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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 OSTI2022

The Spectroscopic Classification of Astronomical Transients (SCAT) Survey: Overview, Pipeline Description, Initial Results, and Future Plans

Here, we present the Spectroscopic Classification of Astronomical Transients (SCAT) survey, which is dedicated to spectrophotometric observations of transient objects such as supernovae and tidal disruption events. SCAT uses the SuperNova Integral-Field Spectrograph (SNIFS) on the University of Hawai’i 2.2 m (UH2.2m) telescope. SNIFS was designed specifically for accurate transient spectrophotometry, including absolute flux calibration and host-galaxy removal. We describe the data reduction and calibration pipeline including spectral extraction, telluric correction, atmospheric characterization, nightly photometricity, and spectrophotometric precision. We achieve ≲5% spectrophotometry across the full optical wavelength range (3500–9000 Å) under photometric conditions. The inclusion of photometry from the SNIFS multi-filter mosaic imager allows for decent spectrophotometric calibration (10%–20%) even under unfavorable weather/atmospheric conditions. SCAT obtained ≈640 spectra of transients over the first 3 yr of operations, including supernovae of all types, active galactic nuclei, cataclysmic variables, and rare transients such as superluminous supernovae and tidal disruption events. These observations will provide the community with benchmark spectrophotometry to constrain the next generation of hydrodynamic and radiative transfer models.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The La Silla Schmidt Southern Survey

We present the La Silla Schmidt Southern Survey (LS4), a new wide-field, time-domain survey to be conducted with the 1 m ESO Schmidt telescope. The 268 megapixel LS4 camera mosaics 32 2k × 4k fully depleted CCDs, providing a ∼20 deg 2 field of view with 1″ pixel −1 resolution. The LS4 camera will have excellent performance at longer wavelengths: in a standard 45 s exposure the expected 5σ limiting magnitudes in g, i, z are ∼21.5, ∼20.9, and ∼20.3 mag (AB), respectively. The telescope design requires a novel filter holder that fixes different bandpasses over each quadrant of the detector. Two quadrants will have i band, while the other two will be g and z band with color information obtained by dithering targets across the different quadrants. The majority (90%) of the observing time will be used to conduct a public survey that monitors the extragalactic sky at both moderate (3 days) and high (1 day) cadence, as well as focused observations within the Galactic plane and bulge. Alerts from the public survey will be broadcast to the community via established alert brokers. LS4 will run concurrently with the Vera C. Rubin Observatory’s Legacy Survey of Space and Time (LSST). The combination of LS4+LSST will enable detailed holistic monitoring of many nearby transients: high-cadence LS4 observations will resolve the initial rise and peak of the light curve while less-frequent but deeper observations by LSST will characterize the years before and after explosion. Here, we summarize the primary science objectives of LS4 including microlensing events in the Galaxy, extragalactic transients powered by massive black holes or stellar explosions, the search for electromagnetic counterparts to multi-messenger events, and supernova cosmology.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

The role of local shipping emissions in aerosol-cloud interactions in the central Arctic

Arctic shipping is projected to increase as sea ice retreats, yet the impact of modern low-sulfur ship emissions on Arctic clouds and radiation remain poorly constrained. We use year-long in situ observations from the MOSAiC expedition to characterize ship-aerosol-cloud interactions for an icebreaker burning ultra-low sulfur fuel (0.1% mass per mass). Exhaust plumes were found to be strongly enriched in Aitken-mode particles, organic aerosol, and black carbon, but showed no detectable enhancement in particulate sulfate. Despite reduced hygroscopicity relative to ambient aerosols, ship emissions substantially increased local cloud condensation nuclei concentrations. A droplet activation parameterization was applied to quantify responses in cloud droplet number concentration ( N d ) to ship-induced perturbations in low-level Arctic clouds. In winter, abundant background accumulation-mode particles from Arctic haze supplied nearly all cloud droplets, while additional particles from ship emissions had little impact on N d . In contrast, during summer months, when unperturbed background aerosol concentrations are low, ship emissions nearly doubled N d compared to average background conditions and increased N d by a factor of five compared to very clean background conditions (25th percentile of background aerosol number concentrations). Longwave radiative transfer simulations for typical conditions of summer Arctic low-level clouds/fog suggest that these ship-induced increases in N d locally (i.e. <100 km downwind) lead to enhanced net surface longwave fluxes and consequent warming, primarily for optically thin clouds (liquid water path (LWP) ⩽ 30 g·m −2 ). For LWP = 10 g · m −2 , ship emissions lead to an increase of 1 W · m −2 in cloud longwave forcing at the surface compared to average unperturbed conditions (+7% relative increase), and up to 4 W · m −2 when compared to very clean background conditions (+22% relative increase). Even ultra-low sulfur fuel emissions can therefore locally and episodically modify Arctic cloud microphysics and radiative properties, especially during summer, implying that future increases in Arctic shipping could have non-negligible regional climate impacts.

