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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Non-averaged single-molecule tertiary structures reveal RNA self-folding through individual-particle cryo-electron tomography

Large-scale and continuous conformational changes in the RNA self-folding process present significant challenges for structural studies, often requiring trade-offs between resolution and observational scope. Here, we utilize individual-particle cryo-electron tomography (IPET) to examine the post-transcriptional self-folding process of designed RNA origami 6-helix bundle with a clasp helix (6HBC). By avoiding selection, classification, averaging, or chemical fixation and optimizing cryo-ET data acquisition parameters, we reconstruct 120 three-dimensional (3D) density maps from 120 individual particles at an electron dose of no more than 168 e - Å -2 , achieving averaged resolutions ranging from 23 to 35 Å, as estimated by Fourier shell correlation (FSC) at 0.5. Each map allows us to identify distinct RNA helices and determine a unique tertiary structure. Statistical analysis of these 120 structures confirms two reported conformations and reveals a range of kinetically trapped, intermediate, and highly compacted states, demonstrating a maturation folding landscape likely driven by helix-helix compaction interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Biosynthesis, Microstructural Characterisations and Investigation of In-Vitro Mutagenic and Eco-Toxicological Response of a Novel Microbial Exopolysaccharide Based Biopolymer

A modified microbial polysaccharide based biopolymer has been investigated as a potential candidate towards development of sustainable biomaterials and bioplastics. An in-depth study was carried out to biosynthesize, characterize and assess any possible mutagenic potential and ecotoxicity of the microbial polysaccharide biopolymer. Microstructural investigations using confocal microscopy, Fourier transform (FT)-Raman depth profile mapping and scanning electron microscopy (SEM) of the biosynthetically modified polysaccharide revealed internal structural perturbations, as well as occlusion of granular pores by extraneous materials. The Raman 3D mapping depth profile along with time-of-flight (MALDI-TOF) mass spectrometry also indicated important structural and surface modifications, which could be correlated to the production of microbial exopolysaccharides and secondary metabolites. The study then looked into any possible genetic mutation and ecological risks associated with the biosynthetically modified polysaccharide through the investigation of genotoxicity and ecotoxicity. The genotoxicity study was carried out through bacterial reverse gene mutation (Ames) test by using two different strains (TA98 and TA100) of bacteria. The results did not indicate any mutagenic effect against either of the strains used for the biopolymer samples and was found to be genotoxically safe. Ecotoxicity tests, carried out using bioluminescent bacteria Vibrio fisheri further indicated no ecotoxicity within the given experimental conditions. The study measured the half maximal effective concentration (EC50) to cause a 50% decrease in the light output of the bacteria, a measure of ecotoxicological response of the biopolymer. Overall, results from this study indicated that the novel biopolymer was genotoxically and ecotoxically safe, which offers immense potential for future use of this biopolymer.

36 MATERIALS SCIENCE↗
DOE OSTI2016

THE PHASE COHERENCE OF INTERSTELLAR DENSITY FLUCTUATIONS

Studies of MHD turbulence often investigate the Fourier power spectrum to provide information on the nature of the turbulence cascade. However, the Fourier power spectrum only contains the Fourier amplitudes and rejects all information regarding the Fourier phases. Here, we investigate the utility of two statistical diagnostics for recovering information on Fourier phases in ISM column density maps: the averaged amplitudes of the bispectrum and the phase coherence index (PCI), a new phase technique for the ISM. We create three-dimensional density and two-dimensional column density maps using a set of simulations of isothermal ideal MHD turbulence with a wide range of sonic and Alfvénic Mach numbers. We find that the bispectrum averaged along different angles with respect to either the k {sub 1} or k {sub 2} axis is primarily sensitive to the sonic Mach number while averaging the bispectral amplitudes over different annuli is sensitive to both the sonic and Alfvénic Mach numbers. The PCI of density suggests that the most correlated phases occur in supersonic sub-Alfvénic turbulence and near the shock scale. This suggests that nonlinear interactions with correlated phases are strongest in shock-dominated regions, in agreement with findings from the solar wind. Our results suggest that the phase information contained in the bispectrum and PCI can be used to find the turbulence parameters in column density maps.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

