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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Molecular recognition of a host protein by NS1 of pandemic and seasonal influenza A viruses

The 1918 influenza A virus (IAV) caused the most severe flu pandemic in recorded human history. Nonstructural protein 1 (NS1) is an important virulence factor of the 1918 IAV. NS1 antagonizes host defense mechanisms through interactions with multiple host factors. One pathway by which NS1 increases virulence is through the activation of phosphoinositide 3-kinase (PI3K) by binding to its p85β subunit. Here we present the mechanism underlying the molecular recognition of the p85β subunit by 1918 NS1. Using X-ray crystallography, we determine the structure of 1918 NS1 complexed with p85β of human PI3K. We find that the 1918 NS1 effector domain (1918 NS1 ED ) undergoes a conformational change to bind p85β. Using NMR relaxation dispersion and molecular dynamics simulation, we identify that free 1918 NS1 ED exists in a dynamic equilibrium between p85β-binding–competent and –incompetent conformations in the submillisecond timescale. Moreover, we discover that NS1 ED proteins of 1918 (H1N1) and Udorn (H3N2) strains exhibit drastically different conformational dynamics and binding kinetics to p85β. These results provide evidence of strain-dependent conformational dynamics of NS1. Using kinetic modeling based on the experimental data, we demonstrate that 1918 NS1 ED can result in the faster hijacking of p85β compared to Ud NS1 ED , although the former has a lower affinity to p85β than the latter. Our results suggest that the difference in binding kinetics may impact the competition with cellular antiviral responses for the activation of PI3K. We anticipate that our findings will increase the understanding of the strain-dependent behaviors of influenza NS1 proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dynamic land use implications of rapidly expanding and evolving wind power deployment

Abstract The expansion of wind power poses distinct and varied geographic challenges to a sustainable energy transition. However, current knowledge of its land use impacts and synergies is limited by reliance on static characterizations that overlook the role of turbine technology and plant design in mediating interactions with the environment. Here, we investigate how wind technology development and innovation have shaped landscape interactions with social and ecological systems within the United States and contribute to evolving land area requirements. This work assesses trends in key land use facets of wind power using a holistic set of metrics to establish an evidence base that researchers, technology designers, land use managers, and policymakers can use in envisioning how future wind-intensive energy systems may be jointly optimized for clean energy, social, and environmental objectives. Since 2000, we find dynamic land occupancy patterns and regional trends that are driven by advancing technology and geographic factors. Though most historical U.S. wind deployment has been confined to the temperate grassland biome in the nation’s interior, regional expansion has implicated diverse land use and cover types. A large percentage of the typical wind plant footprint (∼96% to > 99%) is not directly impacted by permanent physical infrastructure, allowing for multiple uses in the spaces between turbines. Surprisingly, turbines are commonly close to built structures. Moreover, rangeland and cropland have supported 93.4% of deployment, highlighting potential synergies with agricultural lands. Despite broadly decreasing capacity densities, offsetting technology improvements have stabilized power densities. Land use intensity, defined as the ratio of direct land usage to lifetime power generation of wind facilities, has also trended downwards. Although continued deployment on disturbed lands, and in close proximity to existing wind facilities and other infrastructure, could minimize the extent of impacts, ambitious decarbonization trajectories may predispose particular biomes to cumulative effects and risks from regional wind power saturation. Increased land-use and sustainability feedback in technology and plant design will be critical to sustainable management of wind power.

17 WIND ENERGY↗
DOE OSTI2024

Surface molecular pump enables ultrahigh catalyst activity

The performance of electrocatalysts is critical for renewable energy technologies. While the electrocatalytic activity can be modulated through structural and compositional engineering following the Sabatier principle, the insufficiently explored catalyst-electrolyte interface is promising to promote microkinetic processes such as physisorption and desorption. By combining experimental designs and molecular dynamics simulations with explicit solvent in high accuracy, we demonstrated that dimethylformamide can work as an effective surface molecular pump to facilitate the entrapment of oxygen and outflux of water. Dimethylformamide disrupts the interfacial network of hydrogen bonds, leading to enhanced activity of the oxygen reduction reaction by a factor of 2 to 3. This strategy works generally for platinum-alloy catalysts, and we introduce an optimal model PtCuNi catalyst with an unprecedented specific activity of 21.8 ± 2.1 mA/cm 2 at 0.9 V versus the reversible hydrogen electrode, nearly double the previous record, and an ultrahigh mass activity of 10.7 ± 1.1 A/mg Pt .

