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At least 235 records · Page 13

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NASA NTRS2009

Shock Structure and Magnetic Fields Generation Associated with Relativistic Jets Unmagnetized Pair Plasma

Using 3D and 2D particle-in-cell simulations we investigate a shock structure, magnetic field generation, and particle acceleration associated with an unmagnetized relativistic electron-positron jet propagating into an unmagnetized pair plasma. The simulations use long computational grids which allow to study the formation and dynamics of the system in a spatial and temporal way. We find for the first time a relativistic shock system comparable to a predicted magnetohydrodynamic shock structure consisting of leading and trailing shocks separated by a contact discontinuity. Strong electromagnetic fields resulting from the Weibel two-stream instability are generated in the trailing shock where jet matter is thermalized and decelerated. We analyze the formation and nonlinear development through saturation and dissipation of those fields and associated particle acceleration. In the AGN context the trailing shock corresponds to the jet shock at the head of a relativistic astrophysical jet. In the GRB context this trailing shock can be identified with the bow shock driven by relativistic ejecta. The strong electromagnetic field region in the trailing shock provides the emission site for the hot spot at the leading edge of AGN jets and for afterglow emission from GRBs.

Niemiec, J.↗

NASA NTRS1993

Analysis and sizing of Mars aerobrake structure

A cone-sphere aeroshell structure for aerobraking into Martian atmosphere is studied. Using this structural configuration, a space frame load-bearing structure is proposed. To generate this structure efficiently and to perform a variety of studies of several configurations, a mesh generator that utilizes only a few configurational parameters is developed. A finite element analysis program that analyzes space frame structures was developed. A sizing algorithm that arrives at a minimum mass configuration was developed and integrated into the finite element analysis program. A typical 135-ft-diam aerobrake configuration was analyzed and sized. The minimum mass obtained in this study using high modulus graphite/epoxy composite material members is compared with the masses obtained from two other aerobrake structures using lightweight erectable tetrahedral truss and part-spherical truss configurations. Excellent agreement for the minimum mass was obtained with the three different aerobrake structures. Also, the minimum mass using the present structure was obtained when the supports were not at the base but at about 75 percent of the base diameter.

Raju, I. S.↗

NASA NTRS1973

On the inviscid rolled-up structure of lift-generated vortices

A simple form is presented of the relationships derived by Betz for the inviscid, fully developed structure of lift-generated vortices behind aircraft. An extension is then made to arbitrary span-load distributions by inferring guidelines for the selection of rollup centers for the vortex sheet. These techniques are easier to use and yield more realistic estimates of the rolled-up structure of vortices than the original form of Betz' theory when the span loading differs appreciably from elliptic loading.

Rossow, V. J.↗

DOE OSTI2025

Tutorial: Machine-Learning-Based CREASE-2D Analysis of 2D SAXS Profiles to Characterize Anisotropic Nanostructures in Soft Materials

We present a tutorial to guide users on how to extend the Computational Reverse Engineering Analysis of Scattering Experiments-2D (CREASE-2D) framework to interpret their experimental two-dimensional small-angle scattering (SAS) data from soft materials (e.g., polymers, peptide amphiphiles, biomolecular fibrils). Unlike most traditional SAS analysis approaches, which typically rely on azimuthally averaged onedimensional (1D) profiles, CREASE-2D utilizes the complete 2D scattering profile to reveal information about anisotropy in the structure. In past applications, CREASE has provided insights into complex structural features, including the cross-sectional shapes of assembled nanostructures and dispersity in these features, which are difficult to discern with existing analytical models. While (1D- ) CREASE has been applied to SANS and SAXS data, this tutorial shares the steps for implementing CREASE-2D using an example of a dipeptide solution system, for which we have SAXS data. We present details for these steps involved in using CREASE-2D to interpret SAXS profiles: how to preprocess SAXS data, define relevant structural features, generate three-dimensional real-space structures for specific values of these features, train a machine learning (ML) surrogate model to predict scattering profiles for given structural features, and optimize these features using genetic algorithms (GA). Then, we use these steps to interpret complex 2DSAXS data collected from dipeptide solutions that, in microscopy images, exhibit nanoscale structures that could be elliptical tubes/ flat tapes/cylinders or a combination of these cross sections. Open-source codes, computational hardware, and software requirements, as well as the strengths and limitations of this protocol, are also presented. We expect researchers working with (soft) biomaterials, peptide amphiphiles, amphiphilic polymer solutions, polymer nanocomposites, and blends of particles/polymers will find this CREASE-2D method and this tutorial of use.

