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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

SAXS Assistant: Automated SAXS analysis for structural discovery in biologics and polymeric nanoparticles

Small-angle x-ray scattering (SAXS) is a powerful technique for assessing macromolecular structure. High-throughput SAXS is limited by the time-consuming and, at times, subjective nature of SAXS data interpretation. Here, we present SAXS Assistant, a Python-based script that streamlines SAXS data analysis to extract features for machine learning (ML) and key structural parameters, including the Guinier radius of gyration (R g ), pair distance distribution function (PDDF)-derived R g , maximum particle dimension (D max ), and Kratky plots. The script builds upon BioXTAS RAW and validates reliability via Guinier/PDDF R g agreement, an important indicator of well-measured data sets. For assistance in D max estimation, a multilayer perceptron regressor was trained with 1940 data files from the Small Angle Scattering Biological Data Bank. The model achieved a test set performance R 2 = 0.90 and mean absolute error = 11.7 Å. Training exclusively with experimental data translates analyses from researchers, including experts in the field, to the ML model, which helps assess D max estimations from PDDF. Gaussian mixture model clustering was implemented to classify profiles into structural classes based on entries in the Small Angle Scattering Biological Data Bank. Users may therefore assess the similarity between experimental samples and known biomolecular shapes within the mapped repository entries. This probabilistic clustering aids in quantifying information from Kratky and generating shape-descriptive features. SAXS Assistant accelerates SAXS data analysis through enforced quality control, ML-ready outputs, and flags for low-confidence results. In addition to providing the ability to analyze large data sets at high throughput, this tool is versatile and may serve researchers in both biological and synthetic polymer research fields.

36 MATERIALS SCIENCE↗
NASA NTRS1994

The SAX Italian scientific satellite. The on-board implemented automation as a support to the ground control capability

This paper presents the capabilities implemented in the SAX system for an efficient operations management during its in-flight mission. SAX is an Italian scientific satellite for x-ray astronomy whose major mission objectives impose quite tight constraints on the implementation of both the space and ground segment. The most relevant mission characteristics require an operative lifetime of two years, performing scientific observations both in contact and in noncontact periods, with a low equatorial orbit supported by one ground station, so that only a few minutes of communications are available each orbit. This operational scenario determines the need to have a satellite capable of performing the scheduled mission automatically and reacting autonomously to contingency situations. The implementation approach of the on-board operations management, through which the necessary automation and autonomy are achieved, follows a hierarchical structure. This has been achieved adopting a distributed avionic architecture. Nine different on-board computers, in fact, constitute the on-board data management system. Each of them performs the local control and monitors its own functions while the system level control is performed at a higher level by the data handling applications software. The SAX on-board architecture provides the ground operators with different options of intervention by three classes of telecommands. The management of the scientific operations will be scheduled by the operation control center via dedicated operating plans. The SAX satellite flight mode is presently being integrated at Alenia Spazio premises in Turin for a launch scheduled for the end of 1995. Once in orbit, the SAX satellite will be subject to intensive check-out activities in order to verify the required mission performances. An overview of the envisaged procedure and of the necessary on-ground activities is therefore depicted as well.

Martelli, Andrea↗
DOE OSTI2027

A multi-region approach for the analysis of porous materials and gas-solid reactions using USAXS-SAXS-WAXS: application to CaO carbonation

The reaction rate of gas-solid non-catalytic reactions is typically investigated using reactant conversion data over time and ex-situ measurements of the porous solid reactant textural properties; these data enable the experimental estimation of the initial intrinsic reaction rate, whereas the evolution of the textural properties and the reaction rate over time are evaluated theoretically using reaction models. In this work, a different methodology is presented, based on: a) in-situ time-resolved USAXS-SAXS-WAXS measurements of the solid sample, and b) a multi-region modeling approach; this methodology allows for the estimation of the textural properties and the intrinsic reaction rate at any time during the reaction. Referring to a reaction in which a solid product is obtained from a solid reactant and a gaseous reactant, the porous particle is described as consisting of several distinct regions with different microstructural properties, and both a gas-solid reaction model and a SAXS model are derived and applied to the carbonation of porous CaO. The proposed reaction model highlights the role of the inaccessible reactant and accurately predicts the solid reactant conversion versus time profile. The SAXS model accurately predicts the measured linear trends of the Porod invariant and of the pre-factor of the power law scattering profile versus CaO mass fraction; in the absence of chemical reactions, the proposed equations extend classical SAXS theory to porous materials containing macropores and nonporous solid phases in addition to standard nanoscale inhomogeneous regions.

