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DOE OSTI2020

Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor

Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. In this work, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2013

Upper Bounds on r-Mode Amplitudes from Observations of Low-Mass X-Ray Binary Neutron Stars

We present upper limits on the amplitude of r-mode oscillations and gravitational-radiation-induced spin-down rates in low-mass X-ray binary neutron stars, under the assumption that the quiescent neutron star luminosity is powered by dissipation from a steady-state r-mode. For masses <2M solar mass we find dimensionless r-mode amplitudes in the range from about 1×10(exp−8) to 1.5×10(exp−6). For the accreting millisecond X-ray pulsar sources with known quiescent spin-down rates, these limits suggest that approx. less than 1% of the observed rate can be due to an unstable r-mode. Interestingly, the source with the highest amplitude limit, NGC 6440, could have an r-mode spin-down rate comparable to the observed, quiescent rate for SAX J1808−3658. Thus, quiescent spin-down measurements for this source would be particularly interesting. For all sources considered here, our amplitude limits suggest that gravitational wave signals are likely too weak for detection with Advanced LIGO. Our highest mass model (2.21M solar mass) can support enhanced, direct Urca neutrino emission in the core and thus can have higher r-mode amplitudes. Indeed, the inferred r-mode spin-down rates at these higher amplitudes are inconsistent with the observed spin-down rates for some of the sources, such as IGR J00291+5934 and XTE J1751−305. In the absence of other significant sources of internal heat, these results could be used to place an upper limit on the masses of these sources if they were made of hadronic matter, or alternatively it could be used to probe the existence of exotic matter in them if their masses were known.

gravitational waves↗

NASA NTRS2003

NASA Tech Briefs, November 2003

Topics covered include: Computer Program Recognizes Patterns in Time-Series Data; Program for User-Friendly Management of Input and Output Data Sets; Noncoherent Tracking of a Source of a Data-Modulated Signal; Software for Acquiring Image Data for PIV; Detecting Edges in Images by Use of Fuzzy Reasoning; A Timer for Synchronous Digital Systems; Prototype Parts of a Digital Beam-Forming Wide-Band Receiver; High-Voltage Droplet Dispenser; Network Extender for MIL-STD-1553 Bus; MMIC HEMT Power Amplifier for 140 to 170 GHz; Piezoelectric Diffraction-Based Optical Switches; Numerical Modeling of Nanoelectronic Devices; Organizing Diverse, Distributed Project Information; Eigensolver for a Sparse, Large Hermitian Matrix; Modified Polar-Format Software for Processing SAR Data; e-Stars Template Builder; Software for Acoustic Rendering; Functionally Graded Nanophase Beryllium/Carbon Composites; Thin Thermal-Insulation Blankets for Very High Temperatures; Prolonging Microgravity on Parabolic Airplane Flights; Device for Locking a Control Knob; Cable-Dispensing Cart; Foam Sensor Structures Would be Self-Deployable and Survive Hard Landings; Real-Gas Effects on Binary Mixing Layers; Earth-Space Link Attenuation Estimation via Ground Radar Kdp; Wedge Heat-Flux Indicators for Flash Thermography; Measuring Diffusion of Liquids by Common-Path Interferometry; Zero-Shear, Low-Disturbance Optical Delay Line; Whispering-Gallery Mode-Locked Lasers; Spatial Light Modulators as Optical Crossbar Switches; Update on EMD and Hilbert-Spectra Analysis of Time Series; Quad-Tree Visual-Calculus Analysis of Satellite Coverage; Dyakonov-Perel Effect on Spin Dephasing in n-Type GaAs; Update on Area Production in Mixing of Supercritical Fluids; and Quasi-Sun-Pointing of Spacecraft Using Radiation Pressure.