CREASE↗

NASA NTRS1990

A three-dimensional application with the numerical grid generation code: EAGLE (utilizing an externally generated surface)

Program EAGLE (Eglin Arbitrary Geometry Implicit Euler) is a multiblock grid generation and steady-state flow solver system. This system combines a boundary conforming surface generation, a composite block structure grid generation scheme, and a multiblock implicit Euler flow solver algorithm. The three codes are intended to be used sequentially from the definition of the configuration under study to the flow solution about the configuration. EAGLE was specifically designed to aid in the analysis of both freestream and interference flow field configurations. These configurations can be comprised of single or multiple bodies ranging from simple axisymmetric airframes to complex aircraft shapes with external weapons. Each body can be arbitrarily shaped with or without multiple lifting surfaces. Program EAGLE is written to compile and execute efficiently on any CRAY machine with or without Solid State Disk (SSD) devices. Also, the code uses namelist inputs which are supported by all CRAY machines using the FORTRAN Compiler CF177. The use of namelist inputs makes it easier for the user to understand the inputs and to operate Program EAGLE. Recently, the Code was modified to operate on other computers, especially the Sun Spare4 Workstation. Several two-dimensional grid configurations were completely and successfully developed using EAGLE. Currently, EAGLE is being used for three-dimension grid applications.

Houston, Johnny L.↗

NASA NTRS1990

Velocity and pressure fields associated with near-wall turbulence structures

Computer generated databases containing velocity and pressure fields in three-dimensional space at a sequence of time-steps, were used for the investigation of near-wall turbulence structures, their space-time evolution, and their associated pressure fields. The main body of the results were obtained from simulation data for turbulent channel flow at a Reynolds number of 180 (based on half-channel height and friction velocity) with a grid of 128 x 129 x and 128 points. The flow was followed over a total time of 141 viscous time units. Spanwise centering of the detected structures was found to be essential in order to obtain a correct magnitude of the associated Reynolds stress contribution. A positive wall-pressure peak is found immediately beneath the center of the structure. The maximum amplitude of the pressure pattern was, however, found in the buffer region at the center of the shear-layer. It was also found that these flow structures often reach a maximum strength in connection with an asymmetric spanwise motion, which motivated the construction of a conditional sampling scheme that preserved this asymmetry.

Johansson, Arne V.↗

NASA NTRS1981

The structure of trailing vortices generated by model rotor blades

Hot-wire anemometry to analyze the structure and geometry of rotary wing trailing vortices is studied. Tests cover a range of aspect ratios and blade twist. For all configurations, measured vortex strength correlates well with maximum blade-bound circulation. Measurements of wake geometry are in agreement with classical data for high-aspect ratios. The detailed vortex structure is similar to that found for fixed wings and consists of four well defined regions--a viscous core, a turbulent mixing region, a merging region, and an inviscid outer region. A single set of empirical formulas for the entire set of test data is described.

Tung, C.↗

NASA NTRSDate not supplied

Precision in Assembled Discrete Lattice Space Structures for Next-Generation ISAM Applications

Robust autonomous robotic assembly of large-scale space structures has been a long-term and challenging goal to enable higher quality in-space communication and science instrumentation. For optical observatory support structures and antenna structures, the challenge is the strict dimensional precision requirements (generally RMS surface error) driven by the operational radiation wavelength. Early theoretical work in the area linked RMS surface error of a reflector support truss plate to the natural passive dynamic mode frequencies of the structure, as well as to the error distribution in dimensions of constituent structural elements. Prior robotic truss assembly demonstrations focused on designing ultra-high precision structural elements, joints, and robotic actuators. Recently, an alternative space structure assembly strategy based on a programmable matter approach (NASA ARMADAS) was demonstrated. This approach uses lattice building blocks (voxels) that are reversibly, mechanically joined into a bulk lattice structure by robots that locomote in and on the structure itself. Such a system can achieve high-level autonomy with low computation, robustly assemble utilizing inexpensive and imprecise robots, and efficiently build structures several orders of magnitude larger than the assembly robots. However, for instrumentation support structure applications, the resulting precision of these building block-based lattice structures is not well studied. Since they are demonstrated with many more assembly units than prior art trusses, it is unclear whether the same precision design approaches apply. In this work, we study in simulation the effects of voxel geometry, error in distribution, assembly resolution (module size), and assembly geometry on the error of both beam and plate lattice structures. While average RMS error of a plate increases with plate size, increasing plate thickness quickly collapses RMS error towards a limit that is on the order of the error of the constituent parts. We validate our models against previously published precision measurements of built systems. Results from this study will guide manufacturing precision requirements, as well as designs, for future robotically assembled structural applications and establish feasibility for different applications.