CO2 solid sorbents↗
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 NTRS1994

Space simulation techniques and facilities for SAX STM test campaign

SAX is a satellite for X-Ray astronomy. It is a major element of the overall basic Science Program of the Italian Space Agency (ASI) and is being developed with the contribution of the Netherlands Agency for Aerospace Programs (NIVR). The scientific objectives of SAX are to carry out systematic and comprehensive observations of celestial X-Ray sources over the 0.1 - 300 KeV energy range with special emphasis on spectral and timing measurements. The satellite will also monitor the X-Ray sky to investigate long-term source variability and to permit localization and study of X-Ray transients. Alenia Spazio is developing the satellite that is intended for launch in the second half of 1995 in a low, near-equatorial Earth orbit. At system level a Structural Thermal Model (STM) has been conceived to verify the environmental requirements by validating the mechanical and thermal analytical models and qualifying satellite structure and thermal control. In particular, the following tests have been carried out in Alenia Spazio, CEA/CESTA and ESTEC facilities: Modal Survey, Centrifuge, Acoustic, Sinusoidal/Random Vibration and Thermal Balance. The paper, after a short introduction of the SAX satellite, summarizes the environmental qualification program performed on the SAX STM. It presents test objectives, methodologies and relevant test configurations. Peculiar aspects of the test campaign are highlighted. Problems encountered and solutions adopted in performing the tests are described as well. Furthermore, test results are presented and assessed.

Giordano, Pietro↗
DOE OSTI2025

Ion Clusters in Multicomponent Solutions Determined from X-ray PDF and SAXS Analysis: The NaNO 2 –NaOH–H 2 O System

Here, this study explores ion cluster formation in the NaNO 2 –NaOH–H 2 O system to understand how ion cluster formation is influenced by the composition in multicomponent mixtures. X-ray pair distribution function (PDF) and small-angle X-ray scattering (SAXS) identified complex ion clusters in concentrated NaNO 2 and NaOH solutions as well as their mixtures. PDF analysis showed that the Na–O distance depended primarily on total Na + concentrations rather than anion composition, whereas the nitrite-water oxygen distance stayed the same regardless of concentration or composition. This result indicates that the nitrite ion hydration was relatively independent of composition. SAXS confirms local fluctuations and coherent clusters with notable size differences between NaOH and NaNO 2 solutions. SAXS analysis of mixed solutions shows that their clusters are an average of the individual solutions, indicating mixed clusters.

Reynolds, Jacob G. [Central Plateau Cleanup Compan↗
DOE OSTI2024

SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0

Amelogenin is an intrinsically disordered protein essential to tooth enamel formation in mammals. Here, using advanced small angle X-ray scattering (SAXS) capabilities at synchrotrons and computational models, we revisited measuring the quaternary structure of murine amelogenin as a function of pH and phosphorylation at serine-16. The SAXS data shows that at the pH extremes, amelogenin exists as an extended monomer at pH 3.0 (R g = 38.4 Å) and nanospheres at pH 8.0 (R g = 84.0 Å), consistent with multiple previous observations. At pH 5.0 and above there was no evidence for a significant population of monomeric species. Instead, at pH 5.0 ~ 80% of the population is a heterogenous dimeric species that increases to ~ 100% at pH 5.5. The dimer population was observed at all pH > 5 conditions in dynamic equilibrium with a species in the pentamer range at pH < 6.5 and nanospheres at pH 8.0. At pH 8.0 ~ 40% of the amelogenin still remained in the dimeric state. In general, serine-16 phosphorylation of amelogenin appears to modestly stabilize the population of the dimeric species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗
NASA NTRS1992