SU-E-I-41: Non-Cartesian MR Image Reconstruction with Integrated Gradient Non-Linearity Correction

Purpose: Nonlinearities in the spatial encoding gradients of MRI systems cause geometric distortion in images. Typically, this is retrospectively corrected via image-domain interpolation (a.k.a., “gradwarp”) albeit with a loss of spatial resolution. For non-Cartesian MRI, the latter problem is exaggerated by noise and undersampling artifact. In this study, we describe a novel correction strategy that accounts for gradient nonlinearities during — rather than after — non-Cartesian MRI reconstruction, and demonstrate that this approach mitigates the resolution loss that can occur with standard methods. Methods: To test the proposed method, the American College of Radiology (ACR) quality control phantom was scanned on at 1.5 T (General Electric, v16.0, “zoom” gradient) using a 1.6x undersampled 3D non- Cartesian Shells trajectory (GRE, FOV=24 cm3, 120 shells, 16552 shots, 512 readout, matrix=2403). Image reconstruction was first performed via standard k-space density-compensated gridding and retrospectively corrected via cubic spline interpolation. Image reconstruction was then separately performed using a k-space and image-domain densitycompensated type-3 non-uniform fast Fourier transform (NUFFT), which provides a direct mapping between non-Cartesian k-space samples and warped image space voxel locations. Thus, no separate distortion correction procedure is needed for the proposed approach. The gradient distortion field was determined using vendor provided calibration data. Results: Phantom scan results show that both processing approaches successfully correct geometric distortion. However, visual inspection of the ACR phantom spatial resolution inserts shows that the proposed strategy preserves the resolution of the nominal (uncorrected) reconstruction while “gradwarp” imparts marked spatial blurring (especially for the 1.0 and 1.1 mm inserts) and thus resolution loss. Conclusion: We've presented a novel reconstruction strategy for non-Cartesian MRI that corrects for gradient nonlinearities during — rather than after — reconstruction, and thus better preserves image resolution than traditional interpolation-based methods. This approach is expected to be especially advantageous when imaging with non-standard magnet geometries. NIH RR018898; NIH EB10065.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Analog In-Memory Computing for the Synthetic Aperture Radar Polar Format Algorithm

As the utility of synthetic aperture radar (SAR) systems increases in autonomous vehicles, satellites, and other power- and space-constrained edge applications, there is a growing need for processors that can form SAR images at low power. In recent years, analog in-memory compute (AIMC) has shown immense promise for accelerating neural networks and other matrix-vector multiplication (MVM) heavy workloads at the edge. Here, in this work, we examine how the polar format algorithm (PFA), a popular SAR image formation algorithm, can be mapped to these AIMC systems. The PFA maps readily onto analog MVMs because it primarily consists of two linear operations: interpolation of frequency-domain data to a Cartesian grid, followed by a 2-D Fourier transform. This work presents two approaches to map the interpolation operation onto MVMs in analog hardware: a chirp transform and a modified form of sinc interpolation. These mappings introduce algorithmic errors, and their effect on the quality of SAR image formation is examined, both quantitatively and qualitatively. In addition, the impact of errors introduced by the analog hardware is explored to determine which approach is optimal under varying assumptions about the underlying analog memory devices and circuits.

Analog computing↗
DOE OSTI2020

Microstructural characterization and assessment of mechanical properties of concrete based on combined elemental analysis techniques and Fast-Fourier transform-based simulations

This paper presents a pixel-based modeling approach of concrete which combines an experimental characterization of concrete and the Fast-Fourier transform simulations. High-resolution phase maps created from experimental characterization by micro X-ray fluorescence, energy dispersive X-ray analysis, and X-ray diffraction contain 9 different phases, including 22.17 vol.% of hydrated cement paste, 54.21 vol.% of minerals, and 23.62 vol.% of interfaces. These phases provide the input for determining the effective elastic properties, coupled with Fast-Fourier transform-based simulation. The simulation results show that the effective range of Young’s modulus of concrete is comparable with the range of experimental values ~ 37 ± 4 GPa with the assumption of realistic properties of interfaces.