Christine E Gregg↗

DOE OSTI2021

A deep generative model enables automated structure elucidation of novel psychoactive substances

Over the past decade, the illicit drug market has been reshaped by the proliferation of clandestinely produced designer drugs. These agents, referred to as new psychoactive substances (NPSs), are designed to mimic the physiological actions of better-known drugs of abuse while skirting drug control laws. The public health burden of NPS abuse obliges toxicological, police and customs laboratories to screen for them in law enforcement seizures and biological samples. However, the identification of emerging NPSs is challenging due to the chemical diversity of these substances and the fleeting nature of their appearance on the illicit market. Here, in this study, we present DarkNPS, a deep learning-enabled approach to automatically elucidate the structures of unidentified designer drugs using only mass spectrometric data. Our method employs a deep generative model to learn a statistical probability distribution over unobserved structures, which we term the structural prior. We show that the structural prior allows DarkNPS to elucidate the exact chemical structure of an unidentified NPS with an accuracy of 51% and a top-10 accuracy of 86%. Our generative approach has the potential to enable de novo structure elucidation for other types of small molecules that are routinely analysed by mass spectrometry.

Cheminformatics↗

NASA NTRS1995

Statistically generated weighted curve fit of residual functions for modal analysis of structures

A statistically generated weighting function for a second-order polynomial curve fit of residual functions has been developed. The residual flexibility test method, from which a residual function is generated, is a procedure for modal testing large structures in an external constraint-free environment to measure the effects of higher order modes and interface stiffness. This test method is applicable to structures with distinct degree-of-freedom interfaces to other system components. A theoretical residual function in the displacement/force domain has the characteristics of a relatively flat line in the lower frequencies and a slight upward curvature in the higher frequency range. In the test residual function, the above-mentioned characteristics can be seen in the data, but due to the present limitations in the modal parameter evaluation (natural frequencies and mode shapes) of test data, the residual function has regions of ragged data. A second order polynomial curve fit is required to obtain the residual flexibility term. A weighting function of the data is generated by examining the variances between neighboring data points. From a weighted second-order polynomial curve fit, an accurate residual flexibility value can be obtained. The residual flexibility value and free-free modes from testing are used to improve a mathematical model of the structure. The residual flexibility modal test method is applied to a straight beam with a trunnion appendage and a space shuttle payload pallet simulator.

Bookout, P. S.↗

DOE OSTI2025

Surface structure of water from soft X-ray second harmonic generation

The microscopic structure of water’s surface is crucial to many natural and industrial processes, but studying its hydrogen bond (H-bond) network directly remains challenging due to the required interfacial sensitivity of experimental techniques. By leveraging advances in flat liquid sheet microjets and terawatt-scale attosecond soft X-ray pulses from the LCLS X-ray free electron laser, we employed soft X-ray second harmonic generation (SXSHG) spectroscopy to examine the liquid water/vapor interface. SXSHG combines the elemental selectivity of X-ray spectroscopies with the surface selectivity of SHG and gives access to the electronic structure of interfacial species. Here, we show the SXSHG spectrum differs from bulk water’s X-ray absorption, with its peak shifted several eV, indicating a vastly different electronic environment at the interface as compared to the bulk. First-principles electronic structure calculations show the signal is highly sensitive to H-bond interactions, such as water molecules accepting a single H-bond, which are surface abundant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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 NTRS1988

Heat flow, heat generation and crustal thermal structure of the northern block of the South Indian Craton

Heat flow values and heat generation data calculated from the concentration of heat producing radioactive elements, U, Th and K in surface rocks were analyzed. The South Indian Craton according to Drury et al., can be divided into various blocks, separated by late Proterozoic shear belts. The northern block comprises Eastern and Western Dharwar Cratons of Rogers (1986), Naqvi and Rogers (1987) and a part of the South Indian granulite terrain up to a shear system occupying the Palghat-Cauvery low lands. The geothermal data analysis clearly demonstrates that the present thermal characteristics of the above two Archaean terrains of the Indian and Australian Shields are quite similar. Their crustal thermal structures are likely to be similar also.