Source record↗

DOE OSTI2025

FIRM image analysis: A machine learning workflow for quantifying extracellular matrix components from electron microscopy images

The extracellular matrix (ECM) is a complex network of biomolecules that plays an integral role in the structure, processes, and signaling mechanisms of cells and tissues. Identifying and quantifying changes in these matrix components provides insight into the mechanisms behind specific tissue remodeling processes; however, quantifying these changes is challenging due to difficult imaging conditions, complexity of the ECM, and the subtlety of these changes. Current imaging techniques allow us to visualize these critical remodeling events and developments in image analysis have employed a combination of analysis software and machine learning techniques to improve the efficiency and accuracy with which features are measured. Although image analysis has seen much improvement in recent years, there has been no technique developed to address ambiguity in feature edges in electron microscopy images. Presented here is a new machine learning-based workflow for the analysis of microscopy images named FIRM (Feature Identification from Raw Microscopy) that uses a random forest classifier to identify ECM features of interest and generate binary segmentation masks for quantification with ImageJ-FIJI. FIRM performed with an F1 score of 0.794 and greater than 80% accuracy for number and size of features detected. FIRM had similar deviation from the ground truth in the number of identified fibrils, fibril size, and size distributions when compared to human analyses. The results suggest that FIRM performs as well as manual analysis and requires a fraction of the time. This analysis technique is more efficient, eliminates user bias, and can be easily optimized to identify a variety of features, making it useful for any discipline requiring image analysis.

Science & Technology - Other Topics↗

NASA NTRS1990

New multi-level codes over GF(q)

Set partitioning to multi-dimensional signal spaces over GF(q), particularly GF sup q-1(q) and GF sup q (q), and show how to construct both multi-level block codes and multi-level trellis codes over GF(q). Two classes of multi-level (n, k, d) block codes over GF(q) with block length n, number of information symbols k, and minimum distance d sub min greater than or = d, are presented. These two classes of codes use Reed-Solomon codes as component codes. They can be easily decoded as block length q-1 Reed-Solomon codes or block length q or q + 1 extended Reed-Solomon codes using multi-stage decoding. Many of these codes have larger distances than comparable q-ary block codes, as component codes. Low rate q-ary convolutional codes, work error correcting convolutional codes, and binary-to-q-ary convolutional codes can also be used to construct multi-level trellis codes over GF(q) or binary-to-q-ary trellis codes, some of which have better performance than the above block codes. All of the new codes have simple decoding algorithms based on hard decision multi-stage decoding.

Wu, Jiantian↗

NASA NTRS1992

New multilevel codes over GF(q)

Wu, Jiantian↗

NASA NTRS2000

Gravitational Waves from Rotating Neutron Stars and Evaluation of fast Chirp Transform Techniques

X-ray observations suggest that neutron stars in low mass X-ray binaries (LMXB) are rotating with frequencies from 300 - 600 Hz. These spin rates are significantly less than the break-up rates for essentially all realistic neutron star equations of state, suggesting that some process may limit the spin frequencies of accreting neutron stars to this range. If the accretion induced spin up torque is in equilibrium with gravitational radiation losses, these objects could be interesting sources of gravitational waves. I present a brief summary of current measurements of neutron star spins in LMXBs based on the observations of high-Q oscillations during thermonuclear bursts (so called 'burst oscillations'). Further measurements of neutron star spins will be important in exploring the gravitational radiation hypothesis in more detail. To this end I also present a study of fast chirp transform (FCT) techniques as described by Jenet and Prince in the context of searching for the chirping signals observed during X-ray bursts.

Strohmayer, Tod E.↗

NASA NTRS2001

Oscillations During Thermonuclear X-ray Bursts

High amplitude, nearly coherent X-ray brightness oscillations during thermonuclear X-ray bursts were discovered with the Rossi X-ray Timing Explorer (RXTE) in early 1996. Spectral and timing evidence strongly supports the conclusion that these oscillations are caused by rotational modulation of the burst emission and that they reveal the spin frequency of neutron stars in low mass X-ray binaries, a long sought goal of X-ray astronomy. Studies carried out over the past year have led to the discovery of burst oscillations in four new sources, bringing to ten the number with confirmed burst oscillations. I review the status of our knowledge of these oscillations and indicate how they can be used to probe the physics of neutron stars. For a few burst oscillation sources it has been proposed that the strongest and most ubiquitous frequency is actually the first overtone of the spin frequency and hence that two nearly antipodal hot spots are present on the neutron star. This inference has important implications for both the physics of thermonuclear burning as well as the mass - radius relation for neutron stars, so its confirmation is crucial. I discuss recent attempts to confirm this hypothesis for 4U 1636-53, the source for which a signal at the putative fundamental (290Hz) has, been claimed.