Science & Technology - Other Topics↗
DOE OSTI2023

Dark Field Proton Radiography (Los Alamos LDRD Report)

Proton radiography at LANL (pRad) takes advantage of the high flux, high proton energy, and flexible timing structure of LANSCE's 800-MeV proton beam to visualize dense, dynamic systems under extreme strain. With recent needs identified for the development of the W93, the pRad team has been actively searching for ways to increase the facility's radiographic capabilities. Recently, we discovered that utilizing two magnetic lenses (one upstream and one downstream of the object), and specific combinations of collimator choices within the two lenses, that the signal-to-noise ratio was improved by more than a factor of two. However, we did not fully understand the mechanism, and found that results did not match forward modeling predictions. This work specifically sought to implement an engineering solution to solve this problem, through the development of an actuated collimator that reduced the time required to swap collimator settings from a typical 4-8 hours, to less than 30 seconds. This allowed, in combination with a unique multi-material, multi-resolution stepwedge, to acquire an unprecedently enormous dataset, with in total 24 collimation combinations, and multiple diffuser settings and pulse patterns, equivalent to almost a full run cycle's worth of data in a few days. This massive dataset is currently being harnessed to make a fully-predictive, ultra-fast Python-based model of the system, to dial in specific settings for any future experiments that fully optimize that radiographic sensitivity to the material of interest.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
NASA NTRS1995

Interactive flutter analysis and parametric study for conceptual wing design

An interactive computer program was developed for wing flutter analysis in the conceptual design stage. The objective was to estimate the flutter instability boundary of a flexible cantilever wing, when well defined structural and aerodynamic data are not available, and then study the effect of change in Mach number, dynamic pressure, torsional frequency, sweep, mass ratio, aspect ratio, taper ratio, center of gravity, and pitch inertia, to guide the development of the concept. The software was developed on MathCad (trademark) platform for Macintosh, with integrated documentation, graphics, database and symbolic mathematics. The analysis method was based on nondimensional parametric plots of two primary flutter parameters, namely Regier number and Flutter number, with normalization factors based on torsional stiffness, sweep, mass ratio, aspect ratio, center of gravity location and pitch inertia radius of gyration. The plots were compiled in a Vaught Corporation report from a vast database of past experiments and wind tunnel tests. The computer program was utilized for flutter analysis of the outer wing of a Blended Wing Body concept, proposed by McDonnell Douglas Corporation. Using a set of assumed data, preliminary flutter boundary and flutter dynamic pressure variation with altitude, Mach number and torsional stiffness were determined.

Mukhopadhyay, Vivek↗
DOE OSTI2023

Effective sensor location for detection of change in structural dynamic response

This paper investigates the sensitivity of structural system response to the sensor location by investigating consequences of small changes in the location to the structural system response. The paper discusses how maximum observability (based on mode shape and the participation of that mode in the input provided) drives optimal location. The structural responses were investigated in terms of the g-rms response for various low-frequency inputs (pure sinusoids and real-life inputs such as an earthquake and trains). Results were then analyzed in the context of Modal Contributions Factors (MCF) and changes to the Force-to-response Transfer Functions (TRFs). A modal-matching process is first presented using a Matlab TM -based Finite Element Method (FEM) model of a cantilever beam and instrumentation to determine the location of a small mass based on three different criteria. Subsequently, the structural response is investigated using experiments and the FEM model. The accelerometer of small mass (at 1/3 height) was moved up or down to obtain changes in the structural response (TRF) to various realistic low-frequency inputs. Modal Contribution Factor (MCF) and derivative (slope) of the associated mode-shapes were correlated to the observed changes in TRFs. Results show how optimal sensor locations for detecting change in structural response can be based on the MCFs and the associated mode-shapes.

