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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Hallucination of closed repeat proteins containing central pockets

In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Repeated gravitational wave bursts from cosmic strings

A characteristic observational signature of cosmic strings are short duration gravitational wave (GW) bursts. These have been searched for by the LIGO-Virgo-KAGRA (LVK) Collaboration and will be searched for with LISA. We point out that these burst signals are repeated, since cosmic string loops evolve quasiperiodically in time, and will always appear from essentially the same position in the sky. We estimate the number of GW repeaters for LVK and LISA and show that the string tension that can be probed scales as detector sensitivity to the sixth power, which raises hope for detection in future GW detectors. Furthermore, the observation of repeated GW bursts from the same cosmic string loop helps distinguish between the GW waveform parameters and the sky localization.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
NASA NTRS1972

An assessment of repeated loads on general aviation and transport aircraft.

An assessment is made of recent repeated loads data from short-haul jet transports and several general aviation airplanes. The jet transport data indicate that except for check flight maneuvers the load histories are essentially independent of operator and airplane type. General aviation data show a large amount of scatter in the repeated load history. The use and geographical location of operations may be the primary means of specifying the repeated loads environment.

Donely, P.↗
NASA NTRS1978

Performances of regenerative and non-regenerative satellite repeaters with MPSK signalling

Linear (translation), hard-limited, and demod/remod types of satellite repeaters are considered in this paper. Both uncoded and coded multiple phase shift keyed (MPSK) signals are assumed to be transmitted through these repeaters. Relative performances of these repeaters in the presence of uplink and downlink noises are then compared quantitatively. Probabilities of bit errors and the computational cutoff rates are computed for 2, 4, and 8 phases PSK signals, with uplink and downlink SNRs as parameters.

Woo, K. T.↗
NASA NTRS1992

More About Gravitational Bumps And Repeating Orbits

Improved algorithm reduces computation needed to estimate dynamics affecting trajectory of satellite in orbit around Earth with approximately repeating ground track. Underlying concepts presented in "Computing Gravitational Bumps From Repeating-Orbit Data", (NPO-17925). Satellite presumed to undergo same gravitational perturbation upon each near-repetition. Tracking data from multiple nearly repeating arcs collected into segments called "bins" and processed together to reduce effects of random errors, and thereby obtain more-accurate estimates of dynamical parameters. Bumps in gravitational field of Earth estimated with less computation.

Wu, Jiun-Tsong↗
NASA NTRS1993

Extending substructure based iterative solvers to multiple load and repeated analyses

Direct solvers currently dominate commercial finite element structural software, but do not scale well in the fine granularity regime targeted by emerging parallel processors. Substructure based iterative solvers--often called also domain decomposition algorithms--lend themselves better to parallel processing, but must overcome several obstacles before earning their place in general purpose structural analysis programs. One such obstacle is the solution of systems with many or repeated right hand sides. Such systems arise, for example, in multiple load static analyses and in implicit linear dynamics computations. Direct solvers are well-suited for these problems because after the system matrix has been factored, the multiple or repeated solutions can be obtained through relatively inexpensive forward and backward substitutions. On the other hand, iterative solvers in general are ill-suited for these problems because they often must restart from scratch for every different right hand side. In this paper, we present a methodology for extending the range of applications of domain decomposition methods to problems with multiple or repeated right hand sides. Basically, we formulate the overall problem as a series of minimization problems over K-orthogonal and supplementary subspaces, and tailor the preconditioned conjugate gradient algorithm to solve them efficiently. The resulting solution method is scalable, whereas direct factorization schemes and forward and backward substitution algorithms are not. We illustrate the proposed methodology with the solution of static and dynamic structural problems, and highlight its potential to outperform forward and backward substitutions on parallel computers. As an example, we show that for a linear structural dynamics problem with 11640 degrees of freedom, every time-step beyond time-step 15 is solved in a single iteration and consumes 1.0 second on a 32 processor iPSC-860 system; for the same problem and the same parallel processor, a pair of forward/backward substitutions at each step consumes 15.0 seconds.

Farhat, Charbel↗
NASA NTRS1994

Postburst nebular emission of soft gamma-ray repeaters

The soft gamma ray repeater SGR 1806-20 has been shown to be unambiguously associated with the central region of the radio nebula G10.0-0.3. The nebula surrounding SGR 1806-20 is probably a supernova remnant and has a nonthermal radio spectrum typical of a 'plerion,' circumstellar gas energized by a relativistic particle outflow from a central source. The association of soft gamma ray repeaters (SGRs) with supernova remnants is supported by the likely association of another repeater, SGR 0525-66, with the nebula N49 in the Large Magellanic Cloud. Gas nebulae surrounding SGRs provide ideal calorimeters to tap both the impulsive and steady state energy released from these bursting sources. We discuss in this Letter a simple model of high-energy emission produced by impulsive release of relativistic particles in nebulae surrounding SGRs following bursting episodes. This nebular X-ray and gamma ray emission can be detected and monitored by ROSAT, ASCA, and the Compton Gamma Ray Observatory.