Strohmayer, Tod E.↗

DOE OSTI2024

Machine learning for precise hit position reconstruction in Resistive Silicon Detectors

RSDs are LGAD silicon sensors with 100% fill factor, based on the principle of AC-coupled resistive read-out. Signal sharing and internal charge multiplication are the RSD key features to achieve picosecond-level time resolution and micron-level spatial resolution, thus making these sensors promising candidates as 4D-trackers for future experiments. This paper describes the use of a neural network to reconstruct the hit position of ionizing particles, an approach that can boost the performance of the RSD with respect to analytical models. The neural network has been trained in the laboratory and then validated on test beam data. The device-under-test in this work is a 450 μm-pitch matrix from the FBK RSD2 production, which achieved a resolution of about 65 μm at the DESY Test Beam Facility, a 50% improvement compared to a simple analytical reconstruction method, and a factor two better than the resolution of a standard pixel sensor of equal pitch size with binary read-out. The test beam result is compatible with the laboratory ones obtained during the neural network training, confirming the ability of the machine learning model to provide accurate predictions even in environments very different from the training one. Prospects for future improvements are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

NASA NTRS1995

A study of coronal X-ray emission from short-period Algol binaries

A study of X-ray emission from five short-period Algol-type binaries based on observations with Advanced Satellite for Cosmology and Astrophysics (ASCA) and ROSAT is presented. We have observed RZ Cas with both satellites, and beta Per, U Cep, delta Lib, and TW Dra with ROSAT. Significant intensity variations are seen in the X-ray emission from RZ Cas, U Cep, TW Dra, and delta Lib. These variations seem unrelated to the eclipsing behavior of these systems and are probably due to either rotational modulation of compact active regions on the surfaces of the chromospherically active secondary components or to flaring activity in the systems. The spectra of all but one of the systems require the presence of at least two discrete plasma components with different temperatures (0.6 - 0.7 keV, and approximately 2 keV) and the abundances of the medium-Z elements 20% - 50% of the solar photospheric values. The high resolving power and signal-to-noise ratio of the ASCA spectra allow us to individually constrain the coronal abundances of O, Ne, Mg, Si, S, and Fe in RZ Cas. We demonstrate that, if we use the elemental abundances and temperatures obtained from the analysis of their ASCA spectra as (fixed) inputs, to fit the ROSAT PSPC spectra well requires the presence of a third component (kT approximately 0.2 - 0.3 keV) in RZ Cas and beta Per. A continuous emission measure model of the power-law type (EM(T) variesas (T/T(sub max)(sup alpha)) generally gives a poor fit to the ASCA and ROSAT data on most sources. Circumstellar or circumbinary absorbing matter seems to be present in some of these systems, as indicated by the variable total column density needed to fit their X-ray spectra.

Singh, K. P.↗

NASA NTRS1993

Optimizing the fine lock performance of the Hubble Space Telescope fine guidance sensors