36 MATERIALS SCIENCE↗
NASA NTRS1994

On determining the spectrum of primordial inhomogeneity from the COBE DMR sky maps: Results of two-year data analysis

A new technique of Fourier analysis on a cut sky has been applied to the two-year Cosmic Background Explorer (COBE) Differential Microwave Radiometer (DMR) 53 and 90 GHz sky maps. The Bayesian power spectrum estimation results are consistent with the Harrison-Zel'dovich n = 1 model. The maximum likelihood estimates of the usual parameters defining the power spectrum of primordial perturbations are n = 1.22 (1.02) and Q(sub rms-PS) = 17 (20) microK including (excluding) the quadrupole. A spectral-index-independent normalization is naturally expressed for the two-year maps in terms of the multipole amplitude a(sub 9) = 8.2 (8.3) microK (to approximately 12 sigma significance). The marginal likelihood function on n obtained by intergration with respect to a(sub 9) renders n = 1.17 +/- 0.31 (0.96 +/- 0.36).

Gorski, K. M.↗
NASA NTRS1979

A method of mapping compact structure in radio sources using VLBI observations

A two-part technique is described for determining the angular structure of the compact components of radio sources from VLBI observations. With this technique, the source structure is first approximated, using both amplitudes and closure phases, by a model consisting of circularly symmetric Gaussian components located on a grid of positions on the sky. The second part begins by employing this model to predict the visibility phase corresponding to each observed visibility amplitude; these estimated visibility phases are then adjusted to agree with the observed closure phases. The resulting estimates of the visibility phases and the observed visibility amplitudes are then combined in a direct Fourier transform to produce a 'dirty' source map that is deconvolved via the CLEAN procedure on the basis of the point-source response. Some examples based on data generated from test models are provided.

Cotton, W. D.↗
NASA NTRS1989

The 3.3 micron emission feature: Map of the galactic disk, 10 deg less than 1 less than 35 deg, - 6 deg less than b less than 6 deg

The 3.3 micron aromatic feature has been detected in the diffuse galactic emission with the AROME balloon-borne instrument. The results are presented in the form of an map of the 3.3 micron feature's intensity. The AROME instrument consists in a Cassegrain telescope with wobbling secondary mirrors and a liquid/solid nitrogen cooled photometer. The instrumental output is modified by the impulse response of the system. So the galactic surface brightness was restored in Fourier space by an inverse optimal filtering. The map of the feature's intensity is presented for a region of galactic coordinates. All the known H II giant molecular cloud complexes are visible in the 3.3 micron feature emission showing a good correlation with the infrared dust emission.

Giard, Martin↗
DOE OSTI2012

Implementation of moire-schlieren deflectometry on a small scale fast capillary plasma discharge

We present the results of an implementation of a refractive diagnostic to study fast dynamics in capillary discharges. It consists of a moire-schlieren deflectometry technique that provides a quantitative analysis of the refractive index gradients. The technique is composed of an angular deflection mapping system (moire deflectometry) and a spatial Fourier filter (schlieren). Temporal resolution of 12 ps, 50 {mu}m of spatial resolution and minimum detectable gradient of ({nabla}n{sub e}){sub min}=6x10{sup 18}cm{sup -4} were obtained. With these parameters, a large aspect ratio capillary discharge of 15 ns half period current was studied; the diagnostic was implemented axially along the alumina tube of 1.6 mm inner diameter and 21 mm length. The detectable electron density for these conditions was 1x10{sup 17}cm{sup -3}. From the interpretation of the fringe displacement, we are able to measure the velocity of the radial compression wave and the compression ratio due to the Lorentz force. On axis, electron densities of the order of 5x10{sup 17}cm{sup -3} were obtained at the time of maximum soft x-ray emission.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2012