Tavani, Marco↗
NASA NTRS1995

Photon-splitting limits to the hardness of emission in strongly magnetized soft gamma repeaters

Soft gamma repeaters are characterized by recurrent activity consisting of short-duration outbursts of high-energy emission that is typically of temperature less than 40 keV. One recent model of repeaters is that they originate in the environs of neutron stars with superstrong magnetic fields, perhaps greater than 10(exp 14) G. In such fields, the exotic process of magnetic photon splitting gamma yields gamma gamma acts very effectively to reprocess gamma-ray radiation down to hard X-ray energies. In this Letter, the action of photon splitting is considered in some detail, via the solution of photon kinetic equations, determining how it limits the hardness of emission in strongly magnetized repeaters, and thereby obtaining observational constraints to the field in SGR 1806-20.

Baring, Matthew G.↗
NASA NTRS1995

Repeating sources of classical gamma-ray bursts

From an analysis of the first catalog of the Burst and Transient Source Experiment (BATSE) experiment (Fishman et al. 1993, 1994a) on the Compton Gamma Ray Observatory (CGRO), we find an excessive number of pairs of gamma-ray bursts which are clustered in both a space and time . The angular separation between the two bursts in each pair is less than their positional uncertainties, and the interval between their occurrence times is within several days. Optimizing the signal, we find that the probability of observing such a clustered excess froma Poisson ensemble is approximately 2 x 10(exp -5). We suggest that these bursts arise from repeating sources. A detailed study of the most prolific source, GBS 0855-00, is presented in a separate paper (Wang & Lingenfelter 1993a, b). Unlike most of the 'soft' gamma-ray repeaters, these repeating bursts have relatively hard spectra, complex light curves, and widely varying durations, that are indistinguishable from classical gamma-ray bursts. Although the significance of the clustered excess was optimized a posteriori, because it depends on temporal and spatial bin sized that could not be defined a priori, we can use the optimizations from the first catalog to test subsequent BATSE data sets. Unfortunately, the failure of the on-board tape recorders during the second catalog period seriously reduced the number of accurately positioned bursts (Fishman et al. 1994b), so that we can neither confirm, nor refute, the predicted repitition in that sample, and we must await the results of the third catalog.

Wang, V. C.↗
NASA NTRS1994

Do gamma-ray burst sources repeat?

The demonstration of repeated gamma-ray bursts from an individual source would severely constrain burst source models. Recent reports of evidence for repetition in the first BATSE burst catalog have generated renewed interest in this issue. Here, we analyze the angular distribution of 585 bursts of the second BATSE catalog (Meegan et al. 1994). We search for evidence of burst recurrence using the nearest and farthest neighbor statistic ad the two-point angular correlation function. We find the data to be consistent with the hypothesis that burst sources do not repeat; however, a repeater fraction of up to about 20% of the bursts cannot be excluded.

Meegan, C. A.↗
NASA NTRS1995

Do gamma-ray burst sources repeat?

The demonstration of repeated gamma-ray bursts from an individual source would severely constrain burst source models. Recent reports (Quashnock and Lamb, 1993; Wang and Lingenfelter, 1993) of evidence for repetition in the first BATSE burst catalog have generated renewed interest in this issue. Here, we analyze the angular distribution of 585 bursts of the second BATSE catalog (Meegan et al., 1994). We search for evidence of burst recurrence using the nearest and farthest neighbor statistic and the two-point angular correlation function. We find the data to be consistent with the hypothesis that burst sources do not repeat; however, a repeater fraction of up to about 20% of the observed bursts cannot be excluded.

Meegan, Charles A.↗
NASA NTRS1995

Capillary Pressure Balance with Repeated Head-Up Tilt in Humans

We measured blood density (BD). plasma density (PD) and hematocrit (Ht) during repeated 70 deg head-up tilt (HUT) consisting of a pre-drink period with two supine (P and P3) and two HUT (P2 and P4) phases of 45 min each. At the end of P4 test subjects (N=8) drank 10 ml/kg body weight of isotonic (290 mOsm/kg) sodium chloride (ISO) or hypotonic (<10 mOsm/kg) unsweetened us (HYP), or nothing (control: CON). The following periods continued the supine (P5, P7) / upright (P6) sequence. Mass density of plasma and whole blood using a "mechanical oscillation" technique were measured from ear lobe blood. Tilting altered (p<0.001) BD, PD, and Ht in all consecutive Phases. BD and PD were different (p<0.05) between CON. HYP. and ISO Phases 6 and 7. The computed mass density of fluid (FD). which moved between intra. and extravascular compartments. averaged 1008 g/l and was the same in any conditions. In the non-drink treatment (P3, P5, P7), supine PV steadly decreased when compared to P1. Tilt-induced PV shifts ranged from 9.7 to 16.7% when compared to PV du. ring the respective previous Phases. After drinking, PV increased above CON values at the end of Phase 7 by 12.9% with ISO, and by 6.6% with HYP. Progressive hemoconcentration. occurred during non-drink supine; isotonic saline ingestion increased supine PV a control level but did not stop or reverse the decrease of upright hemoconcentration. Upright density values were not slowed with repeated upright tilting; decreased fluid loss occurred in consecutive upright periods. Upright capillary pressure balance was achieved with diminished plasma volume loss during repeated tilting.