This paper summarizes the on-orbit performance to date of the three Hubble Space Telescope Fine Guidance Sensors (FGS's) in Fine Lock mode, with respect to acquisition success rate, ability to maintain lock, and star brightness range. The process of optimizing Fine Lock performance, including the reasoning underlying the adjustment of uplink parameters, and the effects of optimization are described. The Fine Lock optimization process has combined theoretical and experimental approaches. Computer models of the FGS have improved understanding of the effects of uplink parameters and fine error averaging on the ability of the FGS to acquire stars and maintain lock. Empirical data have determined the variation of the interferometric error characteristics (so-called 's-curves') between FGS's and over each FGS field of view, identified binary stars, and quantified the systematic error in Coarse Track (the mode preceding Fine Lock). On the basis of these empirical data, the values of the uplink parameters can be selected more precisely. Since launch, optimization efforts have improved FGS Fine Lock performance, particularly acquisition, which now enjoys a nearly 100 percent success rate. More recent work has been directed towards improving FGS tolerance of two conditions that exceed its original design requirements. First, large amplitude spacecraft jitter is induced by solar panel vibrations following day/night transitions. This jitter is generally much greater than the FGS's were designed to track, and while the tracking ability of the FGS's has been shown to exceed design requirements, losses of Fine Lock after day/night transitions are frequent. Computer simulations have demonstrated a potential improvement in Fine Lock tracking of vehicle jitter near terminator crossings. Second, telescope spherical aberration degrades the interferometric error signal in Fine Lock, but use of the FGS two-thirds aperture stop restores the transfer function with a corresponding loss of throughput. This loss requires the minimum brightness of acquired stars to be about one magnitude brighter than originally planned.

Eaton, David J.↗

DOE OSTI2025

SpecDis: Value Added Distance Catalog for 4 Million Stars from DESI Year-1 Data

We present the SpecDis value-added stellar distance catalog accompanying DESI Data Release 1. SpecDis trains a feed-forward neural network (NN) with Gaia parallaxes and gets the distance estimates. To build up an unbiased training sample, we do not apply selections on parallax error or signal-to-noise (S/N) of the stellar spectra, and instead, we incorporate parallax error into the loss function. Moreover, we employ principal component analysis to reduce the noise and dimensionality of stellar spectra. Validated by independent external samples of member stars with precise distances from globular clusters, dwarf galaxies, stellar streams, combined with blue horizontal branch stars, we demonstrate that our distance measurements show no significant bias up to 100 kpc, and are much more precise than Gaia parallax beyond 7 kpc. The median distance uncertainties are 23%, 19%, 11%, and 7% for S/N < 20, 20 ≤ S/N < 60, 60 ≤ S/N < 100, and S/N ≥ 100. Selecting stars with ${\mathrm{log}}\,g\lt 3.8$ and distance uncertainties smaller than 25%, we have more than 74,000 giant candidates within 50 kpc of the Galactic center and 1500 candidates beyond this distance. Additionally, we develop a Gaussian mixture model to identify unresolvable equal-mass binaries by modeling the discrepancy between the NN-predicted and the geometric absolute magnitudes from Gaia parallaxes and identify 120,000 equal-mass binary candidates. Our final catalog provides distances and distance uncertainties for >4 million stars, offering a valuable resource for Galactic astronomy.

astronomy data analysis↗

DOE OSTI2021

Updated universal relations for tidal deformabilities of neutron stars from phenomenological equations of state

Equation of state (EOS) insensitive relations, so-called universal relations, between the neutron star (NS) compactness, its multipolar tidal deformability coefficients, and between the tidal parameters for binary systems are essential to break degeneracies in gravitational wave data analysis. Here, we validate and recalibrate these universal relations using a large set of almost 2 million phenomenological EOSs that are consistent with current observations. In doing so, we extend universal relations to a larger region of the EOS parameter space, most notably to softer EOSs and larger compactnesses. We show that waveform models that neglect higher-than-leading-order tidal deformations of the NSs accumulate as much as 3.5 radians of dephasing from 20Hz to merger. Further, we also perform a full Bayesian parameter estimation of the GW170817 data, and we compare the NS radius constraints produced using universal relations from the literature and the updated fits we propose here. We find that the new fits yield a NS radius that is smaller by about 500 meters. This difference is less than the statistical uncertainty on the radius at the signal-to-noise-ratio of GW170817, but it is significantly larger than the precision anticipated for next-generation detectors.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS2010

