the vein density trait, including chromosome positions and corresponding P values, in gwas_results.csv.

09 BIOMASS FUELS↗
DOE OSTI2026

Intrinsic energy and time resolution of the Jefferson Lab Hall C Neutral Particle Spectrometer

The Neutral Particle Spectrometer (NPS) is an advanced calorimeter designed to measure neutral electro- magnetic particles with high precision in energy, time, and position, under conditions of high luminosity and significant background. Integrated into the experimental setup of Hall C at Thomas Jefferson National Accelerator Facility, the NPS plays a critical role in studies of nucleon structure through exclusive and semi- inclusive reaction channels. Here, this paper presents an assessment of the detector’s performance characteristics, specifically its energy and timing resolution, derived from elastic electron–proton scattering data. We report an energy resolution between 1.2% and 1.3% in the 4.5–7.3 GeV range, and an intrinsic timing resolution better than 200 ps for energies above 500 MeV. These results serve as a reference for current and future precision measurements in hadronic physics.

Detector performance↗
DOE OSTI2020

A versatile Johansson-type tender x-ray emission spectrometer

We present a high energy resolution x-ray spectrometer for the tender x-ray regime (1.6–5.0 keV) that was designed and operated at Stanford Synchrotron Radiation Lightsource. The instrument is developed on a Rowland geometry (500 mm of radius) using cylindrically bent Johansson analyzers and a position sensitive detector. By placing the sample inside the Rowland circle, the spectrometer operates in an energy-dispersive mode with a subnatural line-width energy resolution (~0.32 eV at 2400 eV), even when an extended incident x-ray beam is used across a wide range of diffraction angles (~30° to 65°). The spectrometer is enclosed in a vacuum chamber, and a sample chamber with independent ambient conditions is introduced to enable a versatile and fast-access sample environment (e.g., solid/gas/liquid samples, in situ cells, and radioactive materials). The design, capabilities, and performance are presented and discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules

Flaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5’ end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5’ guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promoter function. To facilitate identification of small molecule binding sites in flavivirus SLA, we determined high-resolution structures of bottom and top stems of ZIKV SLA, which contain a single U- or G-bulge, respectively. Both bulge nucleotides exhibit multiple orientations, from folded back on the adjacent nucleotide to flipped out of the helix, and are stabilized by stacking or base triple interactions. These structures suggest that even a single unpaired nucleotide can provide flexibility to RNA structures and its conformation is mainly determined by the stabilizing chemical environment. To facilitate discovery of small molecule inhibitors that interfere with the functions of ZIKV SLA, we screened and identified compounds that bind to the bottom and top stems of ZIKV SLA.

Biochemistry & Molecular Biology↗