Hinghofer-Szalkay, H. G.↗
NASA NTRS2004

Measurement of Force Balance Repeatability and Reproducibility in the NTF

A recently published statistical approach for measuring and evaluating wind tunnel force balance repeatability and reproducibility is applied to three check standard tests in the National Transonic Facility at NASA Langley Research Center. Two different airframe models and force balances were used. The short-term repeatability and within-test reproducibility are separately estimated and correlations with tunnel parameters are carried out. Conjectures are presented for the development of scaling laws for predicting the repeatability and reproducibility of other force balance tests in the tunnel.

Hemsch, M. J.↗
NASA NTRS2000

Leech segmental repeats develop normally in the absence of signals from either anterior or posterior segments

We have investigated whether the development of segmental repeats is autonomous in the embryo of the leech Helobdella robusta. The segmental tissues of the germinal band arise from progeny of five stem cells called teloblasts. Asymmetric divisions of the teloblasts form chains of segment founder cells (called primary blast cells) that divide in a stereotypical manner to produce differentiated descendants. Using two distinct techniques, we have looked for potential interactions between neighboring blast cell clones along the anterior-posterior axis. In one technique, we prevented the birth of primary blast cells by injection of DNase I into the teloblast, thereby depriving the last blast cell produced before the ablation of its normal posterior neighbors. We also ablated single blast cells with a laser microbeam, which allowed us to assess potential signals acting on either more anterior or more posterior primary blast cell clones. Our results suggest that interactions along the anterior-posterior axis between neighboring primary blast cell clones are not required for development of normal segmental organization within the blast cell clone. We also examined the possibility that blast cells receive redundant signals from both anterior and posterior neighboring clones and that either is sufficient for normal development. Using double blast cell laser ablations to isolate a primary blast cell clone by removal of both its anterior and its posterior neighbor, we found that the isolated clone still develops normally. These results reveal that the fundamental segmental repeat in the leech embryo, the primary blast cell clone, can develop normally in the apparent absence of signals from adjacent repeats along the anterior-posterior axis.

NASA Discipline Evolutionary Biology↗
NASA NTRS2003

An L-band SAR for repeat pass deformation measurements on a UAV platform

We are proposing to develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for repeat-pass differential interferometric measurements of deformation for rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes that is to be flown on a unmanned aerial vehicle (UAV) or minimally piloted vehicle (MPV). Upon surveying the capabilities and availabilities of such aircraft, the Proteus aircraft and the ALTAIR UAV appear to meet our criteria in terms of payload capabilities, flying altitude, and endurance. To support the repeat pass deformation capability it is necessary to control flight track capability of the aircraft to be within a specified 10 m tube with a goal of 1 m. This requires real-time GPS control of the autopilot to achieve these objectives that has not been demonstrated on these aircraft. Based on the Proteus and ALTAIR's altitude of 13.7 km (45,000 ft), we are designing a fully polarimetric L-band radar with 80 MHz bandwidth and a 16 km range swath. The radar will have an active electronic beam steering antenna to achieve a Doppler centroid stability that is necessary for repeat-pass interferometry. This paper presents some of the trade studies for the platform, instrument and the expected science.

interferometers↗
NASA NTRS2004

Accumulate repeat accumulate codes

In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

Low Density Parity Check codes (LDPC)↗
NASA NTRS2004

Accumulate-Repeat-Accumulate-Accumulate-Codes

Inspired by recently proposed Accumulate-Repeat-Accumulate (ARA) codes [15], in this paper we propose a channel coding scheme called Accumulate-Repeat-Accumulate-Accumulate (ARAA) codes. These codes can be seen as serial turbo-like codes or as a subclass of Low Density Parity Check (LDPC) codes, and they have a projected graph or protograph representation; this allows for a high-speed iterative decoder implementation using belief propagation. An ARAA code can be viewed as a precoded Repeat-and-Accumulate (RA) code with puncturing in concatenation with another accumulator, where simply an accumulator is chosen as the precoder; thus ARAA codes have a very fast encoder structure. Using density evolution on their associated protographs, we find examples of rate-lJ2 ARAA codes with maximum variable node degree 4 for which a minimum bit-SNR as low as 0.21 dB from the channel capacity limit can be achieved as the block size goes to infinity. Such a low threshold cannot be achieved by RA or Irregular RA (IRA) or unstructured irregular LDPC codes with the same constraint on the maximum variable node degree. Furthermore by puncturing the accumulators we can construct families of higher rate ARAA codes with thresholds that stay close to their respective channel capacity thresholds uniformly. Iterative decoding simulation results show comparable performance with the best-known LDPC codes but with very low error floor even at moderate block sizes.

density evolution↗