Performance Bounds on Two Concatenated, Interleaved Codes

A method has been developed of computing bounds on the performance of a code comprised of two linear binary codes generated by two encoders serially concatenated through an interleaver. Originally intended for use in evaluating the performances of some codes proposed for deep-space communication links, the method can also be used in evaluating the performances of short-block-length codes in other applications. The method applies, more specifically, to a communication system in which following processes take place: At the transmitter, the original binary information that one seeks to transmit is first processed by an encoder into an outer code (Co) characterized by, among other things, a pair of numbers (n,k), where n (n > k)is the total number of code bits associated with k information bits and n k bits are used for correcting or at least detecting errors. Next, the outer code is processed through either a block or a convolutional interleaver. In the block interleaver, the words of the outer code are processed in blocks of I words. In the convolutional interleaver, the interleaving operation is performed bit-wise in N rows with delays that are multiples of B bits. The output of the interleaver is processed through a second encoder to obtain an inner code (Ci) characterized by (ni,ki). The output of the inner code is transmitted over an additive-white-Gaussian- noise channel characterized by a symbol signal-to-noise ratio (SNR) Es/No and a bit SNR Eb/No. At the receiver, an inner decoder generates estimates of bits. Depending on whether a block or a convolutional interleaver is used at the transmitter, the sequence of estimated bits is processed through a block or a convolutional de-interleaver, respectively, to obtain estimates of code words. Then the estimates of the code words are processed through an outer decoder, which generates estimates of the original information along with flags indicating which estimates are presumed to be correct and which are found to be erroneous. From the perspective of the present method, the topic of major interest is the performance of the communication system as quantified in the word-error rate and the undetected-error rate as functions of the SNRs and the total latency of the interleaver and inner code. The method is embodied in equations that describe bounds on these functions. Throughout the derivation of the equations that embody the method, it is assumed that the decoder for the outer code corrects any error pattern of t or fewer errors, detects any error pattern of s or fewer errors, may detect some error patterns of more than s errors, and does not correct any patterns of more than t errors. Because a mathematically complete description of the equations that embody the method and of the derivation of the equations would greatly exceed the space available for this article, it must suffice to summarize by reporting that the derivation includes consideration of several complex issues, including relationships between latency and memory requirements for block and convolutional codes, burst error statistics, enumeration of error-event intersections, and effects of different interleaving depths. In a demonstration, the method was used to calculate bounds on the performances of several communication systems, each based on serial concatenation of a (63,56) expurgated Hamming code with a convolutional inner code through a convolutional interleaver. The bounds calculated by use of the method were compared with results of numerical simulations of performances of the systems to show the regions where the bounds are tight (see figure).

Moision, Bruce↗

NASA NTRS2007

Probing the Galactic Binary Black Hole Spin with Photon Timing

It is generally considered that the X-ray emission in AGN and Galactic Black Hole Candidates is produced by flares above the surface of a geometrically thin optically thick accretion disk, which extends down to the Innermost Stable Circular Orbit (ISCO) of the black hole. We consider the influence of the black hole geometry on the light curves of these flares. To this end we follow a large number of photon orbits emitted impulsively in a locally isotropic fashion, at any phase of the disk orbit and examine their arrival times at infinity by an observer near the plane of the disk. We find out that the presence of the black hole spin induces a certain delay in the photon arrivals, as prograde photon orbits reach the observer on shorter (on the average) times than the retrograde ones. We form a histogram of the differences in photon time arrivals and we find that it exhibits several well defined peaks depending on the flare position and the black hole spin separated by $\Delta t \simeq 30 M$, where M is the black hole mass. The peaks disappear as the spin parameter goes to zero, implying that one could in principle measure the value of the black hole spin with timing measurements of sufficiently high signal to noise ratio.