A MEASUREMENT OF GRAVITATIONAL LENSING OF THE MICROWAVE BACKGROUND USING SOUTH POLE TELESCOPE DATA

We use South Pole Telescope data from 2008 and 2009 to detect the non-Gaussian signature in the cosmic microwave background (CMB) produced by gravitational lensing and to measure the power spectrum of the projected gravitational potential. We constrain the ratio of the measured amplitude of the lensing signal to that expected in a fiducial {Lambda}CDM cosmological model to be 0.86 {+-} 0.16, with no lensing disfavored at 6.3{sigma}. Marginalizing over {Lambda}CDM cosmological models allowed by the Wilkinson Microwave Anisotropy Probe (WMAP7) results in a measurement of A{sub lens} 0.90 {+-} 0.19, indicating that the amplitude of matter fluctuations over the redshift range 0.5 {approx}< z {approx}< 5 probed by CMB lensing is in good agreement with predictions. We present the results of several consistency checks. These include a clear detection of the lensing signature in CMB maps filtered to have no overlap in Fourier space, as well as a 'curl' diagnostic that is consistent with the signal expected for {Lambda}CDM. We perform a detailed study of bias in the measurement due to noise, foregrounds, and other effects and determine that these contributions are relatively small compared to the statistical uncertainty in the measurement. We combine this lensing measurement with results from WMAP7 to improve constraints on cosmological parameters when compared to those from WMAP7 alone: we find a factor of 3.9 improvement in the measurement of the spatial curvature of the universe, {Omega}{sub k} = -0.0014 {+-} 0.0172; a 10% improvement in the amplitude of matter fluctuations within {Lambda}CDM, {sigma}{sub 8} = 0.810 {+-} 0.026; and a 5% improvement in the dark energy equation of state, w = -1.04 {+-} 0.40. When compared with the measurement of w provided by the combination of WMAP7 and external constraints on the Hubble parameter, the addition of the lensing data improves the measurement of w by 15% to give w -1.087 {+-} 0.096.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

WE-DE-207B-12: Scatter Correction for Dedicated Cone Beam Breast CT Based On a Forward Projection Model

Purpose: The image quality of dedicated cone-beam breast CT (CBBCT) is fundamentally limited by substantial x-ray scatter contamination, resulting in cupping artifacts and contrast-loss in reconstructed images. Such effects obscure the visibility of soft-tissue lesions and calcifications, which hinders breast cancer detection and diagnosis. In this work, we propose to suppress x-ray scatter in CBBCT images using a deterministic forward projection model. Method: We first use the 1st-pass FDK-reconstructed CBBCT images to segment fibroglandular and adipose tissue. Attenuation coefficients are assigned to the two tissues based on the x-ray spectrum used for imaging acquisition, and is forward projected to simulate scatter-free primary projections. We estimate the scatter by subtracting the simulated primary projection from the measured projection, and then the resultant scatter map is further refined by a Fourier-domain fitting algorithm after discarding untrusted scatter information. The final scatter estimate is subtracted from the measured projection for effective scatter correction. In our implementation, the proposed scatter correction takes 0.5 seconds for each projection. The method was evaluated using the overall image spatial non-uniformity (SNU) metric and the contrast-to-noise ratio (CNR) with 5 clinical datasets of BI-RADS 4/5 subjects. Results: For the 5 clinical datasets, our method reduced the SNU from 7.79% to 1.68% in coronal view and from 6.71% to 3.20% in sagittal view. The average CNR is improved by a factor of 1.38 in coronal view and 1.26 in sagittal view. Conclusion: The proposed scatter correction approach requires no additional scans or prior images and uses a deterministic model for efficient calculation. Evaluation with clinical datasets demonstrates the feasibility and stability of the method. These features are attractive for clinical CBBCT and make our method distinct from other approaches. Supported partly by NIH R21EB019597, R21CA134128 and R01CA195512.The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1990

Initial results in the development of a synthetic aperture microwave radiometer

A radiometer that measures the complex correlation of the voltage from pairs of antennas at many different baselines is being developed. Each baseline produces a sample point in the Fourier transform of the scene, and a map of the scene is obtained after all measurements have been made by inverting the transform. A substantial reduction in the antenna collecting area required compared to a conventional imaging radiometer can be obtained in this manner. An aircraft prototype being developed is a hybrid which uses real aperture antennas to obtain resolution along-track (stick antennas) and uses aperture synthesis to obtain resolution across-track. The prototype was flight-tested aboard the NASA P-3 in June 1988. During this flight a map was made of the Delmarva Peninsula south of NASA's Wallops Flight Facility. This initial map shows the major land/water features and compares very favorably with a Landsat image of the area, suggesting a bright outlook for the development of this technique in the future.