Arctic↗
DOE OSTI2022

A study on the clustering properties of radio-selected sources in the Lockman Hole region at 325 MHz

Studying the spatial distribution of extragalactic source populations is vital in understanding the matter distribution in the Universe. It also enables understanding the cosmological evolution of dark matter density fields and the relationship between dark matter and luminous matter. Clustering studies are also required for EoR foreground studies since it affects the relevant angular scales. This paper investigates the angular and spatial clustering properties and the bias parameter of radio-selected sources in the Lockman Hole field at 325 MHz. The data probes sources with fluxes ≳0.3 mJy within a radius of 1.8° around the phase centre of a 6° × 6° mosaic. Based on their radio luminosity, the sources are classified into Active Galactic Nuclei (AGNs) and Star-Forming Galaxies (SFGs). Clustering and bias parameters are determined for the combined populations and the classified sources. The spatial correlation length and the bias of AGNs are greater than SFGs- indicating that more massive haloes host the former. This study is the first reported estimate of the clustering property of sources at 325 MHz, intermediate between the pre-existing studies at high and low-frequency bands. It also probes a well-studied deep field at an unexplored frequency with moderate depth and area. Clustering studies require such observations along different lines of sight, with various fields and data sets across frequencies to avoid cosmic variance and systematics. Thus, an extragalactic deep field has been studied in this work to contribute to this knowledge.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Chandra measurements of gas homogeneity and turbulence at intermediate radii in the Perseus Cluster

ABSTRACT We present a Chandra study of surface brightness fluctuations in the diffuse intracluster medium of the Perseus Cluster. Our study utilizes deep, archival imaging of the cluster core as well as a new mosaic of 29 short $\, 5\,$-ks observations extending in eight different directions out to radii of $r_{500} \sim 2.2\, r_{2500}$. Under the assumption that the distribution of densities at a given radius is log-normally distributed, two important quantities can be derived from the width of the log-normal density distribution on a given spatial scale: the density bias, that is equal to the square root of the clumping factor C; and the one-component turbulent velocity, vk,1D. We forward-model all contributions to the measured surface brightness, including astrophysical and particle background components, and account for the Poisson nature of the measured signal. Measuring the distribution of surface brightness fluctuations in 1 arcmin2 regions, spanning the radial range $0.3\rm {-}2.2\, r_{2500}$ ($7.8\rm {-}57.3\,$ arcmin), we find a small to moderate average density bias of around $3{{\ \rm per\ cent}}$ at radii below $1.6\, r_{2500}$. We also infer an average turbulent velocity at these radii of V1D < 400 km s−1. Direct confirmation of our results on turbulent velocities inferred from surface brightness fluctuations should be possible using the X-ray calorimeter spectrometers to be flown aboard the XRISM and Athena observatories.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

SDSS IV MaNGA: visual morphological and statistical characterization of the DR15 sample

ABSTRACT We present a detailed visual morphological classification for the 4614 MaNGA galaxies in SDSS Data Release 15, using image mosaics generated from a combination of r band (SDSS and deeper DESI Legacy Surveys) images and their digital post-processing. We distinguish 13 Hubble types and identify the presence of bars and bright tidal debris. After correcting the MaNGA sample for volume completeness, we calculate the morphological fractions, the bi-variate distribution of type and stellar mass M* – where we recognize a morphological transition ‘valley’ around S0a-Sa types – and the variations of the g − i colour and luminosity-weighted age over this distribution. We identified bars in 46.8 per cent of galaxies, present in all Hubble types later than S0. This fraction amounts to a factor ∼2 larger when compared with other works for samples in common. We detected 14 per cent of galaxies with tidal features, with the fraction changing with M* and morphology. For 355 galaxies, the classification was uncertain; they are visually faint, mostly of low/intermediate masses, low concentrations, and discy in nature. Our morphological classification agrees well with other works for samples in common, though some particular differences emerge, showing that our image procedures allow us to identify a wealth of added value information as compared to SDSS-based previous estimates. Based on our classification, we also propose an alternative criteria for the E–S0 separation, in the structural semimajor to semiminor axis versus bulge to total light ratio (b/a − B/T) and concentration versus semimajor to semiminor axis (C − b/a) space.