Woodall, J.↗
DOE OSTI2026

Exploring the impact of nucleotide length on lipid nanoparticle structure and properties

Lipid nanoparticles (LNPs) are versatile carriers for nucleic acid (NA) therapeutics, including ASOs, siRNA, mRNA, and poly-IC. While lipid composition is known to influence LNP properties, the impact of NA length on morphology and internal structure is less understood, particularly during the stages of carrier–cargo assembly. Here, we examine NA length and lipid composition immediately after mixing using high-throughput SAXS, dynamic light scattering, and cryogenic electron microscopy. All LNPs form ordered NA/lipid compartments, with longer NAs promoting inverse hexagonal (H II ) phases and larger intercompartment distances. In contrast, short NAs, especially in formulations with SM102 ionizable lipid, favor lamellar phases. SAXS peak deconvolution quantifies ordered versus disordered phases via a Robustness of Ordered Phase factor, which correlates with particle size and encapsulation efficiency. Formulations with MC3 ionizable and DOPE helper lipids exhibit the most stable H II -phase packing, highlighting the role of helper-lipid curvature in compartment stabilization. Variations in NA compartmentalization indicate differences in payload capacity, offering a framework for rational LNP design across diverse nucleic acid cargos.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures

The first important step in a structure-based virtual screening is the judicious selection of a receptor protein. In cases where the holo protein receptor structure is unavailable, significant reduction in virtual screening performance has been reported. In this work, we present a robust method to generate reliable holo protein structure conformations from apo structures using molecular dynamics (MD) simulation with restraints derived from holo structure binding-site templates. We perform benchmark tests on two different datasets: 40 structures from a directory of useful decoy-enhanced (DUD-E) and 84 structures from the Gunasekaran dataset. Our results show successful refinement of apo binding-site structures toward holo conformations in 82% of the test cases. In addition, virtual screening performance of 40 DUD-E structures is significantly improved using our MD-refined structures as receptors with an average enrichment factor (EF), an EF1% value of 6.2 compared to apo structures with 3.5. Docking of native ligands to the refined structures shows an average ligand root mean square deviation (RMSD) of 1.97 Å (DUD-E dataset and Gunasekaran dataset) relative to ligands in the holo crystal structures, which is comparable to the self-docking (i.e., docking of the native ligand back to its crystal structure receptor) average, 1.34 Å (DUD-E dataset) and 1.36 Å (Gunasekaran dataset). On the other hand, docking to the apo structures yields an average ligand RMSD of 3.65 Å (DUD-E) and 2.90 Å (Gunasekaran). These results indicate that our method is robust and can be useful to improve virtual screening performance of apo structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1991

Surface disordering of Pb(110)

A molecular dynamics simulation of Pb(110), using embedded atom method energy functional and two-body potential derived for the purpose, shows that near 400 K the three surface layers begin to disorder well before the bulk (interior) layers. Transfer of atoms from the first subsurface layer to the surface layer occurs. Disordering propagates beyond the top three layers above 550 K, accompanied by formation of an adlayer and vacancies in the top three layers. Behavior of the two-dimensional layer structure factors indicates that disordering is anisotropic. Simulation results are consistent with experimental observations of surface roughening near 400 K and more extensive surface ordering above 525 K. Results are consistent with simulations for Ni and Al.

Tibbits, P.↗
NASA NTRS2006

Statistical Analyses of Satellite Cloud Object Data From CERES: Boundary-layer Cloud Objects During 1998 El Nino - Part 4

Three boundary-layer cloud object types, stratus, stratocumulus and cumulus, that occurred over the Pacific Ocean during January-August 1998, are identified from the CERES (Clouds and the Earth s Radiant Energy System) single scanner footprint (SSF) data from the TRMM (Tropical Rainfall Measuring Mission) satellite. This study emphasizes the differences and similarities in the characteristics of each cloud-object type between the tropical and subtropical regions and among different size categories and among small geographic areas. Both the frequencies of occurrence and statistical distributions of cloud physical properties are analyzed. In terms of frequencies of occurrence, stratocumulus clouds dominate the entire boundary layer cloud population in all regions and among all size categories. Stratus clouds are more prevalent in the subtropics and near the coastal regions, while cumulus clouds are relatively prevalent over open ocean and the equatorial regions, particularly, within the small size categories. The largest size category of stratus cloud objects occurs more frequently in the subtropics than in the tropics and has much larger average size than its cumulus and stratocumulus counterparts. Each of the three cloud object types exhibits small differences in statistical distributions of cloud optical depth, liquid water path, TOA albedo and perhaps cloud-top height, but large differences in those of cloud-top temperature and OLR between the tropics and subtropics. Differences in the sea surface temperature (SST) distributions between the tropics and subtropics influence some of the cloud macrophysical properties, but cloud microphysical properties and albedo for each cloud object type are likely determined by (local) boundary-layer dynamics and structures. Systematic variations of cloud optical depth, TOA albedo, cloud-top height, OLR and SST with cloud object sizes are pronounced for the stratocumulus and stratus types, which are related to systematic variations of the strength of inversion with cloud object sizes, produced by large-scale subsidence. The differences in cloud macrophysical properties over small regions are significantly larger than those of cloud microphysical properties and TOA albedo, suggesting a greater control of (local) large-scale dynamics and other factors on cloud object properties. When the three cloud object types are combined, the relative population among the three types is the most important factor for determining the cloud object properties in a Pacific transect where the transition of boundary-layer cloud types takes place.