System test approach for the SAX satellite

SAX satellite verification is based on a protoflight approach, in which only one system model is realized at flight standard level, taking into account the utilization of hardware already qualified for other space programs and the necessity to respect the schedule constraints for a scientific objective. In any case, this approach was tailored with some deviations in order to reduce risks inherent in such a choice. The protoflight approach was also pursued at subsystem/unit level in particular for those subsystems and units considered critical from the schedule point of view. Payload Instruments followed the same approach but complete spare units were developed to reduce the risks associated with such an approach. A description of the model philosophy is provided and then, at satellite level, the testing approach and rationale for each model is presented. Finally, a brief description of each test will be given, highlighting objectives, methodologies, and test configurations. Moreover, for the major tests, problems encountered and solutions applied in establishing a correct approach are described.

Giordano, Pietro↗
NASA NTRS2001

Discovery of a Hand X-Ray Source, SAX J0635+0533, in the Error Box of the Gamma-Ray Source 2EG J0635+0521

We have discovered an X-ray source, SAX J0635+0533, with a hard spectrum within the error box of the GeV gamma-ray source in Monoceros, 2EG J0635+0521. The unabsorbed flux from the source is 1.2 x 10(exp -11) ergs /sq cm s in the 2-10 keV band. The X-ray spectrum is consistent with a simple power-law model with absorption. The photon index is 1.50 +/- 0.08, and we detect emission out to 40 keV. Optical observations identify a counterpart with a V magnitude of 12.8. The counterpart has broad emission lines and the colors of an early B-type star. If the identification of the X-ray/optical source with the gamma-ray source is correct, then the source would be a gamma-ray-emitting X-ray binary.

Kaaret, P.↗
NASA NTRS2001

Probing AGN with Masers and X-Rays-SAX Proposals

We have made BeppoSAX observations of the Seyfert 2/1.9 galaxy ESO103-G35, which contains a nuclear maser source and is known to be heavily absorbed in the X-rays. Analysis of the X-ray spectra observed by SAX in October 1996 and 1997 yields an energy index = 0.74 +/- 0.07, typical of Seyfert galaxies and consistent with earlier observations of this source. The strong, soft X-ray absorption has a column density, N_H of (1.79 +/- 0.09)E23 cmE-02, again consistent with earlier results. The best fitting spectrum is that of a power law with a high energy cutoff at 29 +/- 10 keV, a cold (E=6.3 +/- 0.1 keV, rest frame), marginally resolved (sigma = 0.35 +/- 0.14 keV, FWHM approximately (31 +/- 12)E03 km/s) FeKalpha line with EW 290 +100 -80 eV (1996) and a mildly ionized Fe K-edge at 7.37 +0.15 -0.21 keV, tau 0.24 +0.06 -0.09. The Fe Kalpha line and cold absorption are consistent with origin in a accretion disk/torus through which our line-of-sight passes at a radial distance of approximately 0.01 pc. The Fe K-edge is mildly ionized suggesting the presence of ionized gas probably in the inner accretion disk, close to the central source or in a separate warm absorber. The data quality is too low to distinguish between these possibilities but the edge-on geometry implied by the water maser emission favors the former. Comparison with earlier observations of ESO103-G35 shows little/no change in spectral parameters while the flux changes by factors of a few on timescales of a few months. The 2-10 keV flux decreased by a factor of approximately 2.7 between Oct 1996 and Oct 1997 with no detectable change in the count rate greater than 20 keV (i.e. the PDS data). Spectral fits to the combined datasets indicate either a significant hardening of the spectrum (energy index approximately 0.5) or an approximate constant or delayed response reflection component. The high energy cutoff (29 +/- 10 keV) is lower than the typical approximately 300 keV values seen in Seyfert galaxies. A significant subset of similar sources would affect current models of the AGN contribution to the cosmic X-ray background (CXRB) which generally assume a high energy cutoff of approximately 300 keV.