Kazanas, Demosthenes↗

NASA NTRS2007

Probing the Galactic Binary Black Hole Spin with Photon Timing

It is generally considered that the X-ray emission in AGN and Galactic Black Hole Candidates is produced by flares above the surface of a geometrically thin optically thick accretion disk, which extends down to the Innermost Stable Circular Orbit (ISCO) of the black hole. We consider the influence of the black hole geometry on the light curves of these flares. To this end we follow a large number of photon orbits emitted impulsively in a locally isotropic fashion, at any phase of the disk orbit and examine their arrival times at infinity by an observer near the plane of the disk. We find out that the presence of the black hole spin induces a certain delay in the photon arrivals, as prograde photon orbits reach the observer on shorter (on the average) times than the retrograde ones. We form a histogram of the differences in photon time arrivals and we find that it exhibits several well defined peaks depending on the flare position and the black hole spin separated by $\Delta t\slmeq 30 M$, where M is the black hole mass. The peaks disappear as the spin parameter goes to zero, implying that one could in principle measure the value of the black hole spin with timing measurements of sufficiently high signal to noise ratio.

Kazanas, Demos↗

NASA NTRS2012

Goldstone Solar System Radar Waveform Generator

Due to distances and relative motions among the transmitter, target object, and receiver, the time-base between any transmitted and received signal will undergo distortion. Pre-distortion of the transmitted signal to compensate for this time-base distortion allows reception of an undistorted signal. In most radar applications, an arbitrary waveform generator (AWG) would be used to store the pre-calculated waveform and then play back this waveform during transmission. The Goldstone Solar System Radar (GSSR), however, has transmission durations that exceed the available memory storage of such a device. A waveform generator capable of real-time pre-distortion of a radar waveform to a given time-base distortion function is needed. To pre-distort the transmitted signal, both the baseband radar waveform and the RF carrier must be modified. In the GSSR, this occurs at the up-conversion mixing stage to an intermediate frequency (IF). A programmable oscillator (PO) is used to generate the IF along with a time-varying phase component that matches the time-base distortion of the RF carrier. This serves as the IF input to the waveform generator where it is mixed with a baseband radar waveform whose time-base has been distorted to match the given time-base distortion function producing the modulated IF output. An error control feedback loop is used to precisely control the time-base distortion of the baseband waveform, allowing its real-time generation. The waveform generator produces IF modulated radar waveforms whose time-base has been pre-distorted to match a given arbitrary function. The following waveforms are supported: continuous wave (CW), frequency hopped (FH), binary phase code (BPC), and linear frequency modulation (LFM). The waveform generator takes as input an IF with a time varying phase component that matches the time-base distortion of the carrier. The waveform generator supports interconnection with deep-space network (DSN) timing and frequency standards, and is controlled through a 1 Gb/s Ethernet UDP/IP interface. This real-time generation of a timebase distorted radar waveform for continuous transmission in a planetary radar is a unique capability.

Quirk, Kevin J.↗

DOE OSTI2021

Modeling Kilonova Light Curves: Dependence on Nuclear Inputs

The mergers of binary neutron stars, as well as black hole–neutron star systems, are expected to produce an electromagnetic counterpart that can be analyzed to infer the element synthesis that occurred in these events. We investigate one source of uncertainties pertinent to lanthanide-rich outflows: the nuclear inputs to rapid neutron capture nucleosynthesis calculations. We begin by examining 32 different combinations of nuclear inputs: eight mass models, two types of spontaneous fission rates, and two types of fission daughter product distributions. We find that such nuclear physics uncertainties typically generate at least one order of magnitude uncertainty in key quantities such as the nuclear heating (one and a half orders of magnitude at 1 day post-merger), the bolometric luminosity (one order of magnitude at 5 days post-merger), and the inferred mass of material from the bolometric luminosity (factor of 8 when considering the 8–10 day region). Since particular nuclear processes are critical for determining the electromagnetic signal, we provide tables of key nuclei undergoing β-decay, α-decay, and spontaneous fission important for heating at different times, identifying decays that are common among the many nuclear input combinations.

79 ASTRONOMY AND ASTROPHYSICS↗