Xu, Kuan-Man↗
NASA NTRSDate not supplied

Lunar Lander Landing Modeling and Simulation in Simscape

The landing gear is a critical subsystem of a lander for a successful landing on the moon or a planet. During a landing event, structural loading, energy absorption and toppling stability are important factors for the landing gear development. These aspects can be studied using simulations. The landing gear comprising the primary struct, secondary structs, footpad, and joints, is easily modeled using Simscape Multibody toolbox. The energy absorption mechanisms in the structs is readily modeled using Simulink and Multibody blocks based on the relative motions of the inner and outer cylinder of the structures. During touchdown, the footpads strike the lunar surface, and the contact forces can be modeled including the soil mechanical properties. Slosh dynamics are included using a mechanical pendulum model. Tip-over controllers are developed using Simulink blocks and toolboxes. This model was intensively tested manually then additionally with Monte Carlo simulation. It offers the opportunity for landing stability study, i.e. the max slope a lander can land without tipping over in 3D realistic landing situations.

Wei Wu↗
DOE OSTI2021

Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form

The Ebola virus matrix protein VP40 forms distinct structures linked to distinct functions in the virus life cycle. Dimeric VP40 is a structural protein associated with virus assembly, while octameric, ring-shaped VP40 is associated with transcriptional control. In this study, we show that suitable nucleic acid is sufficient to trigger a dynamic transformation of VP40 dimer into the octameric ring. Deep sequencing reveals a binding preference of the VP40 ring for the 3' untranslated region of cellular mRNA and a guanine- and adenine-rich binding motif. Complementary analyses of the nucleic-acid-induced VP40 ring by native mass spectrometry, electron microscopy, and X-ray crystal structures at 1.8 and 1.4 Å resolution reveal the stoichiometry of RNA binding, as well as an interface involving a key guanine nucleotide. The host factor-induced structural transformation of protein structure in response to specific RNA triggers in the Ebola virus life cycle presents unique opportunities for therapeutic inhibition.

3′ UTR↗
DOE OSTI2022

Tolerance Factor for Stabilizing 3D Hybrid Halide Perovskitoids Using Linear Diammonium Cations

Three-dimensional (3D) halide perovskites have attracted enormous research interest, but the choice of the A-site cations is limited by the Goldschmidt tolerance factor. In order to accommodate cations that lie outside the acceptable range of the tolerance factor, low-dimensional structures usually form. To maintain the favorable 3D connection, the links among the metal-halide octahedra need to be rearranged to fit the large cations. This can result in a departure from the proper corner-sharing perovskite architectures and lead to distinctly different perovskitoid motifs with edge- and face-sharing. In this work, we report four new 3D bromide perovskitoids incorporating linear organic diammonium cations, A'Pb 2 Br 6 (A' is a +2 cation). We propose a rule that can guide the further expansion of this class of compounds, analogous to the notion of Goldschmidt tolerance factor widely adopted for 3D AMX 3 perovskites. The fundamental building blocks in A'Pb 2 Br 6 consist of two edge-shared octahedra, which are then connected by corner-sharing to form a 3D network. Different compounds adopt different structural motifs, which can be transformed from one to another by symmetry operations. Electronic structure calculations suggest that they are direct bandgap semiconductors, with relatively large band dispersions created by octahedra connected by corner-sharing. They exhibit similar electronic band structures and dynamic lattice characteristics to the regular 3D AMX 3 perovskites. Structures with smaller Pb–Br–Pb angles and larger octahedra distortion exhibit broad photoluminescence at room temperature. Furthermore, the emerging structure–property relationships in these 3D perovskitoids set the foundation for designing and investigating these compounds for a variety of optoelectronic applications.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Allosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration

The trimeric serine protease HTRA1 is a genetic risk factor associated with geographic atrophy (GA), a currently untreatable form of age-related macular degeneration. Here, we describe the allosteric inhibition mechanism of HTRA1 by a clinical Fab fragment, currently being evaluated for GA treatment. Using cryo-EM, X-ray crystallography and biochemical assays we identify the exposed LoopA of HTRA1 as the sole Fab epitope, which is approximately 30 Å away from the active site. The cryo-EM structure of the HTRA1:Fab complex in combination with molecular dynamics simulations revealed that Fab binding to LoopA locks HTRA1 in a non-competent conformational state, incapable of supporting catalysis. Moreover, grafting the HTRA1-LoopA epitope onto HTRA2 and HTRA3 transferred the allosteric inhibition mechanism. This suggests a conserved conformational lock mechanism across the HTRA family and a critical role of LoopA for catalysis, which was supported by the reduced activity of HTRA1-3 upon LoopA deletion or perturbation. This study reveals the long-range inhibition mechanism of the clinical Fab and identifies an essential function of the exposed LoopA for activity of HTRA family proteases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mass action model of solution activity via speciation by solvation and ion pairing equilibria

Abstract Solutes and their concentrations influence many natural and anthropogenic solution processes. Electrolyte and solution models are used to quantify and predict such behavior. Here we present a mechanistic solution model based on mass action equilibria. Solvation and ion pairing are used to model speciated solute and solvent concentrations such that they correlate to a solution’s vapor pressure (solvent activity) according to Raoult’s law from dilute conditions to saturation. This model introduces a hydration equilibrium constant ( K ha ) that is used with either an ion dissociation constant ( K id ) or a hydration modifier ( m ) with an experimentally determined ion dissociation constant, as adjustable parameters to fit vapor–liquid equilibrium data. The modeled solvation equilibria are accompanied by molecular dynamics (MD) studies that support a decline in the observed degree of solvation with increased concentration. MD calculations indicate this finding is a combination of a solvent that solvates multiple solutes, and changes in a solute’s solvation sphere, with the dominant factor changing with concentration. This speciation-based solution model is lateral to established electrostatics-based electrolyte theories. With its basis in mass action, the model can directly relate experimental data to the modeled solute and solvent speciated concentrations and structures.

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

Nucleon and pion PDFs: large-x asymptotics meets functional mimicry

We review strategies to unveil the primordial large- x x structure of the nucleons as well as the pion from hard-scattering experiments. Ideas are presented for learning about the x\to 1 x → 1 limit of nonperturbative QCD dynamics at energy scales of order 1 GeV from collider experiments at much higher scales. The behavior of parton distributions at x\to 1 x → 1 predicted by the quark counting rules and other low-energy theoretical approaches is contrasted with phenomenological PDFs. Polynomial mimicry of PDF parametrizations is one of many factors that influence the apparent power of the (1-x) ( 1 − x ) falloff. We discuss implications of the mimicry for the large- x x falloff of the pion PDFs.

Courtoy, Aurore↗
NASA NTRS1982

Small scale structure in the interstellar medium: Orion's threadbare cloak

The interstellar medium in the central portion of the Orion Cloak dynamical feature was examined for evidence of fine structure. Four stars in the Ori OB I association, HD 37017, 37468, 37479, and 37776 bracket the stars in the lower belt region that were studied previously. Two are members of the sigma Ori subcluster. A lower limit to the scale inhomogeneity can be set using these at 0.1 pc, while on a scale of about 10 pc, the high velocity component of the second spectrum ions shows optical depth variation of more than a factor of 5. Neutral lines do not display the high velocity component. Some preliminary abundances are also given.

Shore, S. N.↗
NASA NTRS1985

Directional reflectance factor distributions for cover types of Northern Africa

Directional reflectance factors that spanned the entire exitance hemisphere were collected on the ground throughout the morning period for common cover types in Tunisia, Africa. NOAA 7/8 AVHRR bands 1(0.58-0.68 micron) and 2 (0.7301.1 micron) were used in data collection. The cover types reported were a plowed field, annual grassland, steppe grassland, hard wheat, salt plain, and irrigated wheat. Several of these cover types had geometric structures that are extreme as compared to those reported in the literature. Comparisons were made between the dynamics of the observed reflectance distributions and those reported in the literature. It was found that the dynamics of the measured data could be explained by a combination of soil and vegetation scattering components. The data and analysis further validated physical principles that cause the reflectance distribution dynamics as proposed by field and simulation studies in the literature. Finally, the normalized difference transformation (Band 2 - Band 1)/(Band 1 + Band 2), which is useful in monitoring vegetation cover, generally decreased the variation in signal with changing view angle. However, several exceptions were noted.

Kimes, D. S.↗