Wilkes, Belinda J.↗
NASA NTRS2002

X-ray Spectra and Pulse Frequency Changes in SAX J2103.5+4545

The November 1999 outburst of the transient pulsar SAX J2103.5+4545 was monitored with the large area detectors of the Rossi X-Ray Timing Explorer until the pulsar faded after a year. The 358 s pulsar was spun up for 150 days, at which point the flux dropped quickly by a factor of approximately 7, the frequency saturated and, as the flux continued to decline, a weak spin-down began. The pulses remained strong during the decay and the spin-up/flux correlation can be fit to the Ghosh and Lamb derivations for the spin-up caused by accretion from a thin, pressure-dominated disk, for a distance approximately 3.2 kpc and a surface magnetic field approximately 1.2 x 10(exp 13) Gauss. During the bright spin-up part of the outburst, the flux was subject to strong orbital modulation, peaking approximately 3 days after periastron of the eccentric 12.68 day orbit, while during the faint part, there was little orbital modulation. The X-ray spectra were typical of accreting pulsars, describable by a cut-off power-law, with an emission line near the 6.4 keV of Kappa(sub alpha) fluorescence from cool iron. The equivalent width of this emission did not share the orbital modulation, but nearly doubled during the faint phase, despite little change in the column density. The outburst could have been caused by an episode of increased wind from a Be star, such that a small accretion disk is formed during each periastron passage. A change in the wind and disk structure apparently occurred after 5 months such that the accretion rate was no longer modulated or the diffusion time was longer. The distance estimate implies the X-ray luminosity observed was between 1 X 10(exp 36) ergs s(exp -1) and 6 x 10(exp 34) ergs s(exp -1), with a small but definite correlation of the intrinsic power-law spectral index.

Baykal, A.↗
NASA NTRS2003

Discovery of Soft Spectral Component and Transient 22.7s Quasi Periodic Oscillations of SAX J2103.5+4545

XMM-Newton observed SAX J2103.5+4545 on January 6, 2003, while RXTE was monitoring the source. Using RXTE-PCA dataset between December 3, 2002 and January 29, 2003, the spin period and average spin-up rate during the XMM-Newton observations were found to be 354.7940+/-0.0008 s and (7.4 +/- 0.9) x 10(exp -13) Hz/s respectively. In the power spectrum of the 0.9-11 keV EPIC-PN lightcurve, we found quasi periodic oscillations around 0.044 Hz (22.7 s) with an rms fractional amplitude approx. 6.6 %. We interpreted this QPO feature as the Keplerian motion of inhomogeneities through the inner disk. In the X-ray spectrum, in addition to the power law component with high energy cutoff and approx. 6.4 keV fluorescent iron emission line, we discovered a soft component consistent with a blackbody emission with kT approx. 1.9 keV. The pulse phase spectroscopy of the source revealed that the blackbody flux peaked at the peak of the pulse with an emission radius approx. 0.3 km, suggesting the polar cap on the neutron star approx. 6.42 keV was shown to peak at the off-pulse phase, supporting the idea that this feature arises from fluorescent emission of the circumstellar material around the neutron star rather than the hot region in the vicinity of the neutron star polar cap.

Inam, S. C.↗
NASA NTRS2005

Spreading of thermonuclear flames on the neutron star in SAX J1808.4-3658: an observational tool

We analyse archival Rossi X-Ray Timing Explorer (RXTE) proportional counter array (PCA) data of thermonuclear X-ray bursts from the 2002 outburst of the accreting millisecond pulsar SAX 51808.4-3658. We present evidence of a complex frequency modulation of oscillations during burst rise, and correlations among the time evolution of the oscillation frequency, amplitude, and the inferred burning region area. We discuss these findings in the context of a model, based on thermonuclear flame spreading on the neutron star surface, that can qualitatively explain these features. From our model, we infer that for the 2002 Oct. 15 thermonuclear burst, the ignition likely occurred in the mid-latitudes, the burning region took approx. 0.2 s to nearly encircle the equatorial region of the neutron star, and after that the lower amplitude oscillation originated from the remaining asymmetry of the burning front in the same hemisphere where the burst ignited. We emphasize that studies of the evolution of burst oscillation properties during burst rise can provide a powerful tool to understand thermonuclear flame spreading on neutron star surfaces under extreme physical conditions.