Le Vine, David M.↗
NASA NTRS1990

Cassini atmospheric chemistry mapper. Volume 1. Investigation and technical plan

The Cassini Atmospheric Chemistry Mapper (ACM) enables a broad range of atmospheric science investigations for Saturn and Titan by providing high spectral and spatial resolution mapping and occultation capabilities at 3 and 5 microns. ACM can directly address the major atmospheric science objectives for Saturn and for Titan, as defined by the Announcement of Opportunity, with pivotal diagnostic measurements not accessible to any other proposed Cassini instrument. ACM determines mixing ratios for atmospheric molecules from spectral line profiles for an important and extensive volume of the atmosphere of Saturn (and Jupiter). Spatial and vertical profiles of disequilibrium species abundances define Saturn's deep atmosphere, its chemistry, and its vertical transport phenomena. ACM spectral maps provide a unique means to interpret atmospheric conditions in the deep (approximately 1000 bar) atmosphere of Saturn. Deep chemistry and vertical transport is inferred from the vertical and horizontal distribution of a series of disequilibrium species. Solar occultations provide a method to bridge the altitude range in Saturn's (and Titan's) atmosphere that is not accessible to radio science, thermal infrared, and UV spectroscopy with temperature measurements to plus or minus 2K from the analysis of molecular line ratios and to attain an high sensitivity for low-abundance chemical species in the very large column densities that may be achieved during occultations for Saturn. For Titan, ACM solar occultations yield very well resolved (1/6 scale height) vertical mixing ratios column abundances for atmospheric molecular constituents. Occultations also provide for detecting abundant species very high in the upper atmosphere, while at greater depths, detecting the isotopes of C and O, constraining the production mechanisms, and/or sources for the above species. ACM measures the vertical and horizontal distribution of aerosols via their opacity at 3 microns and, particularly, at 5 microns. ACM recovers spatially-resolved atmospheric temperatures in Titan's troposphere via 3- and 5-microns spectral transitions. Together, the mixing ratio profiles and the aerosol distributions are utilized to investigate the photochemistry of the stratosphere and consequent formation processes for aerosols. Finally, ring opacities, observed during solar occultations and in reflected sunlight, provide a measurement of the particle size and distribution of ring material. ACM will be the first high spectral resolution mapping spectrometer on an outer planet mission for atmospheric studies while retaining a high resolution spatial mapping capability. ACM, thus, opens an entirely new range of orbital scientific studies of the origin, physio-chemical evolution and structure of the Saturn and Titan atmospheres. ACM provides high angular resolution spectral maps, viewing nadir and near-limb thermal radiation and reflected sunlight; sounds planetary limbs, spatially resolving vertical profiles to several atmospheric scale heights; and measures solar occultations, mapping both atmospheres and rings. ACM's high spectral and spatial resolution mapping capability is achieved with a simplified Fourier Transform spectrometer with a no-moving parts, physically compact design. ACM's simplicity guarantees an inherent stability essential for reliable performance throughout the lengthy Cassini Orbiter mission.