Vázquez-Mata, J. A. (ORCID:0000000186941204)↗
DOE OSTI2024

Simulating image coaddition with the Nancy Grace Roman Space Telescope – I. Simulation methodology and general results

The upcoming Nancy Grace Roman Space Telescope will carry out a wide-area survey in the near-infrared. A key science objective is the measurement of cosmic structure via weak gravitational lensing. Roman data will be undersampled, which introduces new challenges in the measurement of source galaxy shapes; a potential solution is to use linear algebra-based coaddition techniques such as imcom that combine multiple undersampled images to produce a single oversampled output mosaic with a desired ‘target’ point spread function (PSF). We present here an initial application of imcom to 0.64 square degrees of simulated Roman data, based on the Roman branch of the Legacy Survey of Space and Time (LSST) Dark Energy Science Collaboration (DESC) Data Challenge 2 (DC2) simulation. We show that imcom runs successfully on simulated data that includes features such as plate scale distortions, chip gaps, detector defects, and cosmic ray masks. We simultaneously propagate grids of injected sources and simulated noise fields as well as the full simulation. We quantify the residual deviations of the PSF from the target (the ‘leakage’), as well as noise properties of the output images; we discuss how the overall tiling pattern as well as Moiré patterns appear in the final leakage and noise maps. We include appendices on interpolation algorithms and the interaction of undersampling with image processing operations that may be of broader applicability. The companion paper (‘Paper II’) explores the implications for weak lensing analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function

Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for non model organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved Proximal Orthologous Gene (POG) pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte-chlorophyte split, 1,000 million years ago. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid (MAA), "sunscreen", neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene (PGK). Mutants of the ArsJ-like transporter and PGK-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga Auxenochlorella

Auxenochlorella spp. are diploid oleaginous green algae whose streamlined genomes can be readily manipulated by homologous recombination, making them highly amenable to discovery research and bioengineering. Vegetatively diploid organisms experience specific evolutionary phenomena, including allodiploid hybridization, mitotic recombination, loss-of-heterozygosity, and aneuploidy; however, studies of these forces have largely focused on yeasts. Here, we present a telomere-to-telomere phased diploid genome assembly of Auxenochlorella UTEX 250-A (haploid length 22 Mb) and introduce a genetic toolkit for site-specific manipulation of the nuclear genome in multiple strains, featuring several selectable markers, inducible promoters, and fluorescent reporters for protein localization. UTEX 250-A is an allodiploid hybrid of Auxenochlorella protothecoides and Auxenochlorella symbiontica, two species differentiated by extensive chromosomal rearrangements. UTEX 250-A haplotypes are a mosaic of each parental species following mitotic recombination, and two chromosomes are trisomic. Loss-of-heterozygosity events are pervasive across Auxenochlorella and can evolve rapidly in the laboratory. High-quality structural annotation yielded ∼7,500 genes per haplotype. Auxenochlorella have experienced gene family loss and reduction, including core photosynthesis genes, and exhibit periodic adenine and cytosine methylation at promoters and gene bodies, respectively. Approximately 10% of genes, especially those involved in DNA repair and sex, overlap antisense long noncoding RNAs, which may participate in a regulatory mechanism. We demonstrate the utility of Auxenochlorella for fundamental research by knockout of a chlorophyll biosynthesis enzyme, and confirm one trisomy by allele-specific transformation. These results demonstrate the generality of several evolutionary forces associated with vegetative diploidy and provide a foundation for the use of Auxenochlorella as a reference organism.