Bhattacharyya, Sudip↗
NASA NTRS2006

An Unusual Precursor Burst with Oscillations from SAX J1808.4-3658

We report the finding of an unusual, weak precursor to a thermonuclear X-ray burst from the accreting millisecond pulsar SAX 51808.4-3658. The burst in question was observed on Oct. 19, 2002 with the Rossi X-Ray Timing Explorer (RXTE) proportional counter array (PCA). The precursor began approx. equal to 1 s prior to the onset of a strong radius expansion burst, lasted for about 0.4 s, and exhibited strong oscillations at the 401 Hz spin frequency. Oscillations are not detected in the approx. equal to 0.5 s interval between the precursor and the main burst. The estimated peak photon flux and energy fluence of the precursor are about 1/25, and 1/500 that of the main burst, respectively. From joint spectral and temporal modeling, we find that an expanding burning region with a relatively low temperature on the spinning neutron star surface can explain the oscillations, as well as the faintness of the precursor with respect to the main part of the burst. We discuss some of the implications of our findings for the ignition and spreading of thermonuclear flames on neutron stars.

Bhattacharyya, Sudip↗
NASA NTRS2018

A Possible Phase-Dependent Absorption Feature in the Transient X-Ray Pulsar SAX J2103.5+4545

We present an X-ray spectral and timing analysis of two Nuclear Spectroscopic Telescope Array (NuSTAR) observations of the transient Be X-ray binary SAX J2103.5+4545 during its 2016 April outburst, which was characterized by the highest flux since NuSTAR's launch. These observations provide detailed hard X-ray spectra of this source during its bright precursor flare and subsequent fainter regular outburst for the first time. In this work, we model the phase-averaged spectra for these observations with a negative and positive power law with an exponential cutoff (NPEX - Negative and Positive power-laws EXponential) model and compare the pulse profiles at different flux states. We found that the broadband pulse profile changes from a three-peaked pulse in the first observation to a two-peaked pulse in the second observation, and that each of the pulse peaks has some energy dependence. We also perform pulse-phase spectroscopy and fit phase-resolved spectra with NPEX to evaluate how spectral parameters change with pulse phase. We find that while the continuum parameters are mostly constant with pulse phase, a weak absorption feature at approximately 12 kiloelectronvolts which might, with further study, be classified as a cyclotron line, does show strong pulse-phase dependence.

Brumback, M.C.↗
NASA NTRS2019

A NICER Thermonuclear Burst from the Millisecond X-Ray Pulsar SAX J1808.4–3658

The Neutron Star Interior Composition Explorer (NICER) has extensively monitored the 2019 August outburst of the 401 Hz millisecond X-ray pulsar SAX J1808.4–3658. In this Letter, we report on the detection of a bright helium-fueled Type I X-ray burst. With a bolometric peak flux of (2.3 ± 0.1) × 10(exp −7) erg/s sq.cm, this was the brightest X-ray burst among all bursting sources observed with NICER to date. The burst shows a remarkable two-stage evolution in flux, emission lines at 1.0 and 6.7 keV, and burst oscillations at the known pulsar spin frequency, with ≈4% fractional sinusoidal amplitude. We interpret the burst flux evolution as the detection of the local Eddington limits associated with the hydrogen and helium layers of the neutron star envelope. The emission lines are likely associated with Fe, due to reprocessing of the burst emission in the accretion disk.

Bult, Peter↗