Gupta, Mohan L.↗

NASA NTRS2023

Structured Type III Radio Bursts Observed in Interplanetary Space

Context . The last few decades have seen numerous studies dedicated to fine structures of type III radio bursts observed in the meter–decameter wavelengths. Most of the explanations of the structured radio emission involve the propagation of electron beams through the strongly inhomogeneous plasma in the low corona. To date, only a few type III bursts with fine structures, observed at hecto-kilometric wavelengths, have been reported. Aims . We report here the existence of numerous structured type III radio bursts observed during the STEREO era by all three WAVES instruments on board STEREO A, B, and Wind. The aim of the study is to report and classify structured type III bursts, and to present the characteristics of their fine structures. The final goal is to try to understand the physical mechanism responsible for the generation of structured radio emission. Methods . In this study we used data from all available spacecraft, specifically STEREO and Wind. We employed 1D density models to obtain the speed of the source of type III radio emission, the electron beam. We also performed a spectral analysis of the fine structures in order to compare their characteristics with the metric–decametric fine structures. Results . The presented similarities of the type III fine structures in the metric to decametric and interplanetary wavelengths indicate that the physical processes responsible for the generation of structured type III radio bursts could be the same, at heights from the low corona to the interplanetary range. We show that the observed structuring and intermittent nature of the type III bursts can be explained by the variation in the level of density fluctuations, at different distances from the Sun.

Non-thermal radiation mechanisms↗

DOE OSTI2024

Feeling the Strain: Quantifying Ligand Deformation in Photosynthesis

Structural distortion of protein-bound ligands can play a critical role in enzyme function by tuning the electronic and chemical properties of the ligand molecule. However, quantifying these effects is difficult due to the limited resolution of protein structures and the difficulty of generating accurate structural restrains for non-protein ligands. Here, we seek to quantify these effects through a statistical analysis of ligand distortion in Chlorophyll (Chl) proteins (CP), where ring deformation is thought to play a role in energy and electron transfer. To assess the accuracy of ring-deformation estimates from available structural data, we take advantage of the C 2 symmetry of Photosystem II (PSII), comparing ring-deformation estimates for equivalent sites both within and between 113 distinct X-ray and Cryogenic electron microscopy (CryoEM) PSII structures. Significantly, we find that several deformation modes exhibit considerable variability in predictions, even for equivalent monomers, down to 2 Å resolution, to an extent that probably prevents their utilization in optical calculations. We further find that refinement restrains play a critical role in determining deformation values to resolution as low as 2 Å. However, for those modes that are well-resolved in the structural data, ring deformation in PSII is strongly conserved across all species tested, from cyanobacteria to algae. Furthermore, these results highlight both the opportunities and limitations inherent in the structure-based analysis of the bioenergetic and optical properties of CPs and other protein-ligand complexes.

14 SOLAR ENERGY↗

DOE OSTI2023

Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge

Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1971

Frame modal analysis

Computer model calculates natural frequencies and modal displacements of three-dimensional frame structures, and generates stiffness and mass matrices. Structures may be divided into several substructures prior to calculation of modal characteristics.

Guyan, R. J.↗

NASA NTRS2011

Defining Dynamic Route Structure

This poster describes a method for defining route structure from flight tracks. Dynamically generated route structures could be useful in guiding dynamic airspace configuration and helping controllers retain situational awareness under dynamically changing traffic conditions. Individual merge and diverge intersections between pairs of flights are identified, clustered, and grouped into nodes of a route structure network. Links are placed between nodes to represent major traffic flows. A parametric analysis determined the algorithm input parameters producing route structures of current day flight plans that are closest to todays airway structure. These parameters are then used to define and analyze the dynamic route structure over the course of a day for current day flight paths. Route structures are also compared between current day flight paths and more user preferred paths such as great circle and weather avoidance routing.

Zelinski, Shannon↗