CHL27↗
DOE OSTI2023

Ancient Rapid Radiation Explains Most Conflicts Among Gene Trees and Well-Supported Phylogenomic Trees of Nostocalean Cyanobacteria

Prokaryotic genomes are often considered to be mosaics of genes that do not necessarily share the same evolutionary history due to widespread horizontal gene transfers (HGTs). Consequently, representing evolutionary relationships of prokaryotes as bifurcating trees has long been controversial. However, studies reporting conflicts among gene trees derived from phylogenomic data sets have shown that these conflicts can be the result of artifacts or evolutionary processes other than HGT, such as incomplete lineage sorting, low phylogenetic signal, and systematic errors due to substitution model misspecification. Here, we present the results of an extensive exploration of phylogenetic conflicts in the cyanobacterial order Nostocales, for which previous studies have inferred strongly supported conflicting relationships when using different concatenated phylogenomic data sets. We found that most of these conflicts are concentrated in deep clusters of short internodes of the Nostocales phylogeny, where the great majority of individual genes have low resolving power. We then inferred phylogenetic networks to detect HGT events while also accounting for incomplete lineage sorting. Our results indicate that most conflicts among gene trees are likely due to incomplete lineage sorting linked to an ancient rapid radiation, rather than to HGTs. Moreover, the short internodes of this radiation fit the expectations of the anomaly zone, i.e., a region of the tree parameter space where a species tree is discordant with its most likely gene tree. In this work, we demonstrated that concatenation of different sets of loci can recover up to 17 distinct and well-supported relationships within the putative anomaly zone of Nostocales, corresponding to the observed conflicts among well-supported trees based on concatenated data sets from previous studies. Our findings highlight the important role of rapid radiations as a potential cause of strongly conflicting phylogenetic relationships when using phylogenomic data sets of bacteria. We propose that polytomies may be the most appropriate phylogenetic representation of these rapid radiations that are part of anomaly zones, especially when all possible genomic markers have been considered to infer these phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Permafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970 to 2014

Permafrost thaw increases active layer thickness, changes landscape hydrology and influences vegetation species composition. These changes alter belowground microbial and geochemical processes, affecting production, consumption and net emission rates of climate forcing trace gases. Net carbon dioxide (CO 2 ) and methane (CH 4 ) fluxes determine the radiative forcing contribution from these climate-sensitive ecosystems. Permafrost peatlands may be a mosaic of dry frozen hummocks, semi-thawed or perched sphagnum dominated areas, wet permafrost-free sedge dominated sites and open water ponds. We revisited estimates of climate forcing made for 1970 and 2000 for Stordalen Mire in northern Sweden and found the trend of increasing forcing continued into 2014. The Mire continued to transition from dry permafrost to sedge and open water areas, increasing by 100% and 35%, respectively, over the 45-year period, causing the net radiative forcing of Stordalen Mire to shift from negative to positive. This trend is driven by transitioning vegetation community composition, improved estimates of annual CO 2 and CH 4 exchange and a 22% increase in the IPCC's 100-year global warming potential (GWP_100) value for CH 4 . These results indicate that discontinuous permafrost ecosystems, while still remaining a net overall sink of C, can become a positive feedback to climate change on decadal timescales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Gaps in topological magnon spectra: Intrinsic versus extrinsic effects

Determining and explaining the presence of a gap at a magnon crossing point is a critical step to characterize the topological properties of a material. An inelastic neutron scattering study of a single crystal is a powerful experimental technique to probe the magnetic excitation spectra of topological materials. Here, we show that when the scattering intensity rapidly disperses in the vicinity of a crossing point, such as a Dirac point, the apparent topological gap size is extremely sensitive to experimental conditions including sample mosaic, resolution, and momentum integration range. In this work, we demonstrate these effects using comprehensive neutron scattering measurements of CrCl 3 . Our measurements confirm the gapless nature of the Dirac magnon in CrCl 3 , but also reveal an artificial, i.e., extrinsic, magnon gap unless the momentum integration range is carefully controlled. Our study provides an explanation of the discrepancies between spectroscopic and first-principles estimates of Dirac magnon gap sizes and provides guidelines for accurate measurement of topological magnon gaps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Imaging the Progression of Radiolytic Damage in Molecular Crystals with Scanning Nanobeam Electron Diffraction

Almost every electron microscopy experiment is fundamentally limited by radiation damage. Nevertheless, little is known about the onset and progression of radiolysis in beam-sensitive materials. Here we apply ambient-temperature scanning nanobeam electron diffraction to record simultaneous dual-space movies of organic and organometallic nanocrystals at sequential stages of beam-induced radiolytic decay. We show that the underlying mosaic of coherently diffracting domains undergoes internal rearrangement as a function of accumulating electron fluence, causing the intensities of some associated Bragg reflections to fade nonmonotonically. Furthermore, we demonstrate that repeated irradiation at a single probe position leads to the isotropic propagation of delocalized radiolytic damage well beyond the direct footprint of the incident beam. We refer to these expanding tides of amorphization as “impact craters.”