Smith, William Hayden↗
NASA NTRS2010

Two-Dimensional Synthetic-Aperture Radiometer

A two-dimensional synthetic-aperture radiometer, now undergoing development, serves as a test bed for demonstrating the potential of aperture synthesis for remote sensing of the Earth, particularly for measuring spatial distributions of soil moisture and ocean-surface salinity. The goal is to use the technology for remote sensing aboard a spacecraft in orbit, but the basic principles of design and operation are applicable to remote sensing from aboard an aircraft, and the prototype of the system under development is designed for operation aboard an aircraft. In aperture synthesis, one utilizes several small antennas in combination with a signal processing in order to obtain resolution that otherwise would require the use of an antenna with a larger aperture (and, hence, potentially more difficult to deploy in space). The principle upon which this system is based is similar to that of Earth-rotation aperture synthesis employed in radio astronomy. In this technology the coherent products (correlations) of signals from pairs of antennas are obtained at different antenna-pair spacings (baselines). The correlation for each baseline yields a sample point in a Fourier transform of the brightness-temperature map of the scene. An image of the scene itself is then reconstructed by inverting the sampled transform. The predecessor of the present two-dimensional synthetic-aperture radiometer is a one-dimensional one, named the Electrically Scanned Thinned Array Radiometer (ESTAR). Operating in the L band, the ESTAR employs aperture synthesis in the cross-track dimension only, while using a conventional antenna for resolution in the along-track dimension. The two-dimensional instrument also operates in the L band to be precise, at a frequency of 1.413 GHz in the frequency band restricted for passive use (no transmission) only. The L band was chosen because (1) the L band represents the long-wavelength end of the remote- sensing spectrum, where the problem of achieving adequate spatial resolution is most critical and (2) imaging airborne instruments that operate in this wavelength range and have adequate spatial resolution are difficult to build and will be needed in future experiments to validate approaches for remote sensing of soil moisture and ocean salinity. The two-dimensional instrument includes a rectangular array of patch antennas arranged in the form of a cross. The ESTAR uses analog correlation for one dimension, whereas the two-dimensional instrument uses digital correlation. In two dimensions, many more correlation pairs are needed and low-power digital correlators suitable for application in spaceborne remote sensing will help enable this technology. The two-dimensional instrument is dual-polarized and, with modification, capable of operating in a polarimetric mode. A flight test of the instrument took place in June 2003 and it participated in soil moisture experiments during the summers of 2003 and 2004.

LeVine, David M.↗
DOE OSTI2026

Narrow operator models of stellarator equilibria in Fourier Zernike basis

Numerical computation of the ideal magnetohydrodynamic (MHD) equilibrium magnetic field is at the base of stellarator optimisation and provides the starting point for solving more sophisticated partial differential equations like transport or turbulence models. Conventional approaches solve for a single stationary point of the ideal MHD equations, which is fully defined by three invariants and the numerical scheme employed by the solver. We present the first numerical approach that can solve for a continuous distribution of equilibria with fixed boundary and rotational transform, varying only the pressure invariant. This approach minimises the force residual by optimising parameters of multilayer perceptrons that map from a scalar pressure multiplier to the Fourier Zernike basis as implemented in the modern stellarator equilibrium solver DESC.

fusion plasma↗
DOE OSTI2012

Nonlinear, noniterative, single-distance phase retrieval and developmental biology

For coherent X-ray imaging, based on phase contrast through free-space Fresnel propagation, we discuss two noniterative, nonlinear approaches to the phase-retrieval problem from a single-distance intensity map of a pure-phase object. On one hand, a perturbative set-up is proposed where nonlinear corrections to the linearized transport-of-intensity situation are expanded in powers of the object-detector distance z and are evaluated in terms of the linear estimate. On the other hand, a nonperturbative projection algorithm, which is based on the (linear and local) contrast-transfer function (CTF), works with an effective phase in Fourier space. This effective phase obeys a modified CTF relation between intensity contrast at z > 0 and phase contrast at z= 0: Unphysical singularities of the local CTF model are cut off to yield 'quasiparticles' in analogy to the theory of the Fermi liquid. By identifying the positions of the zeros of the Fourier transformed intensity contrast as order parameters for the dynamical breaking of scaling symmetry we investigate the phase structure of the forward-propagation problem when interpreted as a statistical system. Results justify the quasiparticle approach for a wide range of intermediary phase variations. The latter algorithm is applied to data from biological samples recorded at the beamlines TopoTomo and ID19 at ANKA and ESRF, respectively.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