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Coordinate-based simulation of pair distance distribution functions for small and large molecular assemblies: implementation and applications

X-ray scattering has become a major tool in the structural characterization of nanoscale materials. Thanks to the widely available experimental and computational atomic models, coordinate-based X-ray scattering simulation has played a crucial role in data interpretation in the past two decades. However, simulation of real-space pair distance distribution functions (PDDFs) from small- and wide-angle X-ray scattering, SAXS/WAXS, has been relatively less exploited. This study presents a comparison of PDDF simulation methods, which are applied to molecular structures that range in size from β-cyclodextrin [1 kDa molecular weight (MW), 66 non-hydrogen atoms] to the satellite tobacco mosaic virus capsid (1.1 MDa MW, 81 960 non-hydrogen atoms). The results demonstrate the power of interpretation of experimental SAXS/WAXS from the real-space view, particularly by providing a more intuitive method for understanding of partial structure contributions. Furthermore, the computational efficiency of PDDF simulation algorithms makes them attractive as approaches for the analysis of large nanoscale materials and biological assemblies. The simulation methods demonstrated in this article have been implemented in stand-alone software, SolX 3.0 , which is available to download from https://12idb.xray.aps.anl.gov/solx.html.

Zuo, Xiaobing (ORCID:0000000201344804)↗
DOE OSTI2021

Understanding nanoscale structural distortions in Pb(Zr 0.2 Ti 0.8 )O 3 by utilizing X-ray nanodiffraction and clustering algorithm analysis

Hard X-ray nanodiffraction provides a unique nondestructive technique to quantify local strain and structural inhomogeneities at nanometer length scales. However, sample mosaicity and phase separation can result in a complex diffraction pattern that can make it challenging to quantify nanoscale structural distortions. In this work, a k-means clustering algorithm was utilized to identify local maxima of intensity by partitioning diffraction data in a three-dimensional feature space of detector coordinates and intensity. This technique has been applied to X-ray nanodiffraction measurements of a patterned ferroelectric PbZr 0.2 Ti 0.8 O 3 sample. The analysis reveals the presence of two phases in the sample with different lattice parameters. A highly heterogeneous distribution of lattice parameters with a variation of 0.02 Å was also observed within one ferroelectric domain. This approach provides a nanoscale survey of subtle structural distortions as well as phase separation in ferroelectric domains in a patterned sample.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Beyond integration: modeling every pixel to obtain better structure factors from stills

Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (10 4 -10 6 ) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb 3+ L -III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

FiXR : a framework to reconstruct fiber cross-sections from X-ray fiber diffraction experiments

Ab initio reconstruction methods have revolutionized the capabilities of small-angle X-ray scattering (SAXS), allowing the data-driven discovery of previously unknown molecular conformations, exploiting optimization heuristics and assumptions behind the composition of globular molecules. While these methods have been successful for the analysis of small particles, their impact on fibrillar assemblies has been more limited. The micrometre-range size of these assemblies and the complex interaction of their periodicities in their scattering profiles indicate that the discovery of fibril structures from SAXS measurements requires novel approaches beyond extending existing tools for molecular discovery. In this work, it is proposed to use SAXS measurements, together with diffraction theory, to infer the electron distribution of the average cross-section of a fiber. This cross-section is modeled as a discrete electron density with continuous support, allowing representations beyond binary distributions. Additional constraints, such as non-negativity or smoothness/connectedness, can also be added to the framework. The proposed approach is tested using simulated SAXS data from amyloid β fibril models and using measured data of Tobacco mosaic virus from SAXS experiments, recovering the geometry and density of the cross-sections in all cases. The approach is further tested by analyzing SAXS data from different amyloid β fibril assemblies, with results that are in agreement with previously proposed models from cryo-EM measurements. The limitations of the proposed method, together with an analysis of the robustness of the method and the combination with different experimental sources, are also discussed.

Biochemistry & Molecular Biology↗